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Sample records for structurally similar segment

  1. Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

    Directory of Open Access Journals (Sweden)

    Yunyun Liang

    2015-01-01

    Full Text Available Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM. Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS, segmented PsePSSM, and segmented autocovariance transformation (ACT based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640 are adopted in this paper. Then a 700-dimensional (700D feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA. To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

  2. Optimally segmented magnetic structures

    DEFF Research Database (Denmark)

    Insinga, Andrea Roberto; Bahl, Christian; Bjørk, Rasmus

    We present a semi-analytical algorithm for magnet design problems, which calculates the optimal way to subdivide a given design region into uniformly magnetized segments.The availability of powerful rare-earth magnetic materials such as Nd-Fe-B has broadened the range of applications of permanent...... is not available.We will illustrate the results for magnet design problems from different areas, such as electric motors/generators (as the example in the picture), beam focusing for particle accelerators and magnetic refrigeration devices.......We present a semi-analytical algorithm for magnet design problems, which calculates the optimal way to subdivide a given design region into uniformly magnetized segments.The availability of powerful rare-earth magnetic materials such as Nd-Fe-B has broadened the range of applications of permanent...... magnets[1][2]. However, the powerful rare-earth magnets are generally expensive, so both the scientific and industrial communities have devoted a lot of effort into developing suitable design methods. Even so, many magnet optimization algorithms either are based on heuristic approaches[3...

  3. Asymmetric similarity-weighted ensembles for image segmentation

    DEFF Research Database (Denmark)

    Cheplygina, V.; Van Opbroek, A.; Ikram, M. A.

    2016-01-01

    Supervised classification is widely used for image segmentation. To work effectively, these techniques need large amounts of labeled training data, that is representative of the test data. Different patient groups, different scanners or different scanning protocols can lead to differences between...... the images, thus representative data might not be available. Transfer learning techniques can be used to account for these differences, thus taking advantage of all the available data acquired with different protocols. We investigate the use of classifier ensembles, where each classifier is weighted...... and the direction of measurement needs to be chosen carefully. We also show that a point set similarity measure is robust across different studies, and outperforms state-of-the-art results on a multi-center brain tissue segmentation task....

  4. Musical structure analysis using similarity matrix and dynamic programming

    Science.gov (United States)

    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.

  5. Bayesian segmentation of brainstem structures in MRI

    DEFF Research Database (Denmark)

    Iglesias, Juan Eugenio; Van Leemput, Koen; Bhatt, Priyanka

    2015-01-01

    the brainstem structures in novel scans. Thanks to the generative nature of the scheme, the segmentation method is robust to changes in MRI contrast or acquisition hardware. Using cross validation, we show that the algorithm can segment the structures in previously unseen T1 and FLAIR scans with great accuracy...

  6. Optimally segmented permanent magnet structures

    DEFF Research Database (Denmark)

    Insinga, Andrea Roberto; Bjørk, Rasmus; Smith, Anders

    2016-01-01

    We present an optimization approach which can be employed to calculate the globally optimal segmentation of a two-dimensional magnetic system into uniformly magnetized pieces. For each segment the algorithm calculates the optimal shape and the optimal direction of the remanent flux density vector......, with respect to a linear objective functional. We illustrate the approach with results for magnet design problems from different areas, such as a permanent magnet electric motor, a beam focusing quadrupole magnet for particle accelerators and a rotary device for magnetic refrigeration....

  7. DSCImageCalc – Software for Determining Similarity Coefficients for the Analysis of Image Segmentations

    Directory of Open Access Journals (Sweden)

    Tom Lawton

    2017-10-01

    Full Text Available DSCImageCalc is free software for calculating similarity coefficients on segmented images. It is written in Visual BASIC .NET and is available at: https://doi.org/10.6084/m9.figshare.894428. It presently calculates Sørensen-Dice Coefficient, Jaccard Coefficient, Proportional Agreement, Cohen’s Kappa, Goodman & Kruskal’s Gamma, and Rogot-Goldberg Agreement. It also calculates segment centroids and the distance between them. Whilst it was originally designed for calculating Dice coefficients on segmentations of ultrasound images, it has potential for re-use in any field where similarity of image segments is to be analysed; predominantly medical radiology and ecology.

  8. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract 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.

  9. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation.......Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...

  10. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Parrado-Hernandez, Emilio; Meng, Anders

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...... for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation....

  11. Segmentation and Visualisation of Human Brain Structures

    Energy Technology Data Exchange (ETDEWEB)

    Hult, Roger

    2003-10-01

    In this thesis the focus is mainly on the development of segmentation techniques for human brain structures and of the visualisation of such structures. The images of the brain are both anatomical images (magnet resonance imaging (MRI) and autoradiography) and functional images that show blood flow (functional magnetic imaging (fMRI), positron emission tomography (PET), and single photon emission tomography (SPECT)). When working with anatomical images, the structures segmented are visible as different parts of the brain, e.g. the brain cortex, the hippocampus, or the amygdala. In functional images, the activity or the blood flow that be seen. Grey-level morphology methods are used in the segmentations to make tissue types in the images more homogenous and minimise difficulties with connections to outside tissue. A method for automatic histogram thresholding is also used. Furthermore, there are binary operations such as logic operation between masks and binary morphology operations. The visualisation of the segmented structures uses either surface rendering or volume rendering. For the visualisation of thin structures, surface rendering is the better choice since otherwise some voxels might be missed. It is possible to display activation from a functional image on the surface of a segmented cortex. A new method for autoradiographic images has been developed, which integrates registration, background compensation, and automatic thresholding to get faster and more reliable results than the standard techniques give.

  12. Segmentation and Visualisation of Human Brain Structures

    International Nuclear Information System (INIS)

    Hult, Roger

    2003-01-01

    In this thesis the focus is mainly on the development of segmentation techniques for human brain structures and of the visualisation of such structures. The images of the brain are both anatomical images (magnet resonance imaging (MRI) and autoradiography) and functional images that show blood flow (functional magnetic imaging (fMRI), positron emission tomography (PET), and single photon emission tomography (SPECT)). When working with anatomical images, the structures segmented are visible as different parts of the brain, e.g. the brain cortex, the hippocampus, or the amygdala. In functional images, the activity or the blood flow that be seen. Grey-level morphology methods are used in the segmentations to make tissue types in the images more homogenous and minimise difficulties with connections to outside tissue. A method for automatic histogram thresholding is also used. Furthermore, there are binary operations such as logic operation between masks and binary morphology operations. The visualisation of the segmented structures uses either surface rendering or volume rendering. For the visualisation of thin structures, surface rendering is the better choice since otherwise some voxels might be missed. It is possible to display activation from a functional image on the surface of a segmented cortex. A new method for autoradiographic images has been developed, which integrates registration, background compensation, and automatic thresholding to get faster and more reliable results than the standard techniques give

  13. Structural similarity and category-specificity

    DEFF Research Database (Denmark)

    Gerlach, Christian; Law, Ian; Paulson, Olaf B

    2004-01-01

    It has been suggested that category-specific recognition disorders for natural objects may reflect that natural objects are more structurally (visually) similar than artefacts and therefore more difficult to recognize following brain damage. On this account one might expect a positive relationshi...

  14. Segmentation of elongated structures in medical images

    NARCIS (Netherlands)

    Staal, Jozef Johannes

    2004-01-01

    The research described in this thesis concerns the automatic detection, recognition and segmentation of elongated structures in medical images. For this purpose techniques have been developed to detect subdimensional pointsets (e.g. ridges, edges) in images of arbitrary dimension. These

  15. Segmentation of Lung Structures in CT

    DEFF Research Database (Denmark)

    Lo, Pechin Chien Pau

    This thesis proposes and evaluates new algorithms for segmenting various lung structures in computed tomography (CT) images, namely the lungs, airway trees and vessel trees. The main objective of these algorithms is to facilitate a better platform for studying Chronic Obstructive Pulmonary Disease......, 200 randomly selected CT scans were manually evaluated by medical experts, and only negligible or minor errors were found in nine scans. The proposed algorithm has been used to study how changes in smoking behavior affect CT based emphysema quantification. The algorithms for segmenting the airway...

  16. Unveiling Music Structure Via PLSA Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Meng, Anders; Petersen, Kaare Brandt

    2007-01-01

    Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious. In this p......Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious...... observed similarities can be satisfactorily explained using the latent semantics. Additionally, this approach significantly simplifies the song retrieval phase, leading to a more practical system implementation. The suitability of the PLSA model for representing music structure is studied in a simplified...

  17. Measuring structural similarity in large online networks.

    Science.gov (United States)

    Shi, Yongren; Macy, Michael

    2016-09-01

    Structural similarity based on bipartite graphs can be used to detect meaningful communities, but the networks have been tiny compared to massive online networks. Scalability is important in applications involving tens of millions of individuals with highly skewed degree distributions. Simulation analysis holding underlying similarity constant shows that two widely used measures - Jaccard index and cosine similarity - are biased by the distribution of out-degree in web-scale networks. However, an alternative measure, the Standardized Co-incident Ratio (SCR), is unbiased. We apply SCR to members of Congress, musical artists, and professional sports teams to show how massive co-following on Twitter can be used to map meaningful affiliations among cultural entities, even in the absence of direct connections to one another. Our results show how structural similarity can be used to map cultural alignments and demonstrate the potential usefulness of social media data in the study of culture, politics, and organizations across the social and behavioral sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Structural constraints in the packaging of bluetongue virus genomic segments.

    Science.gov (United States)

    Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C; Roy, Polly

    2014-10-01

    The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by biochemical data analysis suggested that a conformational motif formed by interaction of the 5' and 3' ends of the molecule was necessary and sufficient for packaging. A similar structural signal was also identified in S8 of BTV serotype 1. Furthermore, the same conformational analysis of secondary structures for positive-sense ssRNAs was used to generate a chimeric segment that maintained the putative packaging motif but contained unrelated internal sequences. This chimeric segment was packaged successfully, confirming that the motif identified directs the correct packaging of the segment. © 2014 The Authors.

  19. Finding occurrences of melodic segments in folk songs employing symbolic similarity measures

    NARCIS (Netherlands)

    Janssen, Berit; van Kranenburg, P.; Volk, A.

    2017-01-01

    Much research has been devoted to the classification of folk songs, revealing that variants are recognised based on salient melodic segments, such as phrases and motifs, while other musical material in a melody might vary considerably. In order to judge similarity of melodies on the level of melodic

  20. User-assisted Object Detection by Segment Based Similarity Measures in Mobile Laser Scanner Data

    NARCIS (Netherlands)

    Oude Elberink, S.J.; Kemboi, B.J.

    2014-01-01

    This paper describes a method that aims to find all instances of a certain object in Mobile Laser Scanner (MLS) data. In a userassisted approach, a sample segment of an object is selected, and all similar objects are to be found. By selecting samples from multiple classes, a classification can be

  1. A Segment-Based Trajectory Similarity Measure in the Urban Transportation Systems.

    Science.gov (United States)

    Mao, Yingchi; Zhong, Haishi; Xiao, Xianjian; Li, Xiaofang

    2017-03-06

    With the rapid spread of built-in GPS handheld smart devices, the trajectory data from GPS sensors has grown explosively. Trajectory data has spatio-temporal characteristics and rich information. Using trajectory data processing techniques can mine the patterns of human activities and the moving patterns of vehicles in the intelligent transportation systems. A trajectory similarity measure is one of the most important issues in trajectory data mining (clustering, classification, frequent pattern mining, etc.). Unfortunately, the main similarity measure algorithms with the trajectory data have been found to be inaccurate, highly sensitive of sampling methods, and have low robustness for the noise data. To solve the above problems, three distances and their corresponding computation methods are proposed in this paper. The point-segment distance can decrease the sensitivity of the point sampling methods. The prediction distance optimizes the temporal distance with the features of trajectory data. The segment-segment distance introduces the trajectory shape factor into the similarity measurement to improve the accuracy. The three kinds of distance are integrated with the traditional dynamic time warping algorithm (DTW) algorithm to propose a new segment-based dynamic time warping algorithm (SDTW). The experimental results show that the SDTW algorithm can exhibit about 57%, 86%, and 31% better accuracy than the longest common subsequence algorithm (LCSS), and edit distance on real sequence algorithm (EDR) , and DTW, respectively, and that the sensitivity to the noise data is lower than that those algorithms.

  2. The structure of vortex tube segments in fluid turbulence

    International Nuclear Information System (INIS)

    Wang Lipo

    2011-01-01

    Geometrical description of the flow fields is an important direction to understand the physics of turbulence. Recently several new analysis approaches addressing the entire field properties have been developed, such as dissipation element analysis for the scalar fields and streamtube segment analysis (J. Fluid Mech. 2010, 648: 183-203) for the velocity vector field. By decomposing into a fundamental structure, i.e. stream-tube segments, the velocity field can be understood from the statistics of these relative simple units. Similar idea can be adopted to analyze the vorticity field. The classic concept of vortex tube has been remaining as a topic of essential importance in many aspects. However, the vortex tube structure is not complete to represent the entire turbulent fields, because of its ambiguous definition and small volume portion. This work presents tentatively the vorticitytube segment structure to overcome the existing deficiency. Vorticitytube segments reveal an inherent topology of turbulence vorticity fields. Based on statistics conditioned on different vorticitytube segments, some problems can be newly understood, such as the enstrophy production. Results hereof may also serve for turbulence modeling.

  3. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

    Rypdal, Kristoffer; Juul Rasmussen, Jens; Thomsen, Kenneth

    1985-01-01

    Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and...

  4. Deformable meshes for medical image segmentation accurate automatic segmentation of anatomical structures

    CERN Document Server

    Kainmueller, Dagmar

    2014-01-01

    ? Segmentation of anatomical structures in medical image data is an essential task in clinical practice. Dagmar Kainmueller introduces methods for accurate fully automatic segmentation of anatomical structures in 3D medical image data. The author's core methodological contribution is a novel deformation model that overcomes limitations of state-of-the-art Deformable Surface approaches, hence allowing for accurate segmentation of tip- and ridge-shaped features of anatomical structures. As for practical contributions, she proposes application-specific segmentation pipelines for a range of anatom

  5. A novel method for unsteady flow field segmentation based on stochastic similarity of direction

    Science.gov (United States)

    Omata, Noriyasu; Shirayama, Susumu

    2018-04-01

    Recent developments in fluid dynamics research have opened up the possibility for the detailed quantitative understanding of unsteady flow fields. However, the visualization techniques currently in use generally provide only qualitative insights. A method for dividing the flow field into physically relevant regions of interest can help researchers quantify unsteady fluid behaviors. Most methods at present compare the trajectories of virtual Lagrangian particles. The time-invariant features of an unsteady flow are also frequently of interest, but the Lagrangian specification only reveals time-variant features. To address these challenges, we propose a novel method for the time-invariant spatial segmentation of an unsteady flow field. This segmentation method does not require Lagrangian particle tracking but instead quantitatively compares the stochastic models of the direction of the flow at each observed point. The proposed method is validated with several clustering tests for 3D flows past a sphere. Results show that the proposed method reveals the time-invariant, physically relevant structures of an unsteady flow.

  6. Spectral entropy criteria for structural segmentation in genomic DNA sequences

    International Nuclear Information System (INIS)

    Chechetkin, V.R.; Lobzin, V.V.

    2004-01-01

    The spectral entropy is calculated with Fourier structure factors and characterizes the level of structural ordering in a sequence of symbols. It may efficiently be applied to the assessment and reconstruction of the modular structure in genomic DNA sequences. We present the relevant spectral entropy criteria for the local and non-local structural segmentation in DNA sequences. The results are illustrated with the model examples and analysis of intervening exon-intron segments in the protein-coding regions

  7. International Good Market Segmentation and Financial Market Structure

    OpenAIRE

    Basak, Suleyman; Croitoru, Benjamin

    2003-01-01

    While financial markets have recently become more complete and international capital flows well liberalized, markets for goods remain segmented. To investigate how more complete security markets may relieve the effects of this segmentation, we examine a series of two-country economies with internationally segmented good markets, distinguished by the available financial securities. We show that, under heterogeneity within countries, the financial structure matters: even with internationally co...

  8. Study of domain structure in segmented polyether polyurethaneureas by PAT

    International Nuclear Information System (INIS)

    Yin Chuanyuan; Xu Weizheng; Gu Qingchao

    1990-01-01

    The domain structure of segmented polyether polyurethaneureas is investigated by means of positron annihilation technique, small angle X-ray scattering and differential scanning calorimetry. The experimental results show that the decrease of domain volume and free volume results from the increase of hard segment contents, and that the increase of domain volume and free volume results from the increase of molecular weight of soft segments

  9. A transfer-learning approach to image segmentation across scanners by maximizing distribution similarity

    DEFF Research Database (Denmark)

    van Opbroek, Annegreet; Ikram, M. Arfan; Vernooij, Meike W.

    2013-01-01

    Many successful methods for biomedical image segmentation are based on supervised learning, where a segmentation algorithm is trained based on manually labeled training data. For supervised-learning algorithms to perform well, this training data has to be representative for the target data. In pr...

  10. The Activity Structure of Lesson Segments.

    Science.gov (United States)

    Burns, Robert B.; Anderson, Lorin W.

    1987-01-01

    Approaches classroom instruction and teacher effectiveness by conceptualizing the physical milieu shaping teacher-student interactions. Lessons are viewed as a series of segments with three components (purpose, activity format, and assignment) that help characterize the instructional environment. Scripts are suggested to help regulate activity…

  11. Pulmonary parenchyma segmentation in thin CT image sequences with spectral clustering and geodesic active contour model based on similarity

    Science.gov (United States)

    He, Nana; Zhang, Xiaolong; Zhao, Juanjuan; Zhao, Huilan; Qiang, Yan

    2017-07-01

    While the popular thin layer scanning technology of spiral CT has helped to improve diagnoses of lung diseases, the large volumes of scanning images produced by the technology also dramatically increase the load of physicians in lesion detection. Computer-aided diagnosis techniques like lesions segmentation in thin CT sequences have been developed to address this issue, but it remains a challenge to achieve high segmentation efficiency and accuracy without much involvement of human manual intervention. In this paper, we present our research on automated segmentation of lung parenchyma with an improved geodesic active contour model that is geodesic active contour model based on similarity (GACBS). Combining spectral clustering algorithm based on Nystrom (SCN) with GACBS, this algorithm first extracts key image slices, then uses these slices to generate an initial contour of pulmonary parenchyma of un-segmented slices with an interpolation algorithm, and finally segments lung parenchyma of un-segmented slices. Experimental results show that the segmentation results generated by our method are close to what manual segmentation can produce, with an average volume overlap ratio of 91.48%.

  12. Minimal pneumothorax with dynamic changes in ST segment similar to myocardial infarction.

    Science.gov (United States)

    Yeom, Seok-Ran; Park, Sung-Wook; Kim, Young-Dae; Ahn, Byung-Jae; Ahn, Jin-Hee; Wang, Il-Jae

    2017-08-01

    Pneumothorax can cause a variety of electrocardiographic changes. ST segment elevation, which is mainly observed in myocardial infarction, can also be induced by pneumothorax. The mechanism is presumed to be a decrease in cardiac output, due to increased intra-thoracic pressure. We encountered a patient with ST segment elevation with minimal pneumothorax. Coronary angiography with ergonovine provocation test and echocardiogram had normal findings. The ST segment elevation was normalized by decreasing the amount of pneumothorax. We reviewed the literature and present possible mechanisms for this condition. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Multi-atlas pancreas segmentation: Atlas selection based on vessel structure.

    Science.gov (United States)

    Karasawa, Ken'ichi; Oda, Masahiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Chu, Chengwen; Zheng, Guoyan; Rueckert, Daniel; Mori, Kensaku

    2017-07-01

    Automated organ segmentation from medical images is an indispensable component for clinical applications such as computer-aided diagnosis (CAD) and computer-assisted surgery (CAS). We utilize a multi-atlas segmentation scheme, which has recently been used in different approaches in the literature to achieve more accurate and robust segmentation of anatomical structures in computed tomography (CT) volume data. Among abdominal organs, the pancreas has large inter-patient variability in its position, size and shape. Moreover, the CT intensity of the pancreas closely resembles adjacent tissues, rendering its segmentation a challenging task. Due to this, conventional intensity-based atlas selection for pancreas segmentation often fails to select atlases that are similar in pancreas position and shape to those of the unlabeled target volume. In this paper, we propose a new atlas selection strategy based on vessel structure around the pancreatic tissue and demonstrate its application to a multi-atlas pancreas segmentation. Our method utilizes vessel structure around the pancreas to select atlases with high pancreatic resemblance to the unlabeled volume. Also, we investigate two types of applications of the vessel structure information to the atlas selection. Our segmentations were evaluated on 150 abdominal contrast-enhanced CT volumes. The experimental results showed that our approach can segment the pancreas with an average Jaccard index of 66.3% and an average Dice overlap coefficient of 78.5%. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Protein structure similarity from principle component correlation analysis

    Directory of Open Access Journals (Sweden)

    Chou James

    2006-01-01

    Full Text Available Abstract Background Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. Results We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. Conclusion The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum

  15. Color Image Segmentation Based on Statistics of Location and Feature Similarity

    Science.gov (United States)

    Mori, Fumihiko; Yamada, Hiromitsu; Mizuno, Makoto; Sugano, Naotoshi

    The process of “image segmentation and extracting remarkable regions” is an important research subject for the image understanding. However, an algorithm based on the global features is hardly found. The requisite of such an image segmentation algorism is to reduce as much as possible the over segmentation and over unification. We developed an algorithm using the multidimensional convex hull based on the density as the global feature. In the concrete, we propose a new algorithm in which regions are expanded according to the statistics of the region such as the mean value, standard deviation, maximum value and minimum value of pixel location, brightness and color elements and the statistics are updated. We also introduced a new concept of conspicuity degree and applied it to the various 21 images to examine the effectiveness. The remarkable object regions, which were extracted by the presented system, highly coincided with those which were pointed by the sixty four subjects who attended the psychological experiment.

  16. Weighting training images by maximizing distribution similarity for supervised segmentation across scanners

    DEFF Research Database (Denmark)

    van Opbroek, Annegreet; Vernooij, Meike W; Ikram, M.Arfan

    2015-01-01

    Many automatic segmentation methods are based on supervised machine learning. Such methods have proven to perform well, on the condition that they are trained on a sufficiently large manually labeled training set that is representative of the images to segment. However, due to differences between...... scanners, scanning parameters, and patients such a training set may be difficult to obtain. We present a transfer-learning approach to segmentation by multi-feature voxelwise classification. The presented method can be trained using a heterogeneous set of training images that may be obtained with different...... scanners than the target image. In our approach each training image is given a weight based on the distribution of its voxels in the feature space. These image weights are chosen as to minimize the difference between the weighted probability density function (PDF) of the voxels of the training images...

  17. A method for robust segmentation of arbitrarily shaped radiopaque structures in cone-beam CT projections

    International Nuclear Information System (INIS)

    Poulsen, Per Rugaard; Fledelius, Walther; Keall, Paul J.; Weiss, Elisabeth; Lu Jun; Brackbill, Emily; Hugo, Geoffrey D.

    2011-01-01

    Purpose: Implanted markers are commonly used in radiotherapy for x-ray based target localization. The projected marker position in a series of cone-beam CT (CBCT) projections can be used to estimate the three dimensional (3D) target trajectory during the CBCT acquisition. This has important applications in tumor motion management such as motion inclusive, gating, and tumor tracking strategies. However, for irregularly shaped markers, reliable segmentation is challenged by large variations in the marker shape with projection angle. The purpose of this study was to develop a semiautomated method for robust and reliable segmentation of arbitrarily shaped radiopaque markers in CBCT projections. Methods: The segmentation method involved the following three steps: (1) Threshold based segmentation of the marker in three to six selected projections with large angular separation, good marker contrast, and uniform background; (2) construction of a 3D marker model by coalignment and backprojection of the threshold-based segmentations; and (3) construction of marker templates at all imaging angles by projection of the 3D model and use of these templates for template-based segmentation. The versatility of the segmentation method was demonstrated by segmentation of the following structures in the projections from two clinical CBCT scans: (1) Three linear fiducial markers (Visicoil) implanted in or near a lung tumor and (2) an artificial cardiac valve in a lung cancer patient. Results: Automatic marker segmentation was obtained in more than 99.9% of the cases. The segmentation failed in a few cases where the marker was either close to a structure of similar appearance or hidden behind a dense structure (data cable). Conclusions: A robust template-based method for segmentation of arbitrarily shaped radiopaque markers in CBCT projections was developed.

  18. Local-global alignment for finding 3D similarities in protein structures

    Science.gov (United States)

    Zemla, Adam T [Brentwood, CA

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  19. Lipschitz equivalence of self-similar sets with touching structures

    International Nuclear Information System (INIS)

    Ruan, Huo-Jun; Wang, Yang; Xi, Li-Feng

    2014-01-01

    Lipschitz equivalence of self-similar sets is an important area in the study of fractal geometry. It is known that two dust-like self-similar sets with the same contraction ratios are always Lipschitz equivalent. However, when self-similar sets have touching structures the problem of Lipschitz equivalence becomes much more challenging and intriguing at the same time. So far, all the known results only cover self-similar sets in R with no more than three branches. In this study we establish results for the Lipschitz equivalence of self-similar sets with touching structures in R with arbitrarily many branches. Key to our study is the introduction of a geometric condition for self-similar sets called substitutable. (paper)

  20. Automated Glioblastoma Segmentation Based on a Multiparametric Structured Unsupervised Classification

    Science.gov (United States)

    Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V.; Robles, Montserrat; Aparici, F.; Martí-Bonmatí, L.; García-Gómez, Juan M.

    2015-01-01

    Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation. PMID:25978453

  1. GIS: a comprehensive source for protein structure similarities.

    Science.gov (United States)

    Guerler, Aysam; Knapp, Ernst-Walter

    2010-07-01

    A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. alpha-helices and beta-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10,000 protein domains yielding about 55 x 10(6) possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus.

  2. Multi-scale structural similarity index for motion detection

    Directory of Open Access Journals (Sweden)

    M. Abdel-Salam Nasr

    2017-07-01

    Full Text Available The most recent approach for measuring the image quality is the structural similarity index (SSI. This paper presents a novel algorithm based on the multi-scale structural similarity index for motion detection (MS-SSIM in videos. The MS-SSIM approach is based on modeling of image luminance, contrast and structure at multiple scales. The MS-SSIM has resulted in much better performance than the single scale SSI approach but at the cost of relatively lower processing speed. The major advantages of the presented algorithm are both: the higher detection accuracy and the quasi real-time processing speed.

  3. Remote sensing image segmentation using local sparse structure constrained latent low rank representation

    Science.gov (United States)

    Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

    2016-09-01

    Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

  4. A method for rapid similarity analysis of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Liu Na

    2006-11-01

    Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

  5. Examining Similarity Structure: Multidimensional Scaling and Related Approaches in Neuroimaging

    Directory of Open Access Journals (Sweden)

    Svetlana V. Shinkareva

    2013-01-01

    Full Text Available This paper covers similarity analyses, a subset of multivariate pattern analysis techniques that are based on similarity spaces defined by multivariate patterns. These techniques offer several advantages and complement other methods for brain data analyses, as they allow for comparison of representational structure across individuals, brain regions, and data acquisition methods. Particular attention is paid to multidimensional scaling and related approaches that yield spatial representations or provide methods for characterizing individual differences. We highlight unique contributions of these methods by reviewing recent applications to functional magnetic resonance imaging data and emphasize areas of caution in applying and interpreting similarity analysis methods.

  6. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    Science.gov (United States)

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

  7. The Similar Structures and Control Problems of Complex Systems

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In this paper, the naturally evolving complex systems, such as biotic and social ones, are considered. Focusing on their structures, a feature is noteworthy, i.e., the similarity in structures. The relations between the functions and behaviors of these systems and their similar structures will be studied. Owing to the management of social systems and the course of evolution of biotic systems may be regarded as control processes, the researches will be within the scope of control problems. Moreover, since it is difficult to model for biotic and social systems, it will start with the control problems of complex systems, possessing similar structures, in engineering.The obtained results show that for either linear or nonlinear systems and for a lot of control problemssimilar structures lead to a series of simplifications. In general, the original system may be decomposed into reduced amount of subsystems with lower dimensions and simpler structures. By virtue of such subsystems, the control problems of original system can be solved more simply.At last, it turns round to observe the biotic and social systems and some analyses are given.

  8. RNA structural constraints in the evolution of the influenza A virus genome NP segment

    NARCIS (Netherlands)

    A.P. Gultyaev (Alexander); A. Tsyganov-Bodounov (Anton); M.I. Spronken (Monique); S. Van Der Kooij (Sander); R.A.M. Fouchier (Ron); R.C.L. Olsthoorn (René)

    2014-01-01

    textabstractConserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length,

  9. Similar degree of intimal hyperplasia in surgically detected stenotic and nonstenotic arteriovenous fistula segments: a preliminary report.

    Science.gov (United States)

    Duque, Juan C; Tabbara, Marwan; Martinez, Laisel; Paez, Angela; Selman, Guillermo; Salman, Loay H; Velazquez, Omaida C; Vazquez-Padron, Roberto I

    2018-04-01

    Intimal hyperplasia has been historically associated with improper venous remodeling and stenosis after creation of an arteriovenous fistula. Recently, however, we showed that intimal hyperplasia by itself does not explain the failure of maturation of 2-stage arteriovenous fistulas. We seek to evaluate whether intimal hyperplasia plays a role in the development of focal stenosis of an arteriovenous fistula. This study compares intimal hyperplasia lesions in stenotic and nearby nonstenotic segments collected from the same arteriovenous fistula. Focal areas of stenosis were detected in the operating room in patients (n= 14) undergoing the second-stage vein transposition procedure. The entire vein was inspected, and areas of stenosis were visually located with the aid of manual palpation and hemodynamic changes in the vein peripheral and central to the narrowing. Stenotic and nonstenotic segments were documented by photography before tissue collection (14 tissue pairs). Intimal area and thickness, intima-media thickness, and intima to media area ratio were measured in hematoxylin and eosin stained cross-sections followed by pairwise statistical comparisons. The intimal area in stenotic and nonstenotic segments ranged from 1.25 to 11.61 mm 2 and 1.29 to 5.81 mm 2 , respectively. There was no significant difference between these 2 groups (P=.26). Maximal intimal thickness (P=.22), maximal intima-media thickness (P=.13), and intima to media area ratio (P=.73) were also similar between both types of segments. This preliminary study indicates that postoperative intimal hyperplasia by itself is not associated with the development of focal venous stenosis in 2-stage fistulas. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Strategic Planning Process and Organizational Structure: Impacts, Confluence and Similarities

    Directory of Open Access Journals (Sweden)

    Dyogo Felype Neis

    2017-01-01

    Full Text Available This article aims to analyze the relationship between the strategic planning process and organizational structure in the reality of a complex organization: the Public Prosecutor’s Office of Santa Catarina (MPSC. The research is set by the single case study research strategy and data were collected through the following instruments: bibliographical research, documentary research, semi-structured interviews and systematic observation. The conclusion indicates that the phases of the strategic planning process influence and are influenced by the elements of the organizational structure and highlights the confluences, the impacts and similarities between the stages of formulation and implementation of the strategic process with the various constituent elements of the organizational structure.

  11. Structural similarity image quality reliability: Determining parameters and window size

    OpenAIRE

    Silvestre-Blanes, Javier

    2011-01-01

    The need to obtain objective values of the quality of distorted images with respect to the original is fundamental in multimedia and image processing applications. It is generally required that this value correlates well with the human vision system (HVS). In spite of the properties and the general use of the mean square error (MSE) measurement, this has a poor correlation with HSV, which has led to the development of methods such as structural similarity (SSIM). This metric improves the corr...

  12. APPLICABILITY OF SIMILARITY CONDITIONS TO ANALOGUE MODELLING OF TECTONIC STRUCTURES

    Directory of Open Access Journals (Sweden)

    Mikhail A. Goncharov

    2010-01-01

    Full Text Available The publication is aimed at comparing concepts of V.V. Belousov and M.V. Gzovsky, outstanding researchers who established fundamentals of tectonophysics in Russia, specifically similarity conditions in application to tectonophysical modeling. Quotations from their publications illustrate differences in their views. In this respect, we can reckon V.V. Belousov as a «realist» as he supported «the liberal point of view» [Methods of modelling…, 1988, p. 21–22], whereas M.V. Gzovsky can be regarded as an «idealist» as he believed that similarity conditions should be mandatorily applied to ensure correctness of physical modeling of tectonic deformations and structures [Gzovsky, 1975, pp. 88 and 94].Objectives of the present publication are (1 to be another reminder about desirability of compliance with similarity conditions in experimental tectonics; (2 to point out difficulties in ensuring such compliance; (3 to give examples which bring out the fact that similarity conditions are often met per se, i.e. automatically observed; (4 to show that modeling can be simplified in some cases without compromising quantitative estimations of parameters of structure formation.(1 Physical modelling of tectonic deformations and structures should be conducted, if possible, in compliance with conditions of geometric and physical similarity between experimental models and corresponding natural objects. In any case, a researcher should have a clear vision of conditions applicable to each particular experiment.(2 Application of similarity conditions is often challenging due to unavoidable difficulties caused by the following: a Imperfection of experimental equipment and technologies (Fig. 1 to 3; b uncertainties in estimating parameters of formation of natural structures, including main ones: structure size (Fig. 4, time of formation (Fig. 5, deformation properties of the medium wherein such structures are formed, including, first of all, viscosity (Fig. 6

  13. Structural similarities between prokaryotic and eukaryotic 5S ribosomal RNAs

    International Nuclear Information System (INIS)

    Welfle, H.; Boehm, S.; Damaschun, G.; Fabian, H.; Gast, K.; Misselwitz, R.; Mueller, J.J.; Zirwer, D.; Filimonov, V.V.; Venyaminov, S.Yu.; Zalkova, T.N.

    1986-01-01

    5S RNAs from rat liver and E. coli have been studied by diffuse X-ray and dynamic light scattering and by infrared and Raman spectroscopy. Identical structures at a resolution of 1 nm can be deduced from the comparison of the experimental X-ray scattering curves and electron distance distribution functions and from the agreement of the shape parameters. A flat shape model with a compact central region and two protruding arms was derived. Double helical stems are eleven-fold helices with a mean base pair distance of 0.28 nm. The number of base pairs (26 GC, 9 AU for E. coli; 27 GC, 9 AU for rat liver) and the degree of base stacking are the same within the experimental error. A very high regularity in the ribophosphate backbone is indicated for both 5S RNAs. The observed structural similarity and the consensus secondary structure pattern derived from comparative sequence analyses suggest the conclusion that prokaryotic and eukaryotic 5S RNAs are in general very similar with respect to their fundamental structural features. (author)

  14. Retinal Vessel Segmentation via Structure Tensor Coloring and Anisotropy Enhancement

    Directory of Open Access Journals (Sweden)

    Mehmet Nergiz

    2017-11-01

    Full Text Available Retinal vessel segmentation is one of the preliminary tasks for developing diagnosis software systems related to various retinal diseases. In this study, a fully automated vessel segmentation system is proposed. Firstly, the vessels are enhanced using a Frangi Filter. Afterwards, Structure Tensor is applied to the response of the Frangi Filter and a 4-D tensor field is obtained. After decomposing the Eigenvalues of the tensor field, the anisotropy between the principal Eigenvalues are enhanced exponentially. Furthermore, this 4-D tensor field is converted to the 3-D space which is composed of energy, anisotropy and orientation and then a Contrast Limited Adaptive Histogram Equalization algorithm is applied to the energy space. Later, the obtained energy space is multiplied by the enhanced mean surface curvature of itself and the modified 3-D space is converted back to the 4-D tensor field. Lastly, the vessel segmentation is performed by using Otsu algorithm and tensor coloring method which is inspired by the ellipsoid tensor visualization technique. Finally, some post-processing techniques are applied to the segmentation result. In this study, the proposed method achieved mean sensitivity of 0.8123, 0.8126, 0.7246 and mean specificity of 0.9342, 0.9442, 0.9453 as well as mean accuracy of 0.9183, 0.9442, 0.9236 for DRIVE, STARE and CHASE_DB1 datasets, respectively. The mean execution time of this study is 6.104, 6.4525 and 18.8370 s for the aforementioned three datasets respectively.

  15. Monitoring engineering structures by the comparison of similar photographs

    International Nuclear Information System (INIS)

    Jones, A.

    1976-12-01

    A commonly used method of monitoring engineering structures is to compare similar photographs taken at different times. The initial part of this note deals with commercially available equipment, known as a comparascope, which enables differences between photographs to be rapidly (and reliably) detected. A series of practical tests is described in which it is established that a change in dimensions of 0.05mm can be detected between photographs. For typical camera systems, this will usually correspond to detectable displacements of the order of several mm in object space. Perhaps the most serious disadvantages of the technique is that alterations in camera attitude between photographs can cause changes in the recorded image which mask genuine movements in the structure. The changes caused by a given shift in camera attitude are, therefore, investigated theoretically. Since it is desirable that the changes are small enough to go undetected in the comparison, the established detection limit of the comparascope is included in the investigation to specify how accurately the camera attitude must be controlled for a given set of experimental circumstances. As a result, it appears that a special purpose camera mounting will nearly always be required if structural differences as small as several mm are to be reliably detected. Hand-held cameras should only be used for relatively coarse monitoring tasks. (author)

  16. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Krotee, Pascal [Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States; UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States; Rodriguez, Jose A. [Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States; UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States; Sawaya, Michael R. [Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States; UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States; Cascio, Duilio [Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States; UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States; Reyes, Francis E. [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States; Shi, Dan [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States; Hattne, Johan [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States; Nannenga, Brent L. [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States; Oskarsson, Marie E. [Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; Philipp, Stephan [Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States; Griner, Sarah [Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States; UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States; Jiang, Lin [Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States; Brain Research Institute (BRI), University of California, Los Angeles, Los Angeles, United States; Glabe, Charles G. [Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States; Biochemistry Department, Faculty of Science and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Westermark, Gunilla T. [Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; Gonen, Tamir [Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States; Eisenberg, David S. [Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States; UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States

    2017-01-03

    hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19–29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15–25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19–29 S20G may serve as a model for the toxic spine of hIAPP.

  17. Automatic segmentation of liver structure in CT images

    International Nuclear Information System (INIS)

    Bae, K.T.; Giger, M.L.; Chen, C.; Kahn, C.E. Jr.

    1993-01-01

    The segmentation and three-dimensional representation of the liver from a computed tomography (CT) scan is an important step in many medical applications, such as in the surgical planning for a living-donor liver transplant and in the automatic detection and documentation of pathological states. A method is being developed to automatically extract liver structure from abdominal CT scans using a priori information about liver morphology and digital image-processing techniques. Segmentation is performed sequentially image-by-image (slice-by-slice), starting with a reference image in which the liver occupies almost the entire right half of the abdomen cross section. Image processing techniques include gray-level thresholding, Gaussian smoothing, and eight-point connectivity tracking. For each case, the shape, size, and pixel density distribution of the liver are recorded for each CT image and used in the processing of other CT images. Extracted boundaries of the liver are smoothed using mathematical morphology techniques and B-splines. Computer-determined boundaries were compared with those drawn by a radiologist. The boundary descriptions from the two methods were in agreement, and the calculated areas were within 10%

  18. Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.

    Science.gov (United States)

    Loss, Leandro A; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

    2012-10-01

    Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides.

  19. Common neighbour structure and similarity intensity in complex networks

    Science.gov (United States)

    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.

  20. Revelation of the Sun Self-Similarity Skeletal Structures

    International Nuclear Information System (INIS)

    Rantsev-Kartinov, V.A.

    2005-01-01

    The analysis of databases of photographic images of a surface of the Sun, its atmosphere and the closest its space environment taken at various spatial resolutions and for various types of radiation of a surface of the Sun by means of a method multilevel dynamic contrasting, has revealed presence skeletal structures as on the Sun directly such and in its environment. It is demonstrated the revealed a global structures of the Sun and powerful ejections of mass of its corona, as well as the structures of its atmosphere, protuberances, sun-spots and a globular structures of its photosphere

  1. Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

    Energy Technology Data Exchange (ETDEWEB)

    Smart, Oliver S., E-mail: osmart@globalphasing.com; Womack, Thomas O.; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom)

    2012-04-01

    Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled. Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and @@target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -target enables the correct ligand-binding structure to be found, and http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

  2. Assessment of Vegetation Structural Diversity and Similarity Index of ...

    African Journals Online (AJOL)

    Data were analysed using descriptive statistics, relative density, diversity and similarity indices. The result showed that the forest reserve has one hundred and ninety species of plants belonging to sixty three families. The dominant plant families recorded in the forest are Leguminosae (12.63%), Rubiaceae (8.42%), ...

  3. Anatomical pulmonary magnetic resonance imaging segmentation for regional structure-function measurements of asthma

    Energy Technology Data Exchange (ETDEWEB)

    Guo, F. [Robarts Research Institute, University of Western Ontario, London, Ontario N6A 5B7 (Canada); Graduate Program in Biomedical Engineering, University of Western Ontario, London, Ontario N6A 5B9 (Canada); Svenningsen, S.; Eddy, R. L.; Capaldi, D. P. I.; Sheikh, K. [Robarts Research Institute, University of Western Ontario, London, Ontario N6A 5B7 (Canada); Department of Medical Biophysics, University of Western Ontario, London, Ontario N6A 5C1 (Canada); Fenster, A.; Parraga, G., E-mail: gparraga@robarts.ca [Robarts Research Institute, University of Western Ontario, London, Ontario N6A 5B7 (Canada); Graduate Program in Biomedical Engineering, University of Western Ontario, London, Ontario N6A 5B9 (Canada); Department of Medical Biophysics, University of Western Ontario, London, Ontario N6A 5C1 (Canada)

    2016-06-15

    Purpose: Pulmonary magnetic-resonance-imaging (MRI) and x-ray computed-tomography have provided strong evidence of spatially and temporally persistent lung structure-function abnormalities in asthmatics. This has generated a shift in their understanding of lung disease and supports the use of imaging biomarkers as intermediate endpoints of asthma severity and control. In particular, pulmonary {sup 1}H MRI can be used to provide quantitative lung structure-function measurements longitudinally and in response to treatment. However, to translate such biomarkers of asthma, robust methods are required to segment the lung from pulmonary {sup 1}H MRI. Therefore, their objective was to develop a pulmonary {sup 1}H MRI segmentation algorithm to provide regional measurements with the precision and speed required to support clinical studies. Methods: The authors developed a method to segment the left and right lung from {sup 1}H MRI acquired in 20 asthmatics including five well-controlled and 15 severe poorly controlled participants who provided written informed consent to a study protocol approved by Health Canada. Same-day spirometry and plethysmography measurements of lung function and volume were acquired as well as {sup 1}H MRI using a whole-body radiofrequency coil and fast spoiled gradient-recalled echo sequence at a fixed lung volume (functional residual capacity + 1 l). We incorporated the left-to-right lung volume proportion prior based on the Potts model and derived a volume-proportion preserved Potts model, which was approximated through convex relaxation and further represented by a dual volume-proportion preserved max-flow model. The max-flow model led to a linear problem with convex and linear equality constraints that implicitly encoded the proportion prior. To implement the algorithm, {sup 1}H MRI was resampled into ∼3 × 3 × 3 mm{sup 3} isotropic voxel space. Two observers placed seeds on each lung and on the background of 20 pulmonary {sup 1}H MR images

  4. HIV and influenza share a similar structural blueprint

    Science.gov (United States)

    HIV uses a protein called the envelope glycoprotein spike to attach itself and fuse with the cell membrane; NCI scientists have now defined the structure of this spike in its pre-fusion state using cryo-electron microscopy

  5. Structural covariance of brain region volumes is associated with both structural connectivity and transcriptomic similarity.

    Science.gov (United States)

    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

  6. MR brain scan tissues and structures segmentation: local cooperative Markovian agents and Bayesian formulation

    International Nuclear Information System (INIS)

    Scherrer, B.

    2008-12-01

    Accurate magnetic resonance brain scan segmentation is critical in a number of clinical and neuroscience applications. This task is challenging due to artifacts, low contrast between tissues and inter-individual variability that inhibit the introduction of a priori knowledge. In this thesis, we propose a new MR brain scan segmentation approach. Unique features of this approach include (1) the coupling of tissue segmentation, structure segmentation and prior knowledge construction, and (2) the consideration of local image properties. Locality is modeled through a multi-agent framework: agents are distributed into the volume and perform a local Markovian segmentation. As an initial approach (LOCUS, Local Cooperative Unified Segmentation), intuitive cooperation and coupling mechanisms are proposed to ensure the consistency of local models. Structures are segmented via the introduction of spatial localization constraints based on fuzzy spatial relations between structures. In a second approach, (LOCUS-B, LOCUS in a Bayesian framework) we consider the introduction of a statistical atlas to describe structures. The problem is reformulated in a Bayesian framework, allowing a statistical formalization of coupling and cooperation. Tissue segmentation, local model regularization, structure segmentation and local affine atlas registration are then coupled in an EM framework and mutually improve. The evaluation on simulated and real images shows good results, and in particular, a robustness to non-uniformity and noise with low computational cost. Local distributed and cooperative MRF models then appear as a powerful and promising approach for medical image segmentation. (author)

  7. Structure-properties relationships of novel poly(carbonate-co-amide) segmented copolymers with polyamide-6 as hard segments and polycarbonate as soft segments

    Science.gov (United States)

    Yang, Yunyun; Kong, Weibo; Yuan, Ye; Zhou, Changlin; Cai, Xufu

    2018-04-01

    Novel poly(carbonate-co-amide) (PCA) block copolymers are prepared with polycarbonate diol (PCD) as soft segments, polyamide-6 (PA6) as hard segments and 4,4'-diphenylmethane diisocyanate (MDI) as coupling agent through reactive processing. The reactive processing strategy is eco-friendly and resolve the incompatibility between polyamide segments and PCD segments in preparation processing. The chemical structure, crystalline properties, thermal properties, mechanical properties and water resistance were extensively studied by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Differential scanning calorimetry (DSC), Thermal gravity analysis (TGA), Dynamic mechanical analysis (DMA), tensile testing, water contact angle and water absorption, respectively. The as-prepared PCAs exhibit obvious microphase separation between the crystalline hard PA6 phase and amorphous PCD soft segments. Meanwhile, PCAs showed outstanding mechanical with the maximum tensile strength of 46.3 MPa and elongation at break of 909%. The contact angle and water absorption results indicate that PCAs demonstrate outstanding water resistance even though possess the hydrophilic surfaces. The TGA measurements prove that the thermal stability of PCA can satisfy the requirement of multiple-processing without decomposition.

  8. Structural constraints in the packaging of bluetongue virus genomic segments

    OpenAIRE

    Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C.; Roy, Polly

    2014-01-01

    : The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by bioche...

  9. Evaluating the effect of multiple sclerosis lesions on automatic brain structure segmentation

    Directory of Open Access Journals (Sweden)

    Sandra González-Villà

    2017-01-01

    Full Text Available In recent years, many automatic brain structure segmentation methods have been proposed. However, these methods are commonly tested with non-lesioned brains and the effect of lesions on their performance has not been evaluated. Here, we analyze the effect of multiple sclerosis (MS lesions on three well-known automatic brain structure segmentation methods, namely, FreeSurfer, FIRST and multi-atlas fused by majority voting, which use learning-based, deformable and atlas-based strategies, respectively. To perform a quantitative analysis, 100 synthetic images of MS patients with a total of 2174 lesions are simulated on two public databases with available brain structure ground truth information (IBSR18 and MICCAI’12. The Dice similarity coefficient (DSC differences and the volume differences between the healthy and the simulated images are calculated for the subcortical structures and the brainstem. We observe that the three strategies are affected when lesions are present. However, the effects of the lesions do not follow the same pattern; the lesions either make the segmentation method underperform or surprisingly augment the segmentation accuracy. The obtained results show that FreeSurfer is the method most affected by the presence of lesions, with DSC differences (generated − healthy ranging from −0.11 ± 0.54 to 9.65 ± 9.87, whereas FIRST tends to be the most robust method when lesions are present (−2.40 ± 5.54 to 0.44 ± 0.94. Lesion location is not important for global strategies such as FreeSurfer or majority voting, where structure segmentation is affected wherever the lesions exist. On the other hand, FIRST is more affected when the lesions are overlaid or close to the structure of analysis. The most affected structure by the presence of lesions is the nucleus accumbens (from −1.12 ± 2.53 to 1.32 ± 4.00 for the left hemisphere and from −2.40 ± 5.54 to 9.65 ± 9.87 for the right hemisphere, whereas the

  10. Unsupervised Word Mapping Using Structural Similarities in Monolingual Embeddings

    OpenAIRE

    Aldarmaki, Hanan; Mohan, Mahesh; Diab, Mona

    2017-01-01

    Most existing methods for automatic bilingual dictionary induction rely on prior alignments between the source and target languages, such as parallel corpora or seed dictionaries. For many language pairs, such supervised alignments are not readily available. We propose an unsupervised approach for learning a bilingual dictionary for a pair of languages given their independently-learned monolingual word embeddings. The proposed method exploits local and global structures in monolingual vector ...

  11. Structure of the clinical and geriatric depression: Similarities and differences

    Directory of Open Access Journals (Sweden)

    Novović Zdenka

    2006-01-01

    Full Text Available Studies demonstrating the uniqueness of depression in old age are numerous, but conclusions on the fact if the problems of the elderly people cause depression or if they are a part of depression are not unique. The aim of this paper is to compare the structure of depression of old people without the history of mental illness and middle-aged people treated for depression. The sample consists of 82 healthy inmates of different Homes for the Aged and 78 patients diagnosed with some sort of affective disorder. A depression has been assessed with the shorten version of the MMPI D-scale. The structure of the geriatric and clinical depression has been compared with the method of maximum likelihood, over the matrix of co-variances of answers on the items on the depression scale. The results point out to the statistically significant difference in the structure of depression of the old and clinically depressed individuals. However, half of the items of the D-scale have significant loadings on the factor of depression in both groups. The essence of the depression in both samples is made of cognitive subject matters, depressive affect, decline of motivation and a negative estimate of one's basic abilities. Symptoms concerning low self-esteem, experiencing cognitive deficit, energy and impaired physical health have been significant in describing the clinical depression, while a feeling of reduced positive stimulation and the affective liability is typical for the depression of geriatric sample. The conclusion is that, despite the differences, there is a common core of symptoms that makes the essence of depression, apart from the samples.

  12. Synthesis of resorcinolic lipids bearing structural similarities to cytosporone A

    International Nuclear Information System (INIS)

    Santos, Edson dos Anjos dos; Beatriz, Adilson; Lima, Denis Pires de; Marques, Maria Rita; Leite, Carla Braga

    2009-01-01

    Inspired by the structure and biological activities of resorcinolic lipids and, particularly cytosporone A- a potent inhibitor of plantule germination and growth, we have performed the synthesis of the analogs 3-heptyl-3-hydroxy-5,7-dimethoxy-2-benzofuran-1(3H)-one (1) and 3-heptyl-3-hydroxy-4,6-dimethoxy-2-benzofuran-1(3H)-one (2). The intermediates and products were submitted to allelopathic test using Lactuca sativa L. seeds. Target compound 1 showed an inhibitory effect on germination and growth of hypocotyl and radicle in millimolar range. (author)

  13. Synthesis of resorcinolic lipids bearing structural similarities to cytosporone A

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Edson dos Anjos dos; Beatriz, Adilson; Lima, Denis Pires de [Universidade Federal Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Centro de Ciencias Exatas e Tecnologia. Dept. de Quimica], e-mail: dlima@nin.ufms.br; Marques, Maria Rita; Leite, Carla Braga [Universidade Federal Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Centro de Ciencias Biologicas. Dept. de Morfofisiologia

    2009-07-01

    Inspired by the structure and biological activities of resorcinolic lipids and, particularly cytosporone A- a potent inhibitor of plantule germination and growth, we have performed the synthesis of the analogs 3-heptyl-3-hydroxy-5,7-dimethoxy-2-benzofuran-1(3H)-one (1) and 3-heptyl-3-hydroxy-4,6-dimethoxy-2-benzofuran-1(3H)-one (2). The intermediates and products were submitted to allelopathic test using Lactuca sativa L. seeds. Target compound 1 showed an inhibitory effect on germination and growth of hypocotyl and radicle in millimolar range. (author)

  14. Synthesis of resorcinolic lipids bearing structural similarities to cytosporone A

    Directory of Open Access Journals (Sweden)

    Edson dos Anjos dos Santos

    2009-01-01

    Full Text Available Inspired by the structure and biological activities of resorcinolic lipids and, particularly cytosporone A- a potent inhibitor of plantule germination and growth, we have performed the synthesis of the analogs 3-heptyl-3-hydroxy-5,7-dimethoxy-2-benzofuran-1(3H-one (1 and 3-heptyl-3-hydroxy-4,6-dimethoxy-2-benzofuran-1(3H-one (2. The intermediates and products were submitted to allelopathic test using Lactuca sativa L. seeds. Target compound 1 showed an inhibitory effect on germination and growth of hypocotyl and radicle in milimolar range.

  15. Zooplankton structure in two interconnected ponds: similarities and differences

    Directory of Open Access Journals (Sweden)

    Špoljar Maria

    2016-03-01

    Full Text Available The research of zooplankton diversity, abundance and trophic structure was conducted during the summer period in pelagial zone on the longitudinal profile of the Sutla River Backwater. Investigated site consists of two interconnected basins: transparent Upper Basin with submerged macrophytes and turbid Lower Basin without macrophytes in the littoral zone. In the Upper Basin, abundance and diversity of zooplankton in the pelagial was higher in comparison to the Lower Basin, with prevailing species of genus Keratella as microfilter-feeder, and genera of Polyartha and Trihocerca as macrofilter-feeder rotifers. On the contrary, in the Lower Basin, crustaceans dominated in abundance. Microfilter-feeder cladoceran (Bosmina longirostris and larval and adult stages of macrofilter-feeder copepod (Macrocyclops albidus prevailed in the Lower Basin. Fish predation pressure was more pronounced in the pelagial of the Upper Basin, indicated by low cladoceran abundance in the surface layer. Although the studied basins were interconnected, results indicate significant (Mann-Whitney U test, p < 0.05 differences in the zooplankton structure as a potential result of the macrophyte impact on environmental conditions and fish predation pressure.

  16. Straight trajectory planning for keyhole neurosurgery in sheep with automatic brain structures segmentation

    Science.gov (United States)

    Favaro, Alberto; Lad, Akash; Formenti, Davide; Zani, Davide Danilo; De Momi, Elena

    2017-03-01

    In a translational neuroscience/neurosurgery perspective, sheep are considered good candidates to study because of the similarity between their brain and the human one. Automatic planning systems for safe keyhole neurosurgery maximize the probe/catheter distance from vessels and risky structures. This work consists in the development of a trajectories planner for straight catheters placement intended to be used for investigating the drug diffusivity mechanisms in sheep brain. Automatic brain segmentation of gray matter, white matter and cerebrospinal fluid is achieved using an online available sheep atlas. Ventricles, midbrain and cerebellum segmentation have been also carried out. The veterinary surgeon is asked to select a target point within the white matter to be reached by the probe and to define an entry area on the brain cortex. To mitigate the risk of hemorrhage during the insertion process, which can prevent the success of the insertion procedure, the trajectory planner performs a curvature analysis of the brain cortex and wipes out from the poll of possible entry points the sulci, as part of brain cortex where superficial blood vessels are naturally located. A limited set of trajectories is then computed and presented to the surgeon, satisfying an optimality criteria based on a cost function which considers the distance from critical brain areas and the whole trajectory length. The planner proved to be effective in defining rectilinear trajectories accounting for the safety constraints determined by the brain morphology. It also demonstrated a short computational time and good capability in segmenting gyri and sulci surfaces.

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

    Science.gov (United States)

    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

  18. Automated brain structure segmentation based on atlas registration and appearance models

    DEFF Research Database (Denmark)

    van der Lijn, Fedde; de Bruijne, Marleen; Klein, Stefan

    2012-01-01

    Accurate automated brain structure segmentation methods facilitate the analysis of large-scale neuroimaging studies. This work describes a novel method for brain structure segmentation in magnetic resonance images that combines information about a structure’s location and appearance. The spatial...... with different magnetic resonance sequences, in which the hippocampus and cerebellum were segmented by an expert. Furthermore, the method is compared to two other segmentation techniques that were applied to the same data. Results show that the atlas- and appearance-based method produces accurate results...

  19. A study of symbol segmentation method for handwritten mathematical formula recognition using mathematical structure information

    OpenAIRE

    Toyozumi, Kenichi; Yamada, Naoya; Kitasaka, Takayuki; Mori, Kensaku; Suenaga, Yasuhito; Mase, Kenji; Takahashi, Tomoichi

    2004-01-01

    Symbol segmentation is very important in handwritten mathematical formula recognition, since it is the very first portion of the recognition, since it is the very first portion of the recognition process. This paper proposes a new symbol segmentation method using mathematical structure information. The base technique of symbol segmentation employed in theexisting methods is dynamic programming which optimizes the overall results of individual symbol recognition. The new method we propose here...

  20. HOMOLOGY BETWEEN SEGMENTS OF HUMAN HEMOSTATIC PROTEINS AND PROTEINS OF VIRUSES WHICH CAUSE ACUTE RESPIRATORY INFECTIONS OR DISEASES WITH SIMILAR SYMPTOMS

    Directory of Open Access Journals (Sweden)

    I. N. Zhilinskaya

    2017-01-01

    Full Text Available Objectives: To identify homologous segments of human hemostatic and viral proteins and to assess the role of human hemostatic proteins in viral replication. Materials and Methods: The following viruses were chosen for comparison: influenza B (B/Astrakhan/2/2017, coronaviruses (Hcov229E and SARS-Co, type 1 adenovirus (adenoid 71, measles (ICHINOSE-BA and rubella (Therien. The primary structures of viral proteins and 41 human hemostatic proteins were obtained from open–access www.ncbi.nlm.nih. gov and www.nextprot.org databases, respectively. Sequence homology was determined by comparing 12-amino-acid segments. Those sequences identical in ≥ 8 positions were considered homologous. Results: The analysis shows that viral proteins contain segments which mimic a number of human hemostatic proteins. Most of these segments, except those of adenovirus proteins, are homologous with coagulation factors. The increase in viral virulence, as in case of SARS-Co, correlates with an increased number of segments homologous with hemostatic proteins. Conclusion: Hemostasis plays an important role in viral replication and pathogenesis. The conclusion is consistent with the literature data about the relationship of hemostasis and inflammatory response to viral infections.

  1. Marginal space learning for medical image analysis efficient detection and segmentation of anatomical structures

    CERN Document Server

    Zheng, Yefeng

    2014-01-01

    Presents an award winning image analysis technology (Thomas Edison Patent Award, MICCAI Young Investigator Award) that achieves object detection and segmentation with state-of-the-art accuracy and efficiency Flexible, machine learning-based framework, applicable across multiple anatomical structures and imaging modalities Thirty five clinical applications on detecting and segmenting anatomical structures such as heart chambers and valves, blood vessels, liver, kidney, prostate, lymph nodes, and sub-cortical brain structures, in CT, MRI, X-Ray and Ultrasound.

  2. TH-C-18A-02: Machine Learning and STAPLE Based Simultaneous Longitudinal Segmentation of Bone and Marrow Structures From Dual Energy CT

    International Nuclear Information System (INIS)

    Fehr, D; Schmidtlein, C; Hwang, S; Deasy, J; Veeraraghavan, H

    2014-01-01

    Purpose: To develop a fully-automatic longitudinal bone and marrow segmentation method in the pelvic region from dual energy computed tomography (DECT). Methods: We developed a two-step automatic bone and marrow segmentation method for simultaneous longitudinal evaluation of patients with metastatic bone disease using dual energy CT (DECT). Our approach transforms the DECT images into a multi-material decomposition (MMD) model that represents the voxels as a mixture of multiple materials. A support vector machine (SVM) was trained using a single scan. In the first step of the longitudinal segmentation the trained SVM model detects bone and marrow structures on all available longitudinal scans. Segmentation is further refined through active contour segmentation. In the second step, the segmentations from the individual scans are merged by employing the simultaneous truth and performance level estimation (STAPLE) algorithm. The scans are registered using affine and deformable registration. We found that our approach improves the segmentation in all the scans under reliable registration performance between the same scans. Improving registration was not under the scope of this work. Results: We applied our approach to segment bone and marrow in DECT scans in the pelvic regions for multiple patients. Each patient had three to five follow up scans. All the patients in the analysis had artificial metal prostheses which introduced challenges for the registration. Our algorithm achieved reasonable accurate segmentation despite the presence of metal artifacts and high-density oral contrast in neighboring structures. Our approach obtained an overall segmentation accuracy of 80% using DICE metric. Conclusion: We developed a two-step automatic longitudinal segmentation technique for bone and marrow region structures in the pelvic areas from dual energy CT. Our approach achieves robust segmentation despite the presence of confounding structures with similar intensities as the

  3. Structured prediction for urban scene semantic segmentation with geographic contex

    OpenAIRE

    Volpi Michele; Ferrari Vittorio

    2015-01-01

    In this work we address the problem of semantic segmentation of urban remote sensing images into land cover maps. We propose to tackle this task by learning the geographic context of classes and use it to favor or discourage certain spatial configuration of label assignments. For this reason, we learn from training data two spatial priors enforcing different key aspects of the geographical space: local co-occurrence and relative location of land cover classes. We propose to embed these geogra...

  4. Hartley and Itokawa: small comet and asteroid with similar morphologies and structures

    Science.gov (United States)

    Kochemasov, G. G.

    2011-10-01

    at the convex bulge, from the antipodean side (Fig. 5). The smaller rocky asteroid Itokawa (0.5 km long, Fig. 2) is surprisingly similar in shape and structure to the icy core of Hart ley. It is also bent and rich in cross-cutting lineations o 4 direct ions marked by small holes-craters. But here they are ext inct and lack of gas -dust jets. One sees a transition from a volat ile rich comet core to an ext inct mostly rocky mass - asteroid. In both cases (comet core and as teroid) in the middle develops a smooth "wais t". The bulged convex and antipodal concave segments -hemispheres in rotating bodies require somewhat different densities of composing them masses to equilibrate angular momentum of two halves (compare with the Ea rth's hemis pheres : the eas tern continental "granitic" and wes tern Pacific "bas altic"). The near-IR images of two asteroids (Fig.6-7) confirm this. The concave and convex s ides are co mpos itionally d ifferent. In the Eros ' cas e the concave s ide is rich er in pyroxene, thus denser.

  5. Different measures of structural similarity tap different aspects of visual object processing

    DEFF Research Database (Denmark)

    Gerlach, Christian

    2017-01-01

    The structural similarity of objects has been an important variable in explaining why some objects are easier to categorize at a superordinate level than to individuate, and also why some patients with brain injury have more difficulties in recognizing natural (structurally similar) objects than...... artifacts (structurally distinct objects). In spite of its merits as an explanatory variable, structural similarity is not a unitary construct, and it has been operationalized in different ways. Furthermore, even though measures of structural similarity have been successful in explaining task and category-effects...

  6. Self-similar structure in the distribution and density of the partition function zeros

    International Nuclear Information System (INIS)

    Huang, M.-C.; Luo, Y.-P.; Liaw, T.-M.

    2003-01-01

    Based on the knowledge of the partition function zeros for the cell-decorated triangular Ising model, we analyze the similar structures contained in the distribution pattern and density function of the zeros. The two own the same symmetries, and the arising of the similar structure in the road toward the infinite decoration-level is exhibited explicitly. The distinct features of the formation of the self-similar structure revealed from this model may be quite general

  7. Thai Language Sentence Similarity Computation Based on Syntactic Structure and Semantic Vector

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Automated geographic atrophy segmentation for SD-OCT images using region-based C-V model via local similarity factor.

    Science.gov (United States)

    Niu, Sijie; de Sisternes, Luis; Chen, Qiang; Leng, Theodore; Rubin, Daniel L

    2016-02-01

    Age-related macular degeneration (AMD) is the leading cause of blindness among elderly individuals. Geographic atrophy (GA) is a phenotypic manifestation of the advanced stages of non-exudative AMD. Determination of GA extent in SD-OCT scans allows the quantification of GA-related features, such as radius or area, which could be of important value to monitor AMD progression and possibly identify regions of future GA involvement. The purpose of this work is to develop an automated algorithm to segment GA regions in SD-OCT images. An en face GA fundus image is generated by averaging the axial intensity within an automatically detected sub-volume of the three dimensional SD-OCT data, where an initial coarse GA region is estimated by an iterative threshold segmentation method and an intensity profile set, and subsequently refined by a region-based Chan-Vese model with a local similarity factor. Two image data sets, consisting on 55 SD-OCT scans from twelve eyes in eight patients with GA and 56 SD-OCT scans from 56 eyes in 56 patients with GA, respectively, were utilized to quantitatively evaluate the automated segmentation algorithm. We compared results obtained by the proposed algorithm, manual segmentation by graders, a previously proposed method, and experimental commercial software. When compared to a manually determined gold standard, our algorithm presented a mean overlap ratio (OR) of 81.86% and 70% for the first and second data sets, respectively, while the previously proposed method OR was 72.60% and 65.88% for the first and second data sets, respectively, and the experimental commercial software OR was 62.40% for the second data set.

  10. Solution structure of LC4 transmembrane segment of CCR5.

    Directory of Open Access Journals (Sweden)

    Kazuhide Miyamoto

    Full Text Available CC-chemokine receptor 5 (CCR5 is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1. The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region.

  11. Solution structure of LC4 transmembrane segment of CCR5.

    Science.gov (United States)

    Miyamoto, Kazuhide; Togiya, Kayo

    2011-01-01

    CC-chemokine receptor 5 (CCR5) is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1). The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region.

  12. Solution Structure of LC4 Transmembrane Segment of CCR5

    OpenAIRE

    Miyamoto, Kazuhide; Togiya, Kayo

    2011-01-01

    CC-chemokine receptor 5 (CCR5) is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1). The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescdence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 ...

  13. Structural analysis of the large coil segment test

    International Nuclear Information System (INIS)

    Cain, W.D.; Gray, W.H.; Hendrich, W.R.; Nelson, B.E.; Stoddart, W.C.T.

    1977-01-01

    In the analysis of the LCS, it has been demonstrated that it is possible to design complex structures utilizing existing hardware in a highly reliable and efficient manner. It has also been shown that GIFTS is very useful for aiding in the design and analysis of these complex structures. GIFTS' element generation and graphics display capabilities allow for on-line structural analysis to be performed and permit the incorporation and analysis of major design changes in short periods of time. This flexibility means that more design iterations can be analyzed, and thus a better design can often be achieved instead of just an adequate design. The on-line nature of GIFTS allows for continuity of thought and its visual displays highlight trouble areas which can usually be redesigned in an efficient manner. For the LCS, GIFTS was used to generate a working design of the complete system in a logical and efficient manner in a relatively short period of time

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Cherkasov Artem

    2004-05-01

    Full Text Available Abstract 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.

  16. Automated segmentation of pulmonary structures in thoracic computed tomography scans: a review

    International Nuclear Information System (INIS)

    Van Rikxoort, Eva M; Van Ginneken, Bram

    2013-01-01

    Computed tomography (CT) is the modality of choice for imaging the lungs in vivo. Sub-millimeter isotropic images of the lungs can be obtained within seconds, allowing the detection of small lesions and detailed analysis of disease processes. The high resolution of thoracic CT and the high prevalence of lung diseases require a high degree of automation in the analysis pipeline. The automated segmentation of pulmonary structures in thoracic CT has been an important research topic for over a decade now. This systematic review provides an overview of current literature. We discuss segmentation methods for the lungs, the pulmonary vasculature, the airways, including airway tree construction and airway wall segmentation, the fissures, the lobes and the pulmonary segments. For each topic, the current state of the art is summarized, and topics for future research are identified. (topical review)

  17. Structural Segmentation of Toru Takemitsu's Piece, Itinerant, by Advanced Level Music Graduate Students.

    Science.gov (United States)

    Ordoñana, Jose A; Laucirica, Ana

    2017-01-01

    This work attempts to study the way higher music graduate students segment a contemporary music work, Itinerant, and to understand the influence of musical feature on segmentation. It attempts to test the theory stating that saliences contribute to organising the music surface. The 42 students listened to the work several times and, in real time, they were requested to indicate the places on the score where they perceived structural boundaries. This work is characterised by its linearity, which could hinder identification of saliences and thereby, the establishment of structural boundaries. The participants show stability in the points of segmentation chosen. The results show significant coincidences among the participants in strategic places of the work, which leads us to conclude, in line with other researches, although in a work with different characteristics, that listeners can find a structural organisation in contemporary music that could allow them to understand it.

  18. Structural Segmentation of Toru Takemitsu’s Piece, Itinerant, by Advanced Level Music Graduate Students

    Directory of Open Access Journals (Sweden)

    Jose A. Ordoñana

    2017-05-01

    Full Text Available This work attempts to study the way higher music graduate students segment a contemporary music work, Itinerant, and to understand the influence of musical feature on segmentation. It attempts to test the theory stating that saliences contribute to organising the music surface. The 42 students listened to the work several times and, in real time, they were requested to indicate the places on the score where they perceived structural boundaries. This work is characterised by its linearity, which could hinder identification of saliences and thereby, the establishment of structural boundaries. The participants show stability in the points of segmentation chosen. The results show significant coincidences among the participants in strategic places of the work, which leads us to conclude, in line with other researches, although in a work with different characteristics, that listeners can find a structural organisation in contemporary music that could allow them to understand it.

  19. Automated method for structural segmentation of nasal airways based on cone beam computed tomography

    Science.gov (United States)

    Tymkovych, Maksym Yu.; Avrunin, Oleg G.; Paliy, Victor G.; Filzow, Maksim; Gryshkov, Oleksandr; Glasmacher, Birgit; Omiotek, Zbigniew; DzierŻak, RóŻa; Smailova, Saule; Kozbekova, Ainur

    2017-08-01

    The work is dedicated to the segmentation problem of human nasal airways using Cone Beam Computed Tomography. During research, we propose a specialized approach of structured segmentation of nasal airways. That approach use spatial information, symmetrisation of the structures. The proposed stages can be used for construction a virtual three dimensional model of nasal airways and for production full-scale personalized atlases. During research we build the virtual model of nasal airways, which can be used for construction specialized medical atlases and aerodynamics researches.

  20. Design of the segment structure and coolant ducts for a fusion reactor blanket and shield

    International Nuclear Information System (INIS)

    Briaris, D.A.; Stanbridge, J.R.

    1978-05-01

    An outline design and analysis of a support structure for the replaceable first wall of a helium cooled fusion reactor blanket has been undertaken. The proposed structure supports all the segment gravitational loads with maximum deflections limited to < 10 mm, and is itself supported off the outer shield by a simple vee-in-groove arrangement. It is a feature of the design that the coaxial coolant pipes and the segment structure operate at the same temperature, making it possible for them to be integrated, thereby avoiding the necessity for pipe bellows. The requirements of cooling the inner arm of the structure and increasing the major radius of the torus by approximately = 0.5 m, have been identified as problems associated with the 'horseshoe' shaped structure applicable to the reactor with divertor. For a ring structure, i.e. reactor without divertor, these problems do not arise. (author)

  1. A Structural-Lexical Measure of Semantic Similarity for Geo-Knowledge Graphs

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2015-04-01

    Full Text Available Graphs have become ubiquitous structures to encode geographic knowledge online. The Semantic Web’s linked open data, folksonomies, wiki websites and open gazetteers can be seen as geo-knowledge graphs, that is labeled graphs whose vertices represent geographic concepts and whose edges encode the relations between concepts. To compute the semantic similarity of concepts in such structures, this article defines the network-lexical similarity measure (NLS. This measure estimates similarity by combining two complementary sources of information: the network similarity of vertices and the semantic similarity of the lexical definitions. NLS is evaluated on the OpenStreetMap Semantic Network, a crowdsourced geo-knowledge graph that describes geographic concepts. The hybrid approach outperforms both network and lexical measures, obtaining very strong correlation with the similarity judgments of human subjects.

  2. Multidrug transporters from bacteria to man : similarities in structure and function

    NARCIS (Netherlands)

    van Veen, HW; Konings, WN

    Organisms ranging from bacteria to man possess transmembrane transporters which confer resistance to toxic corn pounds. Underlining their biological significance, prokaryotic and eukaryotic multidrug transport proteins are very similar in structure and function. Therefore, a study of the factors

  3. Hospital costs and revenue are similar for resuscitated out-of-hospital cardiac arrest and ST-segment acute myocardial infarction patients.

    Science.gov (United States)

    Swor, Robert; Lucia, Victoria; McQueen, Kelly; Compton, Scott

    2010-06-01

    Care provided to patients who survive to hospital admission after out-of-hospital cardiac arrest (OOHCA) is sometimes viewed as expensive and a poor use of hospital resources. The objective was to describe financial parameters of care for patients resuscitated from OOHCA. This was a retrospective review of OOHCA patients admitted to one academic teaching hospital from January 2004 to October 2007. Demographic data, length of stay (LOS), and discharge disposition were obtained for all patients. Financial parameters of patient care including total cost, net revenue, and operating margin were calculated by hospital cost accounting and reported as median and interquartile range (IQR). Groups were dichotomized by survival to discharge for subgroup analysis. To provide a reference group for context, similar financial data were obtained for ST-segment elevation myocardial infarction (STEMI) patients admitted during the same time period, reported with medians and IQRs. During the study period, there were 72 admitted OOCHA patients and 404 STEMI patients. OOCHA and STEMI groups were similar for age, sex, and insurance type. Overall, 27 (38.6%) OOHCA patients survived to hospital discharge. Median LOS for OOHCA patients was 4 days (IQR = 1-8 days), with most of those hospitalized for Financial parameters for OOHCA patients are similar to those of STEMI patients. Financial issues should not be a negative incentive to providing care for these patients. (c) 2010 by the Society for Academic Emergency Medicine.

  4. Enhancement of nerve structure segmentation by a correntropy-based pre-image approach

    Directory of Open Access Journals (Sweden)

    J. Gil-González

    2017-05-01

    Full Text Available Peripheral Nerve Blocking (PNB is a commonly used technique for performing regional anesthesia and managing pain. PNB comprises the administration of anesthetics in the proximity of a nerve. In this sense, the success of PNB procedures depends on an accurate location of the target nerve. Recently, ultrasound images (UI have been widely used to locate nerve structures for PNB, since they enable a noninvasive visualization of the target nerve and the anatomical structures around it. However, UI are affected by speckle noise, which makes it difficult to accurately locate a given nerve. Thus, it is necessary to perform a filtering step to attenuate the speckle noise without eliminating relevant anatomical details that are required for high-level tasks, such as segmentation of nerve structures. In this paper, we propose an UI improvement strategy with the use of a pre-image-based filter. In particular, we map the input images by a nonlinear function (kernel. Specifically, we employ a correntropybased mapping as kernel functional to code higher-order statistics of the input data under both nonlinear and non-Gaussian conditions. We validate our approach against an UI dataset focused on nerve segmentation for PNB. Likewise, our Correntropy-based Pre-Image Filtering (CPIF is applied as a pre-processing stage to segment nerve structures in a UI. The segmentation performance is measured in terms of the Dice coefficient. According to the results, we observe that CPIF finds a suitable approximation for UI by highlighting discriminative nerve patterns.

  5. The Effect of Vocalic vs. Consonantal Phonetic Structure on Language Segmentability: the Case of Danish

    DEFF Research Database (Denmark)

    Trecca, Fabio; Bleses, Dorthe; Christiansen, Morten Hyllekvist

    Danish-learning children are slower in the acquisition of receptive vocabulary than children in a range of other language groups. We have hypothesized that the phonetic structure of Danish, rich in vocoids and long vocalic stretches, might reduce the segmentability of the language and impede...

  6. On Line Segment Length and Mapping 4-regular Grid Structures in Network Infrastructures

    DEFF Research Database (Denmark)

    Riaz, Muhammad Tahir; Nielsen, Rasmus Hjorth; Pedersen, Jens Myrup

    2006-01-01

    The paper focuses on mapping the road network into 4-regular grid structures. A mapping algorithm is proposed. To model the road network GIS data have been used. The Geographic Information System (GIS) data for the road network are composed with different size of line segment lengths...

  7. A Feature-Based Structural Measure: An Image Similarity Measure for Face Recognition

    Directory of Open Access Journals (Sweden)

    Noor Abdalrazak Shnain

    2017-08-01

    Full Text Available Facial recognition is one of the most challenging and interesting problems within the field of computer vision and pattern recognition. During the last few years, it has gained special attention due to its importance in relation to current issues such as security, surveillance systems and forensics analysis. Despite this high level of attention to facial recognition, the success is still limited by certain conditions; there is no method which gives reliable results in all situations. In this paper, we propose an efficient similarity index that resolves the shortcomings of the existing measures of feature and structural similarity. This measure, called the Feature-Based Structural Measure (FSM, combines the best features of the well-known SSIM (structural similarity index measure and FSIM (feature similarity index measure approaches, striking a balance between performance for similar and dissimilar images of human faces. In addition to the statistical structural properties provided by SSIM, edge detection is incorporated in FSM as a distinctive structural feature. Its performance is tested for a wide range of PSNR (peak signal-to-noise ratio, using ORL (Olivetti Research Laboratory, now AT&T Laboratory Cambridge and FEI (Faculty of Industrial Engineering, São Bernardo do Campo, São Paulo, Brazil databases. The proposed measure is tested under conditions of Gaussian noise; simulation results show that the proposed FSM outperforms the well-known SSIM and FSIM approaches in its efficiency of similarity detection and recognition of human faces.

  8. Identification of similar regions of protein structures using integrated sequence and structure analysis tools

    Directory of Open Access Journals (Sweden)

    Heiland Randy

    2006-03-01

    Full Text Available Abstract Background Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. Results Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. Conclusion With structural genomics initiatives determining structures with little, if any, functional characterization

  9. Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms : VISCERAL Anatomy Benchmarks

    OpenAIRE

    Jimenez-del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andres; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H.; Fernandez, Tomas Salas; Schaer, Roger

    2016-01-01

    Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the ...

  10. ProCKSI: a decision support system for Protein (Structure Comparison, Knowledge, Similarity and Information

    Directory of Open Access Journals (Sweden)

    Błażewicz Jacek

    2007-10-01

    Full Text Available Abstract Background We introduce the decision support system for Protein (Structure Comparison, Knowledge, Similarity and Information (ProCKSI. ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Similarity Metric (USM, the Maximum Contact Map Overlap (MaxCMO of protein structures and other external methods such as the DaliLite and the TM-align methods, the Combinatorial Extension (CE of the optimal path, and the FAST Align and Search Tool (FAST. Additionally, ProCKSI allows the user to upload a user-defined similarity matrix supplementing the methods mentioned, and computes a similarity consensus in order to provide a rich, integrated, multicriteria view of large datasets of protein structures. Results We present ProCKSI's architecture and workflow describing its intuitive user interface, and show its potential on three distinct test-cases. In the first case, ProCKSI is used to evaluate the results of a previous CASP competition, assessing the similarity of proposed models for given targets where the structures could have a large deviation from one another. To perform this type of comparison reliably, we introduce a new consensus method. The second study deals with the verification of a classification scheme for protein kinases, originally derived by sequence comparison by Hanks and Hunter, but here we use a consensus similarity measure based on structures. In the third experiment using the Rost and Sander dataset (RS126, we investigate how a combination of different sets of similarity measures influences the quality and performance of ProCKSI's new consensus measure. ProCKSI performs well with all three datasets, showing its potential for complex, simultaneous multi-method assessment of structural similarity in large protein datasets. Furthermore, combining different similarity measures is usually more robust than

  11. Fast protein tertiary structure retrieval based on global surface shape similarity.

    Science.gov (United States)

    Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

    2008-09-01

    Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

  12. Discrete Self-Similarity in Interfacial Hydrodynamics and the Formation of Iterated Structures.

    Science.gov (United States)

    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.

  13. SEGMENTATION OF 3D MODELS FOR CULTURAL HERITAGE STRUCTURAL ANALYSIS – SOME CRITICAL ISSUES

    Directory of Open Access Journals (Sweden)

    S. Gonizzi Barsanti

    2017-08-01

    Full Text Available Cultural Heritage documentation and preservation has become a fundamental concern in this historical period. 3D modelling offers a perfect aid to record ancient buildings and artefacts and can be used as a valid starting point for restoration, conservation and structural analysis, which can be performed by using Finite Element Methods (FEA. The models derived from reality-based techniques, made up of the exterior surfaces of the objects captured at high resolution, are - for this reason - made of millions of polygons. Such meshes are not directly usable in structural analysis packages and need to be properly pre-processed in order to be transformed in volumetric meshes suitable for FEA. In addition, dealing with ancient objects, a proper segmentation of 3D volumetric models is needed to analyse the behaviour of the structure with the most suitable level of detail for the different sections of the structure under analysis. Segmentation of 3D models is still an open issue, especially when dealing with ancient, complicated and geometrically complex objects that imply the presence of anomalies and gaps, due to environmental agents such as earthquakes, pollution, wind and rain, or human factors. The aims of this paper is to critically analyse some of the different methodologies and algorithms available to segment a 3D point cloud or a mesh, identifying difficulties and problems by showing examples on different structures.

  14. Segmentation of 3d Models for Cultural Heritage Structural Analysis - Some Critical Issues

    Science.gov (United States)

    Gonizzi Barsanti, S.; Guidi, G.; De Luca, L.

    2017-08-01

    Cultural Heritage documentation and preservation has become a fundamental concern in this historical period. 3D modelling offers a perfect aid to record ancient buildings and artefacts and can be used as a valid starting point for restoration, conservation and structural analysis, which can be performed by using Finite Element Methods (FEA). The models derived from reality-based techniques, made up of the exterior surfaces of the objects captured at high resolution, are - for this reason - made of millions of polygons. Such meshes are not directly usable in structural analysis packages and need to be properly pre-processed in order to be transformed in volumetric meshes suitable for FEA. In addition, dealing with ancient objects, a proper segmentation of 3D volumetric models is needed to analyse the behaviour of the structure with the most suitable level of detail for the different sections of the structure under analysis. Segmentation of 3D models is still an open issue, especially when dealing with ancient, complicated and geometrically complex objects that imply the presence of anomalies and gaps, due to environmental agents such as earthquakes, pollution, wind and rain, or human factors. The aims of this paper is to critically analyse some of the different methodologies and algorithms available to segment a 3D point cloud or a mesh, identifying difficulties and problems by showing examples on different structures.

  15. Seismic Structure of the Shallow Mantle Beneath the Endeavor Segment of the Juan de Fuca Ridge

    Science.gov (United States)

    VanderBeek, B. P.; Toomey, D. R.; Hooft, E. E.; Wilcock, W. S.; Weekly, R. T.; Soule, D. C.

    2013-12-01

    We present tomographic images of the seismic structure of the shallow mantle beneath the intermediate-spreading Endeavor segment of the Juan de Fuca ridge. Our results provide insight into the relationship between magma supply from the mantle and overlying ridge crest processes. We use seismic energy refracted below the Moho (Pn), as recorded by the Endeavor tomography (ETOMO) experiment, to image the anisotropic and isotropic P wave velocity structure. The ETOMO experiment was an active source seismic study conducted in August 2009 as part of the RIDGE2000 science program. The experimental area extends 100 km along- and 60 km across-axis and encompasses active hydrothermal vent fields near the segment center, the eastern end of the Heck seamount chain, and two overlapping spreading centers (OSCs) at either end of the segment. Previous tomographic analyses of seismic arrivals refracted through the crust (Pg), and reflected off the Moho (PmP), constrain a three-dimensional starting model of crustal velocity and thickness. These Pg and PmP arrivals are incorporated in our inversion of Pn travel-time data to further constrain the isotropic and anisotropic mantle velocity structure. Preliminary results reveal three distinct mantle low-velocity zones, inferred as regions of mantle melt delivery to the base of the crust, that are located: (i) off-axis near the segment center, (ii) beneath the Endeavor-West Valley OSC, and (iii) beneath the Cobb OSC near Split Seamount. The mantle anomalies are located at intervals of ~30 to 40 km along-axis and the low velocity anomalies beneath the OSCs are comparable in magnitude to the one located near the segment center. The direction of shallow mantle flow is inferred from azimuthal variations in Pn travel-time residuals relative to a homogeneous isotropic mantle. Continuing analysis will focus on constraining spatial variations in the orientation of azimuthal anisotropy. On the basis of our results, we will discuss the transport of

  16. Three-dimensional segmentation and skeletonization to build an airway tree data structure for small animals

    International Nuclear Information System (INIS)

    Chaturvedi, Ashutosh; Lee, Zhenghong

    2005-01-01

    Quantitative analysis of intrathoracic airway tree geometry is important for objective evaluation of bronchial tree structure and function. Currently, there is more human data than small animal data on airway morphometry. In this study, we implemented a semi-automatic approach to quantitatively describe airway tree geometry by using high-resolution computed tomography (CT) images to build a tree data structure for small animals such as rats and mice. Silicon lung casts of the excised lungs from a canine and a mouse were used for micro-CT imaging of the airway trees. The programming language IDL was used to implement a 3D region-growing threshold algorithm for segmenting out the airway lung volume from the CT data. Subsequently, a fully-parallel 3D thinning algorithm was implemented in order to complete the skeletonization of the segmented airways. A tree data structure was then created and saved by parsing through the skeletonized volume using the Python programming language. Pertinent information such as the length of all airway segments was stored in the data structure. This approach was shown to be accurate and efficient for up to six generations for the canine lung cast and ten generations for the mouse lung cast

  17. A higher-order tensor vessel tractography for segmentation of vascular structures.

    Science.gov (United States)

    Cetin, Suheyla; Unal, Gozde

    2015-10-01

    A new vascular structure segmentation method, which is based on a cylindrical flux-based higher order tensor (HOT), is presented. On a vessel structure, the HOT naturally models branching points, which create challenges for vessel segmentation algorithms. In a general linear HOT model embedded in 3D, one has to work with an even order tensor due to an enforced antipodal-symmetry on the unit sphere. However, in scenarios such as in a bifurcation, the antipodally-symmetric tensor embedded in 3D will not be useful. In order to overcome that limitation, we embed the tensor in 4D and obtain a structure that can model asymmetric junction scenarios. During construction of a higher order tensor (e.g. third or fourth order) in 4D, the orientation vectors lie on the unit 3-sphere, in contrast to the unit 2-sphere in 3D tensor modeling. This 4D tensor is exploited in a seed-based vessel segmentation algorithm, where the principal directions of the 4D HOT is obtained by decomposition, and used in a HOT tractography approach. We demonstrate quantitative validation of the proposed algorithm on both synthetic complex tubular structures as well as real cerebral vasculature in Magnetic Resonance Angiography (MRA) datasets and coronary arteries from Computed Tomography Angiography (CTA) volumes.

  18. Similarity between community structures of different online social networks and its impact on underlying community detection

    Science.gov (United States)

    Fan, W.; Yeung, K. H.

    2015-03-01

    As social networking services are popular, many people may register in more than one online social network. In this paper we study a set of users who have accounts of three online social networks: namely Foursquare, Facebook and Twitter. Community structure of this set of users may be reflected in these three online social networks. Therefore, high correlation between these reflections and the underlying community structure may be observed. In this work, community structures are detected in all three online social networks. Also, we investigate the similarity level of community structures across different networks. It is found that they show strong correlation with each other. The similarity between different networks may be helpful to find a community structure close to the underlying one. To verify this, we propose a method to increase the weights of some connections in networks. With this method, new networks are generated to assist community detection. By doing this, value of modularity can be improved and the new community structure match network's natural structure better. In this paper we also show that the detected community structures of online social networks are correlated with users' locations which are identified on Foursquare. This information may also be useful for underlying community detection.

  19. Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery.

    Science.gov (United States)

    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.

  20. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

    Science.gov (United States)

    Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

    2017-08-16

    Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

  1. Identification of structural similarities between putative transmission proteins of Polymyxa and Spongospora transmitted bymoviruses and furoviruses.

    Science.gov (United States)

    Dessens, J T; Meyer, M

    1996-01-01

    Comparison of amino acid sequence and hydropathy profiles shows conserved, structural similarities between the capsid readthrough protein of potato mop top virus (transmitted by Spongospora subterranea) and furovirus and bymovirus proteins implicated in transmission by Polymyxa spp. This suggests that these proteins have a common ancestry and are involved in a common biological process: virus transmission by plasmodiophorid fungi.

  2. Comparison of manual and automatic segmentation methods for brain structures in the presence of space-occupying lesions: a multi-expert study

    International Nuclear Information System (INIS)

    Deeley, M A; Cmelak, A J; Malcolm, A W; Moretti, L; Jaboin, J; Niermann, K; Yang, Eddy S; Yu, David S; Ding, G X; Chen, A; Datteri, R; Noble, J H; Dawant, B M; Donnelly, E F; Yei, F; Koyama, T

    2011-01-01

    The purpose of this work was to characterize expert variation in segmentation of intracranial structures pertinent to radiation therapy, and to assess a registration-driven atlas-based segmentation algorithm in that context. Eight experts were recruited to segment the brainstem, optic chiasm, optic nerves, and eyes, of 20 patients who underwent therapy for large space-occupying tumors. Performance variability was assessed through three geometric measures: volume, Dice similarity coefficient, and Euclidean distance. In addition, two simulated ground truth segmentations were calculated via the simultaneous truth and performance level estimation algorithm and a novel application of probability maps. The experts and automatic system were found to generate structures of similar volume, though the experts exhibited higher variation with respect to tubular structures. No difference was found between the mean Dice similarity coefficient (DSC) of the automatic and expert delineations as a group at a 5% significance level over all cases and organs. The larger structures of the brainstem and eyes exhibited mean DSC of approximately 0.8-0.9, whereas the tubular chiasm and nerves were lower, approximately 0.4-0.5. Similarly low DSCs have been reported previously without the context of several experts and patient volumes. This study, however, provides evidence that experts are similarly challenged. The average maximum distances (maximum inside, maximum outside) from a simulated ground truth ranged from (-4.3, +5.4) mm for the automatic system to (-3.9, +7.5) mm for the experts considered as a group. Over all the structures in a rank of true positive rates at a 2 mm threshold from the simulated ground truth, the automatic system ranked second of the nine raters. This work underscores the need for large scale studies utilizing statistically robust numbers of patients and experts in evaluating quality of automatic algorithms.

  3. Scaling Relations for the Thermal Structure of Segmented Oceanic Transform Faults

    Science.gov (United States)

    Wolfson-Schwehr, M.; Boettcher, M. S.; Behn, M. D.

    2015-12-01

    Mid-ocean ridge-transform faults (RTFs) are a natural laboratory for studying strike-slip earthquake behavior due to their relatively simple geometry, well-constrained slip rates, and quasi-periodic seismic cycles. However, deficiencies in our understanding of the limited size of the largest RTF earthquakes are due, in part, to not considering the effect of short intra-transform spreading centers (ITSCs) on fault thermal structure. We use COMSOL Multiphysics to run a series of 3D finite element simulations of segmented RTFs with visco-plastic rheology. The models test a range of RTF segment lengths (L = 10-150 km), ITSC offset lengths (O = 1-30 km), and spreading rates (V = 2-14 cm/yr). The lithosphere and upper mantle are approximated as steady-state, incompressible flow. Coulomb failure incorporates brittle processes in the lithosphere, and a temperature-dependent flow law for dislocation creep of olivine activates ductile deformation in the mantle. ITSC offsets as small as 2 km affect the thermal structure underlying many segmented RTFs, reducing the area above the 600˚C isotherm, A600, and thus the size of the largest expected earthquakes, Mc. We develop a scaling relation for the critical ITSC offset length, OC, which significantly reduces the thermal affect of adjacent fault segments of length L1 and L2. OC is defined as the ITSC offset that results in an area loss ratio of R = (Aunbroken - Acombined)/Aunbroken - Adecoupled) = 63%, where Aunbroken = C600(L1+L2)1.5V-0.6 is A600 for an RTF of length L1 + L2; Adecoupled = C600(L11.5+L21.5)V-0.6 is the combined A600 of RTFs of lengths L1 and L2, respectively; and Acombined = Aunbroken exp(-O/ OC) + Adecoupled (1-exp(-O/ OC)). C600 is a constant. We use OC and kinematic fault parameters (L1, L2, O, and V) to develop a scaling relation for the approximate seismogenic area, Aseg, for each segment of a RTF system composed of two fault segments. Finally, we estimate the size of Mc on a fault segment based on Aseg. We

  4. Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages.

    Science.gov (United States)

    Rixon, Frazer J; Schmid, Michael F

    2014-04-01

    Structural information can inform our understanding of virus origins and evolution. The herpesviruses and tailed bacteriophages constitute two large families of dsDNA viruses which infect vertebrates and prokaryotes respectively. A relationship between these disparate groups was initially suggested by similarities in their capsid assembly and DNA packaging strategies. This relationship has now been confirmed by a range of studies that have revealed common structural features in their capsid proteins, and similar organizations and sequence conservation in their DNA packaging machinery and maturational proteases. This concentration of conserved traits in proteins involved in essential and primordial capsid/packaging functions is evidence that these structures are derived from an ancient, common ancestor and is in sharp contrast to the lack of such evidence for other virus functions. Copyright © 2014. Published by Elsevier B.V.

  5. Cloud4Psi: cloud computing for 3D protein structure similarity searching.

    Science.gov (United States)

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

    2014-10-01

    Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

  6. Structural similarities between brain and linguistic data provide evidence of semantic relations in the brain.

    Directory of Open Access Journals (Sweden)

    Colleen E Crangle

    Full Text Available This paper presents a new method of analysis by which structural similarities between brain data and linguistic data can be assessed at the semantic level. It shows how to measure the strength of these structural similarities and so determine the relatively better fit of the brain data with one semantic model over another. The first model is derived from WordNet, a lexical database of English compiled by language experts. The second is given by the corpus-based statistical technique of latent semantic analysis (LSA, which detects relations between words that are latent or hidden in text. The brain data are drawn from experiments in which statements about the geography of Europe were presented auditorily to participants who were asked to determine their truth or falsity while electroencephalographic (EEG recordings were made. The theoretical framework for the analysis of the brain and semantic data derives from axiomatizations of theories such as the theory of differences in utility preference. Using brain-data samples from individual trials time-locked to the presentation of each word, ordinal relations of similarity differences are computed for the brain data and for the linguistic data. In each case those relations that are invariant with respect to the brain and linguistic data, and are correlated with sufficient statistical strength, amount to structural similarities between the brain and linguistic data. Results show that many more statistically significant structural similarities can be found between the brain data and the WordNet-derived data than the LSA-derived data. The work reported here is placed within the context of other recent studies of semantics and the brain. The main contribution of this paper is the new method it presents for the study of semantics and the brain and the focus it permits on networks of relations detected in brain data and represented by a semantic model.

  7. Comparison of segmentation techniques to determine the geometric parameters of structured surfaces

    International Nuclear Information System (INIS)

    MacAulay, Gavin D; Giusca, Claudiu L; Leach, Richard K; Senin, Nicola

    2014-01-01

    Structured surfaces, defined as surfaces characterized by topography features whose shape is defined by design specifications, are increasingly being used in industry for a variety of applications, including improving the tribological properties of surfaces. However, characterization of such surfaces still remains an issue. Techniques have been recently proposed, based on identifying and extracting the relevant features from a structured surface so they can be verified individually, using methods derived from those commonly applied to standard-sized parts. Such emerging approaches show promise but are generally complex and characterized by multiple data processing steps making performance difficult to assess. This paper focuses on the segmentation step, i.e. partitioning the topography so that the relevant features can be separated from the background. Segmentation is key for defining the geometric boundaries of the individual feature, which in turn affects any computation of feature size, shape and localization. This paper investigates the effect of varying the segmentation algorithm and its controlling parameters by considering a test case: a structured surface for bearing applications, the relevant features being micro-dimples designed for friction reduction. In particular, the mechanisms through which segmentation leads to identification of the dimple boundary and influences dimensional properties, such as dimple diameter and depth, are illustrated. It is shown that, by using different methods and control parameters, a significant range of measurement results can be achieved, which may not necessarily agree. Indications on how to investigate the influence of each specific choice are given; in particular, stability of the algorithms with respect to control parameters is analyzed as a means to investigate ease of calibration and flexibility to adapt to specific, application-dependent characterization requirements. (paper)

  8. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

    2005-01-01

    detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

  9. Wind loads and competition for light sculpt trees into self-similar structures.

    Science.gov (United States)

    Eloy, Christophe; Fournier, Meriem; Lacointe, André; Moulia, Bruno

    2017-10-18

    Trees are self-similar structures: their branch lengths and diameters vary allometrically within the tree architecture, with longer and thicker branches near the ground. These tree allometries are often attributed to optimisation of hydraulic sap transport and safety against elastic buckling. Here, we show that these allometries also emerge from a model that includes competition for light, wind biomechanics and no hydraulics. We have developed MECHATREE, a numerical model of trees growing and evolving on a virtual island. With this model, we identify the fittest growth strategy when trees compete for light and allocate their photosynthates to grow seeds, create new branches or reinforce existing ones in response to wind-induced loads. Strikingly, we find that selected trees species are self-similar and follow allometric scalings similar to those observed on dicots and conifers. This result suggests that resistance to wind and competition for light play an essential role in determining tree allometries.

  10. Improvement of training set structure in fusion data cleaning using Time-Domain Global Similarity method

    International Nuclear Information System (INIS)

    Liu, J.; Lan, T.; Qin, H.

    2017-01-01

    Traditional data cleaning identifies dirty data by classifying original data sequences, which is a class-imbalanced problem since the proportion of incorrect data is much less than the proportion of correct ones for most diagnostic systems in Magnetic Confinement Fusion (MCF) devices. When using machine learning algorithms to classify diagnostic data based on class-imbalanced training set, most classifiers are biased towards the major class and show very poor classification rates on the minor class. By transforming the direct classification problem about original data sequences into a classification problem about the physical similarity between data sequences, the class-balanced effect of Time-Domain Global Similarity (TDGS) method on training set structure is investigated in this paper. Meanwhile, the impact of improved training set structure on data cleaning performance of TDGS method is demonstrated with an application example in EAST POlarimetry-INTerferometry (POINT) system.

  11. Searching the protein structure database for ligand-binding site similarities using CPASS v.2

    Directory of Open Access Journals (Sweden)

    Caprez Adam

    2011-01-01

    Full Text Available Abstract Background A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2 database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores

  12. Segmentation of internal brain structures in three-dimensional nuclear magnetic resonance imaging

    International Nuclear Information System (INIS)

    Geraud, Th.

    1998-01-01

    For neurological studies, the in vivo aspect of imaging systems is very attractive. Brain images are currently a classical tool used in clinical routine and research. The most appropriate system to observe brain anatomy is tridimensional magnetic resonance imaging, and a major issue of image processing is to segment automatically cerebral structures. This is the scope of our thesis. The number of applications is steadily growing: morphometric measurements, pathology detection, surgery planning, getting a reference for functional studies,a and so forth. The use of pattern recognition to classify the different cerebral tissues from the only radiometric levels of the images is limited. Even supervised, these methods can not lead to distinguish easily several classes of grey matter. When these methods are automatic, their use has to be empirical in order to ensure robust results, and has to be restricted to regions of interest in order to get reliable results. As these methods do not fully respect the spatial consistency of classes in the images, we have introduced contextual information with the help of different formalisms. With Markovian regularization, we have shown that energetic terms of localization permit the separation of two grey classes: cortex and central nuclei. With mathematical morphology, we have proposed processing chains dedicated to several cerebral objects; in particular, brain segmentation is robust and reproducible, and we have successfully obtained individual markers for lateral ventricles, caudate nuclei, putamen and thalami. We have also proposed a contextual method to estimate pure tissue characteristics from a rough segmentation. Our main contribution has been to present a recognition method which is progressive and atlas guided. The originality of this method is manifold. At first, it takes into account structural information processed as flexible spatial constraints the formalism of which relies on fuzzy set theory and information fusion

  13. Local appearance features for robust MRI brain structure segmentation across scanning protocols

    DEFF Research Database (Denmark)

    Achterberg, H.C.; Poot, Dirk H. J.; van der Lijn, Fedde

    2013-01-01

    Segmentation of brain structures in magnetic resonance images is an important task in neuro image analysis. Several papers on this topic have shown the benefit of supervised classification based on local appearance features, often combined with atlas-based approaches. These methods require...... a representative annotated training set and therefore often do not perform well if the target image is acquired on a different scanner or with a different acquisition protocol than the training images. Assuming that the appearance of the brain is determined by the underlying brain tissue distribution...... with substantially different imaging protocols and on different scanners. While a combination of conventional appearance features trained on data from a different scanner with multiatlas segmentation performed poorly with an average Dice overlap of 0.698, the local appearance model based on the new acquisition...

  14. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  15. Self-similarities of periodic structures for a discrete model of a two-gene system

    International Nuclear Information System (INIS)

    Souza, S.L.T. de; Lima, A.A.; Caldas, I.L.; Medrano-T, R.O.; Guimarães-Filho, Z.O.

    2012-01-01

    We report self-similar properties of periodic structures remarkably organized in the two-parameter space for a two-gene system, described by two-dimensional symmetric map. The map consists of difference equations derived from the chemical reactions for gene expression and regulation. We characterize the system by using Lyapunov exponents and isoperiodic diagrams identifying periodic windows, denominated Arnold tongues and shrimp-shaped structures. Period-adding sequences are observed for both periodic windows. We also identify Fibonacci-type series and Golden ratio for Arnold tongues, and period multiple-of-three windows for shrimps. -- Highlights: ► The existence of noticeable periodic windows has been reported recently for several nonlinear systems. ► The periodic window distributions appear highly organized in two-parameter space. ► We characterize self-similar properties of Arnold tongues and shrimps for a two-gene model. ► We determine the period of the Arnold tongues recognizing a Fibonacci-type sequence. ► We explore self-similar features of the shrimps identifying multiple period-three structures.

  16. Self-similarities of periodic structures for a discrete model of a two-gene system

    Energy Technology Data Exchange (ETDEWEB)

    Souza, S.L.T. de, E-mail: thomaz@ufsj.edu.br [Departamento de Física e Matemática, Universidade Federal de São João del-Rei, Ouro Branco, MG (Brazil); Lima, A.A. [Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG (Brazil); Caldas, I.L. [Instituto de Física, Universidade de São Paulo, São Paulo, SP (Brazil); Medrano-T, R.O. [Departamento de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema, SP (Brazil); Guimarães-Filho, Z.O. [Aix-Marseille Univ., CNRS PIIM UMR6633, International Institute for Fusion Science, Marseille (France)

    2012-03-12

    We report self-similar properties of periodic structures remarkably organized in the two-parameter space for a two-gene system, described by two-dimensional symmetric map. The map consists of difference equations derived from the chemical reactions for gene expression and regulation. We characterize the system by using Lyapunov exponents and isoperiodic diagrams identifying periodic windows, denominated Arnold tongues and shrimp-shaped structures. Period-adding sequences are observed for both periodic windows. We also identify Fibonacci-type series and Golden ratio for Arnold tongues, and period multiple-of-three windows for shrimps. -- Highlights: ► The existence of noticeable periodic windows has been reported recently for several nonlinear systems. ► The periodic window distributions appear highly organized in two-parameter space. ► We characterize self-similar properties of Arnold tongues and shrimps for a two-gene model. ► We determine the period of the Arnold tongues recognizing a Fibonacci-type sequence. ► We explore self-similar features of the shrimps identifying multiple period-three structures.

  17. Structure modulates similarity-based interference in sluicing: An eye tracking study.

    Directory of Open Access Journals (Sweden)

    Jesse A. Harris

    2015-12-01

    Full Text Available In cue-based content-addressable approaches to memory, a target and its competitors are retrieved in parallel from memory via a fast, associative cue-matching procedure under a severely limited focus of attention. Such a parallel matching procedure could in principle ignore the serial order or hierarchical structure characteristic of linguistic relations. I present an eye tracking while reading experiment that investigates whether the sentential position of a potential antecedent modulates the strength of similarity-based interference, a well-studied effect in which increased similarity in features between a target and its competitors results in slower and less accurate retrieval overall. The manipulation trades on an independently established Locality bias in sluiced structures to associate a wh-remnant (which ones in clausal ellipsis with the most local correlate (some wines, as in The tourists enjoyed some wines, but I don’t know which ones. The findings generally support cue-based parsing models of sentence processing that are subject to similarity-based interference in retrieval, and provide additional support to the growing body of evidence that retrieval is sensitive to both the structural position of a target antecedent and its competitors, and the specificity of retrieval cues.

  18. TU-AB-303-07: Evaluation of Automatic Segmentation of Critical Structures for Head-And-Neck and Thoracic Radiotherapy Planning

    International Nuclear Information System (INIS)

    Yang, J; Balter, P; Court, L

    2015-01-01

    Purpose: To evaluate the performance of commercially available automatic segmentation tools built into treatment planning systems (TPS) in terms of their segmentation accuracy and flexibility in customization. Methods: Twelve head-and-neck cancer patients and twelve thoracic cancer patients were retrospectively selected to benchmark the model-based segmentation (MBS) and atlas-based segmentation (ABS) in RayStation TPS and the Smart Probabilistic Image Contouring Engine (SPICE) in Pinnacle TPS. Multi-atlas contouring service (MACS) that was developed in-house as a plug-in of Pinnacle TPS was evaluated as well. Manual contours used in clinic were reviewed and modified for consistency and served as ground truth for the evaluation. Head-and-neck evaluation included six regions of interest (ROIs): left and right parotid glands, brainstem, spinal cord, mandible, and submandibular glands. Thoracic evaluation includes seven ROIs: left and right lungs, spinal cord, heart, esophagus, and left and right brachial plexus. Auto-segmented contours were compared with the manual contours using the Dice similarity coefficient (DSC) and the mean surface distance (MSD). Results: In head- and-neck evaluation, only mandible has a high accuracy in all segmentations (DSC>85%); SPICE achieved DSC>70% for parotid glands; MACS achieved this for both parotid glands and submandibular glands; and RayStation ABS achieved this for spinal cord. In thoracic evaluation, SPICE achieved the best in lung and heart segmentation, while MACS achieved the best for all other structures. The less distinguishable structures on CT images, such as brainstem, spinal cord, parotid glands, submandibular glands, esophagus, and brachial plexus, showed great variability in different segmentation tools (mostly DSC<70% and MSD>3mm). The template for RayStation ABS can be easily customized by users, while RayStation MBS and SPICE rely on the vendors to provide the templates/models. Conclusion: Great variability was

  19. TU-AB-303-07: Evaluation of Automatic Segmentation of Critical Structures for Head-And-Neck and Thoracic Radiotherapy Planning

    Energy Technology Data Exchange (ETDEWEB)

    Yang, J; Balter, P; Court, L [MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose: To evaluate the performance of commercially available automatic segmentation tools built into treatment planning systems (TPS) in terms of their segmentation accuracy and flexibility in customization. Methods: Twelve head-and-neck cancer patients and twelve thoracic cancer patients were retrospectively selected to benchmark the model-based segmentation (MBS) and atlas-based segmentation (ABS) in RayStation TPS and the Smart Probabilistic Image Contouring Engine (SPICE) in Pinnacle TPS. Multi-atlas contouring service (MACS) that was developed in-house as a plug-in of Pinnacle TPS was evaluated as well. Manual contours used in clinic were reviewed and modified for consistency and served as ground truth for the evaluation. Head-and-neck evaluation included six regions of interest (ROIs): left and right parotid glands, brainstem, spinal cord, mandible, and submandibular glands. Thoracic evaluation includes seven ROIs: left and right lungs, spinal cord, heart, esophagus, and left and right brachial plexus. Auto-segmented contours were compared with the manual contours using the Dice similarity coefficient (DSC) and the mean surface distance (MSD). Results: In head- and-neck evaluation, only mandible has a high accuracy in all segmentations (DSC>85%); SPICE achieved DSC>70% for parotid glands; MACS achieved this for both parotid glands and submandibular glands; and RayStation ABS achieved this for spinal cord. In thoracic evaluation, SPICE achieved the best in lung and heart segmentation, while MACS achieved the best for all other structures. The less distinguishable structures on CT images, such as brainstem, spinal cord, parotid glands, submandibular glands, esophagus, and brachial plexus, showed great variability in different segmentation tools (mostly DSC<70% and MSD>3mm). The template for RayStation ABS can be easily customized by users, while RayStation MBS and SPICE rely on the vendors to provide the templates/models. Conclusion: Great variability was

  20. Internal structures of self-organized relaxed states and self-similar decay phase

    International Nuclear Information System (INIS)

    Kondoh, Yoshiomi

    1992-03-01

    A thought analysis on relaxation due to nonlinear processes is presented to lead to a set of general thoughts applicable to general nonlinear dynamical systems for finding out internal structures of the self-organized relaxed state without using 'invariant'. Three applications of the set of general thoughts to energy relaxations in resistive MHD plasmas, incompressible viscous fluids, and incompressible viscous MHD fluids are shown to lead to the internal structures of the self-organized relaxed states. It is shown that all of the relaxed states in these three dynamical systems are followed by self-similar decay phase without significant change of the spatial structure. The well known relaxed state of ∇ x B = ±λ B is shown to be derived generally in the low β plasma limit. (author)

  1. Automated torso organ segmentation from 3D CT images using structured perceptron and dual decomposition

    Science.gov (United States)

    Nimura, Yukitaka; Hayashi, Yuichiro; Kitasaka, Takayuki; Mori, Kensaku

    2015-03-01

    This paper presents a method for torso organ segmentation from abdominal CT images using structured perceptron and dual decomposition. A lot of methods have been proposed to enable automated extraction of organ regions from volumetric medical images. However, it is necessary to adjust empirical parameters of them to obtain precise organ regions. This paper proposes an organ segmentation method using structured output learning. Our method utilizes a graphical model and binary features which represent the relationship between voxel intensities and organ labels. Also we optimize the weights of the graphical model by structured perceptron and estimate the best organ label for a given image by dynamic programming and dual decomposition. The experimental result revealed that the proposed method can extract organ regions automatically using structured output learning. The error of organ label estimation was 4.4%. The DICE coefficients of left lung, right lung, heart, liver, spleen, pancreas, left kidney, right kidney, and gallbladder were 0.91, 0.95, 0.77, 0.81, 0.74, 0.08, 0.83, 0.84, and 0.03, respectively.

  2. Investigation of Time Series Representations and Similarity Measures for Structural Damage Pattern Recognition

    Directory of Open Access Journals (Sweden)

    Wenjia Liu

    2013-01-01

    Full Text Available This paper investigates the time series representation methods and similarity measures for sensor data feature extraction and structural damage pattern recognition. Both model-based time series representation and dimensionality reduction methods are studied to compare the effectiveness of feature extraction for damage pattern recognition. The evaluation of feature extraction methods is performed by examining the separation of feature vectors among different damage patterns and the pattern recognition success rate. In addition, the impact of similarity measures on the pattern recognition success rate and the metrics for damage localization are also investigated. The test data used in this study are from the System Identification to Monitor Civil Engineering Structures (SIMCES Z24 Bridge damage detection tests, a rigorous instrumentation campaign that recorded the dynamic performance of a concrete box-girder bridge under progressively increasing damage scenarios. A number of progressive damage test case datasets and damage test data with different damage modalities are used. The simulation results show that both time series representation methods and similarity measures have significant impact on the pattern recognition success rate.

  3. Investigation of Time Series Representations and Similarity Measures for Structural Damage Pattern Recognition

    Science.gov (United States)

    Swartz, R. Andrew

    2013-01-01

    This paper investigates the time series representation methods and similarity measures for sensor data feature extraction and structural damage pattern recognition. Both model-based time series representation and dimensionality reduction methods are studied to compare the effectiveness of feature extraction for damage pattern recognition. The evaluation of feature extraction methods is performed by examining the separation of feature vectors among different damage patterns and the pattern recognition success rate. In addition, the impact of similarity measures on the pattern recognition success rate and the metrics for damage localization are also investigated. The test data used in this study are from the System Identification to Monitor Civil Engineering Structures (SIMCES) Z24 Bridge damage detection tests, a rigorous instrumentation campaign that recorded the dynamic performance of a concrete box-girder bridge under progressively increasing damage scenarios. A number of progressive damage test case datasets and damage test data with different damage modalities are used. The simulation results show that both time series representation methods and similarity measures have significant impact on the pattern recognition success rate. PMID:24191136

  4. Structural similarities and differences between the human and the mouse pancreas

    Science.gov (United States)

    Dolenšek, Jurij; Rupnik, Marjan Slak; Stožer, Andraž

    2015-01-01

    Mice remain the most studied animal model in pancreas research. Since the findings of this research are typically extrapolated to humans, it is important to understand both similarities and differences between the 2 species. Beside the apparent difference in size and macroscopic organization of the organ in the 2 species, there are a number of less evident and only recently described differences in organization of the acinar and ductal exocrine tissue, as well as in the distribution, composition, and architecture of the endocrine islets of Langerhans. Furthermore, the differences in arterial, venous, and lymphatic vessels, as well as innervation are potentially important. In this article, the structure of the human and the mouse pancreas, together with the similarities and differences between them are reviewed in detail in the light of conceivable repercussions for basic research and clinical application. PMID:26030186

  5. Vibration based structural assessment of the rehabilitation intervention in r.c. segmental bridge

    OpenAIRE

    Franchetti Paolo; Frizzarin Michele; Leonardi Andrea; Zeni Fabio

    2015-01-01

    A vibration based structural assessment campaign was carried out on a r.c. segmental bridge in North East Italy. The bridge has a cantilever static scheme, fixed at the top of the piers and with a hinge at the centre of the span. The particular configuration of the hinge consists in a couple of steel elements, each one composed by a tongue and groove joint. Since the year 1960, the hinge was subjected to consumption and degradation, that caused a malfunctioning of the device. An intervention ...

  6. HIGH QUALITY FACADE SEGMENTATION BASED ON STRUCTURED RANDOM FOREST, REGION PROPOSAL NETWORK AND RECTANGULAR FITTING

    Directory of Open Access Journals (Sweden)

    K. Rahmani

    2018-05-01

    Full Text Available In this paper we present a pipeline for high quality semantic segmentation of building facades using Structured Random Forest (SRF, Region Proposal Network (RPN based on a Convolutional Neural Network (CNN as well as rectangular fitting optimization. Our main contribution is that we employ features created by the RPN as channels in the SRF.We empirically show that this is very effective especially for doors and windows. Our pipeline is evaluated on two datasets where we outperform current state-of-the-art methods. Additionally, we quantify the contribution of the RPN and the rectangular fitting optimization on the accuracy of the result.

  7. Structural controls on the megathrust segmentation of the Middle America Trench from multiple geophysical observations

    Science.gov (United States)

    Naif, S.; Bassett, D.

    2016-12-01

    Subduction zone megathrusts display complex seismogenic behaviors that vary at intra- and inter-margin scales. Many different physical properties have been proposed to be primarily responsible for this behavior, such as the composition of subducted sediments, the hydration state of the incoming oceanic plate, and the pore-fluid pressure at the plate interface. Here, we focus on the northern Middle America Trench and show that subducting plate structures control megathrust segmentation. We analyze multiple types of seafloor geophysical observations and compare them to the distinct behavioral and spatial characteristics of the 1992 Nicaragua (Mw7.6), 2012 El Salvador (Mw7.3), 2012 Guatemala (Mw7.4), and 2012 Costa Rica (Mw7.6) events. The residual topography, residual gravity, and magnetic anomaly structure of the incoming oceanic plate and forearc seafloor are correlated. The forearc is composed of multiple unique segments that are bounded by subducting fracture zones. These boundaries correlate with foreshock and aftershock seismicity and also coincide with the hypocenter of all four earthquakes. The relationship between observed structures, earthquake slip inversions, and radiated energy of the four large events will be discussed.

  8. Andoma segment of southeastern margin of fennoscandian shield: Structure and evolution

    Science.gov (United States)

    Kolodyazhny, S. Yu.; Baluev, A. S.; Terekhov, E. N.

    2016-07-01

    The components of deformation related to endogenic (tectonic) and exogenic (glaciotectonic, gravitational sliding) factors are considered in the sedimentary platform cover by a study of Andoma dislocations in the Upper Devonian sedimentary rocks of the Lake Onega district. These structures are localized in the eponymous segment of the southeastern margin of the Fennoscandian (Baltic) Shield; indications of high tectonic activity are noted along this margin. As has been shown by a structural study, the development of the Andoma structure is caused by long-term (Late Devonian-Quaternary) multistage deformations related to tectonic factors and, to a lesser degree, glaciotectonics. The consecutive stages of synsedimentation normal faulting and landsliding, bedding-plane gliding, various forms of shear flow in a regime of transpression, glaciotectonic thrusting, and neotectonic transpression are recognized in the deformation history.

  9. Self-similar spectral structures and edge-locking hierarchy in open-boundary spin chains

    International Nuclear Information System (INIS)

    Haque, Masudul

    2010-01-01

    For an anisotropic Heisenberg (XXZ) spin chain, we show that an open boundary induces a series of approximately self-similar features at different energy scales, high up in the eigenvalue spectrum. We present a nonequilibrium phenomenon related to this fractal structure, involving states in which a connected block near the edge is polarized oppositely to the rest of the chain. We show that such oppositely polarized blocks can be 'locked' to the edge of the spin chain and that there is a hierarchy of edge-locking effects at various orders of the anisotropy. The phenomenon enables dramatic control of quantum-state transmission and magnetization control.

  10. Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity.

    Science.gov (United States)

    Tao, Yunwen; Zou, Wenli; Cremer, Dieter; Kraka, Elfi

    2018-03-05

    Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. Neighborhood Structural Similarity Mapping for the Classification of Masses in Mammograms.

    Science.gov (United States)

    Rabidas, Rinku; Midya, Abhishek; Chakraborty, Jayasree

    2018-05-01

    In this paper, two novel feature extraction methods, using neighborhood structural similarity (NSS), are proposed for the characterization of mammographic masses as benign or malignant. Since gray-level distribution of pixels is different in benign and malignant masses, more regular and homogeneous patterns are visible in benign masses compared to malignant masses; the proposed method exploits the similarity between neighboring regions of masses by designing two new features, namely, NSS-I and NSS-II, which capture global similarity at different scales. Complementary to these global features, uniform local binary patterns are computed to enhance the classification efficiency by combining with the proposed features. The performance of the features are evaluated using the images from the mini-mammographic image analysis society (mini-MIAS) and digital database for screening mammography (DDSM) databases, where a tenfold cross-validation technique is incorporated with Fisher linear discriminant analysis, after selecting the optimal set of features using stepwise logistic regression method. The best area under the receiver operating characteristic curve of 0.98 with an accuracy of is achieved with the mini-MIAS database, while the same for the DDSM database is 0.93 with accuracy .

  12. From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.

    Science.gov (United States)

    Elhanan, Gai; Ochs, Christopher; Mejino, Jose L V; Liu, Hao; Mungall, Christopher J; Perl, Yehoshua

    2017-06-01

    To examine whether disjoint partial-area taxonomy, a semantically-based evaluation methodology that has been successfully tested in SNOMED CT, will perform with similar effectiveness on Uberon, an anatomical ontology that belongs to a structurally similar family of ontologies as SNOMED CT. A disjoint partial-area taxonomy was generated for Uberon. One hundred randomly selected test concepts that overlap between partial-areas were matched to a same size control sample of non-overlapping concepts. The samples were blindly inspected for non-critical issues and presumptive errors first by a general domain expert whose results were then confirmed or rejected by a highly experienced anatomical ontology domain expert. Reported issues were subsequently reviewed by Uberon's curators. Overlapping concepts in Uberon's disjoint partial-area taxonomy exhibited a significantly higher rate of all issues. Clear-cut presumptive errors trended similarly but did not reach statistical significance. A sub-analysis of overlapping concepts with three or more relationship types indicated a much higher rate of issues. Overlapping concepts from Uberon's disjoint abstraction network are quite likely (up to 28.9%) to exhibit issues. The results suggest that the methodology can transfer well between same family ontologies. Although Uberon exhibited relatively few overlapping concepts, the methodology can be combined with other semantic indicators to expand the process to other concepts within the ontology that will generate high yields of discovered issues. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration.

    Science.gov (United States)

    Straube, Ronny

    2017-12-01

    Much of the complexity of regulatory networks derives from the necessity to integrate multiple signals and to avoid malfunction due to cross-talk or harmful perturbations. Hence, one may expect that the input-output behavior of larger networks is not necessarily more complex than that of smaller network motifs which suggests that both can, under certain conditions, be described by similar equations. In this review, we illustrate this approach by discussing the similarities that exist in the steady state descriptions of a simple bimolecular reaction, covalent modification cycles and bacterial two-component systems. Interestingly, in all three systems fundamental input-output characteristics such as thresholds, ultrasensitivity or concentration robustness are described by structurally similar equations. Depending on the system the meaning of the parameters can differ ranging from protein concentrations and affinity constants to complex parameter combinations which allows for a quantitative understanding of signal integration in these systems. We argue that this approach may also be extended to larger regulatory networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Wake structure and similar behavior of wake profiles downstream of a plunging airfoil

    Directory of Open Access Journals (Sweden)

    Ali R. DAVARI

    2017-08-01

    Full Text Available Very limited attention has already been paid to the velocity behavior in the wake region in unsteady aerodynamic problems. A series of tests has been performed on a flapping airfoil in a subsonic wind tunnel to study the wake structure for different sets of mean angle of attack, plunging amplitude and reduced frequency. In this study, the velocity profiles in the wake for various oscillation parameters have been measured using a wide shoulder rake, especially designed for the present experiments. The airfoil under consideration was a critical section of a 660 kW wind turbine. The results show that for a flapping airfoil the wake structure can be of drag producing type, thrust producing or neutral, depending on the mean angle of attack, oscillation amplitude and reduced frequency. In a thrust producing wake, a high-momentum high-velocity jet flow is formed in the core region of the wake instead of the conventional low-momentum flow. As a result, the drag force normally experienced by the body due to the momentum deficit would be replaced by a thrust force. According to the results, the momentum loss in the wake decreases as the reduced frequency increases. The thrust producing wake pattern for the flapping airfoil has been observed for sufficiently low angles of attack in the absence of the viscous effects. This phenomenon has also been observed for either high oscillation amplitudes or high reduced frequencies. According to the results, for different reduced frequencies and plunging amplitudes, such that the product of them be a constant, the velocity profiles exhibit similar behavior and coalesce on each other. This similarity parameter works excellently at small angles of attack. However, at near stall boundaries, the similarity is not as evident as before.

  15. Seismodynamics of extended underground structures and soils: Statement of the problem and self-similar solutions

    Science.gov (United States)

    Georgievskii, D. V.; Israilov, M. Sh.

    2015-07-01

    In the problems of common vibrations of extended underground structures (pipelines and tunnels) and soil, an approach of the one-dimensional deformation of the medium is developed; this approach is based on the assumption that the soil deformation in the direction of seismic wave propagation coinciding with the pipeline axis is prevailing. The analytic solutions are obtained in the cases where the wave velocity in the soil is respectively less or greater than the wave velocity in the pipeline. The parameters influencing the pipeline fracture are revealed and methods for increasing the seismic stability of such structures are given. The possibility of the pipeline fatigue fracture is pointed out. The statements and solutions of parabolic problems modeling the physical phenomena in soils in the case of discontinuous velocity on the boundaries at the initial time are given. The notion of generalized vorticity diffusion is introduced and the cases of self-similarity existence are classified. A detailed analysis is performed for the non-Newtonian polynomial fluid, the medium close in properties to the rigidly ideally plastic body, and the viscoplastic Shvedov—Bingham body. In the case of physically linear medium, new self-similar solutions are obtained which describe the process of unsteady axially symmetric shear in spherical coordinates. The first approximation to the asymptotic solution of the problem of the vortex sheet diffusion is constructed in a medium with small polynomial nonlinearity. The solutions polynomially decreasing to zero as the self-similar variable increases are proposed in the class of two-constant fluids.

  16. Development of scaffold-free elastic cartilaginous constructs with structural similarities to auricular cartilage.

    Science.gov (United States)

    Giardini-Rosa, Renata; Joazeiro, Paulo P; Thomas, Kathryn; Collavino, Kristina; Weber, Joanna; Waldman, Stephen D

    2014-03-01

    External ear reconstruction with autologous cartilage still remains one of the most difficult problems in the fields of plastic and reconstructive surgery. As the absence of tissue vascularization limits the ability to stimulate new tissue growth, relatively few surgical approaches are currently available (alloplastic implants or sculpted autologous cartilage grafts) to repair or reconstruct the auricle (or pinna) as a result of traumatic loss or congenital absence (e.g., microtia). Alternatively, tissue engineering can offer the potential to grow autogenous cartilage suitable for implantation. While tissue-engineered auricle cartilage constructs can be created, a substantial number of cells are required to generate sufficient quantities of tissue for reconstruction. Similarly, as routine cell expansion can elicit negative effects on chondrocyte function, we have developed an approach to generate large-sized engineered auricle constructs (≥3 cm(2)) directly from a small population of donor cells (20,000-40,000 cells/construct). Using rabbit donor cells, the developed bioreactor-cultivated constructs adopted structural-like characteristics similar to native auricular cartilage, including the development of distinct cartilaginous and perichondrium-like regions. Both alterations in media composition and seeding density had profound effects on the formation of engineered elastic tissue constructs in terms of cellularity, extracellular matrix accumulation, and tissue structure. Higher seeding densities and media containing sodium bicarbonate produced tissue constructs that were closer to the native tissue in terms of structure and composition. Future studies will be aimed at improving the accumulation of specific tissue constituents and determining the clinical effectiveness of this approach using a reconstructive animal model.

  17. Structure and floristic similarities of upper montane forests in Serra Fina mountain range, southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Leonardo Dias Meireles

    2015-03-01

    Full Text Available The upper montane forests in the southern and southeastern regions of Brazil have an unusual and discontinuous geographic distribution at the top of the Atlantic coastal mountain ranges. To describe the floristic composition and structure of the Atlantic Forest near its upper altitudinal limit in southeastern Brazil, 30 plots with 10 × 10 m were installed in three forest sites between 2,200 and 2,300 m.a.s.l. at Serra Fina. The floristic composition and phytosociological structure of this forest were compared with other montane and upper montane forests. In total, 704 individuals were included, belonging to 24 species, 15 families, and 19 genera. Myrsinaceae, Myrtaceae, Symplocaceae, and Cunoniaceae were the most important families, and Myrsine gardneriana, Myrceugenia alpigena, Weinmannia humilis, and Symplocos corymboclados were the most important species. The three forest sites revealed differences in the abundance of species, density, canopy height, and number of stems per individual. The upper montane forests showed structural similarities, such as lower richness, diversity, and effective number of species, and they tended to have higher total densities and total dominance per hectare to montane forests. The most important species in these upper montane forests belong to Austral-Antartic genera or neotropical and pantropical genera that are typical of montane areas. The high number of species shared by these forests suggests past connections between the vegetation in southern Brazilian high-altitude areas.

  18. A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

    Science.gov (United States)

    Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben

    2012-01-01

    3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

  19. Nanotoxicity comparison of four amphiphilic polymeric micelles with similar hydrophilic or hydrophobic structure.

    Science.gov (United States)

    Zhao, Bo; Wang, Xue-Qing; Wang, Xiao-You; Zhang, Hua; Dai, Wen-Bing; Wang, Jun; Zhong, Zhen-Lin; Wu, Hou-Nan; Zhang, Qiang

    2013-10-03

    Nanocarriers represent an attractive means of drug delivery, but their biosafety must be established before their use in clinical research. Four kinds of amphiphilic polymeric (PEG-PG-PCL, PEEP-PCL, PEG-PCL and PEG-DSPE) micelles with similar hydrophilic or hydrophobic structure were prepared and their in vitro and in vivo safety were evaluated and compared. In vitro nanotoxicity evaluations included assessments of cell morphology, cell volume, inflammatory effects, cytotoxicity, apoptosis and membrane fluidity. An umbilical vein cell line (Eahy.926) and a kind of macrophages (J774.A1) were used as cell models considering that intravenous route is dominant for micelle delivery systems. In vivo analyses included complete blood count, lymphocyte subset analysis, detection of plasma inflammatory factors and histological observations of major organs after intravenous administration to KM mice. All the micelles enhanced inflammatory molecules in J774.A1 cells, likely resulting from the increased ROS levels. PEG-PG-PCL and PEEP-PCL micelles were found to increase the J774.A1 cell volume. This likely correlated with the size of PEG-PG-PCL micelles and the polyphosphoester structure in PEEP-PCL. PEG-DSPE micelles inhibited the growth of Eahy.926 cells via inducing apoptosis. This might relate to the structure of DSPE, which is a type of phospholipid and has good affinity with cell membrane. No evidence was found for cell membrane changes after treatment with these micelles for 24 h. In the in vivo study, during 8 days of 4 time injection, each of the four nanocarriers altered the hematic phase differently without changes in inflammatory factors or pathological changes in target organs. These results demonstrate that the micelles investigated exhibit diverse nanotoxicity correlated with their structures, their biosafety is different in different cell model, and there is no in vitro and in vivo correlation found. We believe that this study will certainly provide more

  20. Structural and functional similarities between osmotin from Nicotiana tabacum seeds and human adiponectin.

    Science.gov (United States)

    Miele, Marco; Costantini, Susan; Colonna, Giovanni

    2011-02-02

    Osmotin, a plant protein, specifically binds a seven transmembrane domain receptor-like protein to exert its biological activity via a RAS2/cAMP signaling pathway. The receptor protein is encoded in the gene ORE20/PHO36 and the mammalian homolog of PHO36 is a receptor for the human hormone adiponectin (ADIPOR1). Moreover it is known that the osmotin domain I can be overlapped to the β-barrel domain of adiponectin. Therefore, these observations and some already existing structural and biological data open a window on a possible use of the osmotin or of its derivative as adiponectin agonist. We have modelled the three-dimensional structure of the adiponectin trimer (ADIPOQ), and two ADIPOR1 and PHO36 receptors. Moreover, we have also modelled the following complexes: ADIPOQ/ADIPOR1, osmotin/PHO36 and osmotin/ADIPOR1. We have then shown the structural determinants of these interactions and their physico-chemical features and analyzed the related interaction residues involved in the formation of the complexes. The stability of the modelled structures and their complexes was always evaluated and controlled by molecular dynamics. On the basis of these results a 9 residues osmotin peptide was selected and its interaction with ADIPOR1 and PHO36 was modelled and analysed in term of energetic stability by molecular dynamics. To confirm in vivo the molecular modelling data, osmotin has been purified from nicotiana tabacum seeds and its nine residues peptide synthesized. We have used cultured human synovial fibroblasts that respond to adiponectin by increasing the expression of IL-6, TNF-alpha and IL-1beta via ADIPOR1. The biological effect on fibroblasts of osmotin and its peptide derivative has been found similar to that of adiponectin confirming the results found in silico.

  1. A hybrid algorithm for selecting head-related transfer function based on similarity of anthropometric structures

    Science.gov (United States)

    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.

  2. Structural similarities between the tradition of moral philosophy and Durkheim’s social theory

    Directory of Open Access Journals (Sweden)

    Ana Marta González

    2017-05-01

    Full Text Available The first sociological theories are indebted to Enlightenment philosophy of history, which first appeared to provide a framework of meaning for moral action once moral theory had renounced the metaphysical commitments of early modern moral philosophy. While defending the autonomy of sociology from philosophy, Durkheim prescribed a specific task for sociological thought, namely: develop a moral science which, by keeping together the two features with which moral facts appear before conscience —solidarity and coercion— could account for the moral sense of the division of labour, a phenomenon previously considered almost a natural process. The purpose of this article is to show how Durkheim’s approach makes room for us to establish a structural similarity between sociological analysis and the perspective of mutual obligations characteristic of the moral philosophical tradition.

  3. Rapid discovery of peptide capture candidates with demonstrated specificity for structurally similar toxins

    Science.gov (United States)

    Sarkes, Deborah A.; Hurley, Margaret M.; Coppock, Matthew B.; Farrell, Mikella E.; Pellegrino, Paul M.; Stratis-Cullum, Dimitra N.

    2016-05-01

    Peptides have emerged as viable alternatives to antibodies for molecular-based sensing due to their similarity in recognition ability despite their relative structural simplicity. Various methods for peptide capture reagent discovery exist, including phage display, yeast display, and bacterial display. One of the primary advantages of peptide discovery by bacterial display technology is the speed to candidate peptide capture agent, due to both rapid growth of bacteria and direct utilization of the sorted cells displaying each individual peptide for the subsequent round of biopanning. We have previously isolated peptide affinity reagents towards protective antigen of Bacillus anthracis using a commercially available automated magnetic sorting platform with improved enrichment as compared to manual magnetic sorting. In this work, we focus on adapting our automated biopanning method to a more challenging sort, to demonstrate the specificity possible with peptide capture agents. This was achieved using non-toxic, recombinant variants of ricin and abrin, RiVax and abrax, respectively, which are structurally similar Type II ribosomal inactivating proteins with significant sequence homology. After only two rounds of biopanning, enrichment of peptide capture candidates binding abrax but not RiVax was achieved as demonstrated by Fluorescence Activated Cell Sorting (FACS) studies. Further sorting optimization included negative sorting against RiVax, proper selection of autoMACS programs for specific sorting rounds, and using freshly made buffer and freshly thawed protein target for each round of biopanning for continued enrichment over all four rounds. Most of the resulting candidates from biopanning for abrax binding peptides were able to bind abrax but not RiVax, demonstrating that short peptide sequences can be highly specific even at this early discovery stage.

  4. Earthworm coelomocyte extracellular traps: structural and functional similarities with neutrophil NETs.

    Science.gov (United States)

    Homa, Joanna

    2018-03-01

    Invertebrate immunity is associated with natural mechanisms that include cellular and humoral elements, similar to those that play a role in vertebrate innate immune responses. Formation of extracellular traps (ETs) is a newly discovered mechanism to combat pathogens, operating not only in vertebrate leucocytes but also in invertebrate immune cells. The ET components include extracellular DNA (exDNA), antimicrobial proteins and histones. Formation of mammalian ETs depends on enzymes such as neutrophil elastase, myeloperoxidase, the citrullination of histones and protease activity. It was confirmed that coelomocytes-immunocompetent cells of the earthworm Eisenia andrei-are also able to release ETs in a protease-dependent manner, dependent or independent of the formation of reactive oxygen species and rearrangement of the cell cytoskeleton. Similar to vertebrate leukocytes (e.g., neutrophil), coelomocytes are responsible for many immune functions like phagocytosis, cytotoxicity and secretion of humoral factors. ETs formed by coelomocyte analogues to neutrophil ETs consist of exDNA, histone H3 and attached to these structures proteins, e.g., heat shock proteins HSP27. The latter fact confirms that mechanisms of ET release are conserved in evolution. The study on Annelida adds this animal group to the list of invertebrates capable of ET release, but most importantly provides insides into innate mechanisms of ET formation in lower animal taxa.

  5. Graph-based unsupervised segmentation algorithm for cultured neuronal networks' structure characterization and modeling.

    Science.gov (United States)

    de Santos-Sierra, Daniel; Sendiña-Nadal, Irene; Leyva, Inmaculada; Almendral, Juan A; Ayali, Amir; Anava, Sarit; Sánchez-Ávila, Carmen; Boccaletti, Stefano

    2015-06-01

    Large scale phase-contrast images taken at high resolution through the life of a cultured neuronal network are analyzed by a graph-based unsupervised segmentation algorithm with a very low computational cost, scaling linearly with the image size. The processing automatically retrieves the whole network structure, an object whose mathematical representation is a matrix in which nodes are identified neurons or neurons' clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocytochemistry techniques, our non invasive measures entitle us to perform a longitudinal analysis during the maturation of a single culture. Such an analysis furnishes the way of individuating the main physical processes underlying the self-organization of the neurons' ensemble into a complex network, and drives the formulation of a phenomenological model yet able to describe qualitatively the overall scenario observed during the culture growth. © 2014 International Society for Advancement of Cytometry.

  6. Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.

    Science.gov (United States)

    Zheng, Ling; Chen, Yan; Elhanan, Gai; Perl, Yehoshua; Geller, James; Ochs, Christopher

    2018-05-28

    In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often become fertile ground for quality assurance (QA) in ontologies. They should be audited first. One example of complex concepts is given by "overlapping concepts" (to be defined below.) Historically, a different auditing methodology had to be developed for every single ontology. For better scalability and efficiency, it is desirable to identify family-wide QA methodologies. Each such methodology would be applicable to a whole family of similar ontologies. In past research, we had divided the 685 ontologies of BioPortal into families of structurally similar ontologies. We showed for four ontologies of the same large family in BioPortal that "overlapping concepts" are indeed statistically significantly more likely to exhibit errors. In order to make an authoritative statement concerning the success of "overlapping concepts" as a methodology for a whole family of similar ontologies (or of large subhierarchies of ontologies), it is necessary to show that "overlapping concepts" have a higher likelihood of errors for six out of six ontologies of the family. In this paper, we are demonstrating for two more ontologies that "overlapping concepts" can successfully predict groups of concepts with a higher error rate than concepts from a control group. The fifth ontology is the Neoplasm subhierarchy of the National Cancer Institute thesaurus (NCIt). The sixth ontology is the Infectious Disease subhierarchy of SNOMED CT. We demonstrate quality assurance results for both of them. Furthermore, in this paper we observe two novel, important, and useful phenomena during quality assurance of "overlapping concepts." First, an erroneous "overlapping concept" can help with discovering other erroneous "non-overlapping concepts" in its vicinity

  7. Bayes Clustering and Structural Support Vector Machines for Segmentation of Carotid Artery Plaques in Multicontrast MRI

    Directory of Open Access Journals (Sweden)

    Qiu Guan

    2012-01-01

    Full Text Available Accurate segmentation of carotid artery plaque in MR images is not only a key part but also an essential step for in vivo plaque analysis. Due to the indistinct MR images, it is very difficult to implement the automatic segmentation. Two kinds of classification models, that is, Bayes clustering and SSVM, are introduced in this paper to segment the internal lumen wall of carotid artery. The comparative experimental results show the segmentation performance of SSVM is better than Bayes.

  8. Segmentation and fragmentation of melt jets due to generation of large-scale structures. Observation in low subcooling conditions

    International Nuclear Information System (INIS)

    Sugiyama, Ken-ichiro; Yamada, Tsuyoshi

    1999-01-01

    In order to clarify a mechanism of melt-jet breakup and fragmentation entirely different from the mechanism of stripping, a series of experiments were carried out by using molten tin jets of 100 grams with initial temperatures from 250degC to 900degC. Molten tin jets with a small kinematic viscosity and a large thermal diffusivity were used to observe breakup and fragmentation of melt jets enhanced thermally and hydrodynamically. We observed jet columns with second-stage large-scale structures generated by the coalescence of large-scale structures recognized in the field of fluid mechanics. At a greater depth, the segmentation of jet columns between second-stage large-scale structures and the fragmentation of the segmented jet columns were observed. It is reasonable to consider that the segmentation and the fragmentation of jet columns are caused by the boiling of water hydrodynamically entrained within second-stage large-scale structures. (author)

  9. Towards a chromatographic similarity index to establish localised quantitative structure-retention relationships for retention prediction. II Use of Tanimoto similarity index in ion chromatography.

    Science.gov (United States)

    Park, Soo Hyun; Talebi, Mohammad; Amos, Ruth I J; Tyteca, Eva; Haddad, Paul R; Szucs, Roman; Pohl, Christopher A; Dolan, John W

    2017-11-10

    Quantitative Structure-Retention Relationships (QSRR) are used to predict retention times of compounds based only on their chemical structures encoded by molecular descriptors. The main concern in QSRR modelling is to build models with high predictive power, allowing reliable retention prediction for the unknown compounds across the chromatographic space. With the aim of enhancing the prediction power of the models, in this work, our previously proposed QSRR modelling approach called "federation of local models" is extended in ion chromatography to predict retention times of unknown ions, where a local model for each target ion (unknown) is created using only structurally similar ions from the dataset. A Tanimoto similarity (TS) score was utilised as a measure of structural similarity and training sets were developed by including ions that were similar to the target ion, as defined by a threshold value. The prediction of retention parameters (a- and b-values) in the linear solvent strength (LSS) model in ion chromatography, log k=a - blog[eluent], allows the prediction of retention times under all eluent concentrations. The QSRR models for a- and b-values were developed by a genetic algorithm-partial least squares method using the retention data of inorganic and small organic anions and larger organic cations (molecular mass up to 507) on four Thermo Fisher Scientific columns (AS20, AS19, AS11HC and CS17). The corresponding predicted retention times were calculated by fitting the predicted a- and b-values of the models into the LSS model equation. The predicted retention times were also plotted against the experimental values to evaluate the goodness of fit and the predictive power of the models. The application of a TS threshold of 0.6 was found to successfully produce predictive and reliable QSRR models (Q ext(F2) 2 >0.8 and Mean Absolute Error<0.1), and hence accurate retention time predictions with an average Mean Absolute Error of 0.2min. Crown Copyright

  10. Resistivity structure of Sumatran Fault (Aceh segment) derived from 1-D magnetotelluric modeling

    Science.gov (United States)

    Nurhasan, Sutarno, D.; Bachtiar, H.; Sugiyanto, D.; Ogawa, Y.; Kimata, F.; Fitriani, D.

    2012-06-01

    Sumatran Fault Zone is the most active fault in Indonesia as a result of strike-slip component of Indo-Australian oblique convergence. With the length of 1900 km, Sumatran fault was divided into 20 segments starting from the southernmost Sumatra Island having small slip rate and increasing to the north end of Sumatra Island. There are several geophysical methods to analyze fault structure depending on physical parameter used in these methods, such as seismology, geodesy and electromagnetic. Magnetotelluric method which is one of geophysical methods has been widely used in mapping and sounding resistivity distribution because it does not only has the ability for detecting contras resistivity but also has a penetration range up to hundreds of kilometers. Magnetotelluric survey was carried out in Aceh region with the 12 total sites crossing Sumatran Fault on Aceh and Seulimeum segments. Two components of electric and magnetic fields were recorded during 10 hours in average with the frequency range from 320 Hz to 0,01 Hz. Analysis of the pseudosection of phase and apparent resistivity exhibit vertical low phase flanked on the west and east by high phase describing the existence of resistivity contras in this region. Having rotated the data to N45°E direction, interpretation of the result has been performed using three different methods of 1D MT modeling i.e. Bostick inversion, 1D MT inversion of TM data, and 1D MT inversion of the impedance determinant. By comparison, we concluded that the use of TM data only and the impedance determinant in 1D inversion yield the more reliable resistivity structure of the fault compare to other methods. Based on this result, it has been shown clearly that Sumatra Fault is characterized by vertical contras resistivity indicating the existence of Aceh and Seulimeum faults which has a good agreement with the geological data.

  11. Geomorphological and structural characterization of the southern Weihe Graben, central China: Implications for fault segmentation

    Science.gov (United States)

    Cheng, Yali; He, Chuanqi; Rao, Gang; Yan, Bing; Lin, Aiming; Hu, Jianmin; Yu, Yangli; Yao, Qi

    2018-01-01

    The Cenozoic graben systems around the tectonically stable Ordos Block, central China, have been considered as ideal places for investigating active deformation within continental rifts, such as the Weihe Graben at the southern margin with high historical seismicity (e.g., 1556 M 8.5 Huaxian great earthquake). However, previous investigations have mostly focused on the active structures in the eastern and northern parts of this graben. By contrast, in the southwest, tectonic activity along the northern margin of the Qinling Mountains has not been systematically investigated yet. In this study, based on digital elevation models (DEMs), we carried out geomorphological analysis to evaluate the relative tectonic activity along the whole South Border Fault (SBF). On the basis of field observations, high resolution DEMs acquired by small unmanned aerial vehicles (sUVA) using structure-for-motion techniques, radiocarbon (14C) age dating, we demonstrate that: 1) Tectonic activity along the SBF changes along strike, being higher in the eastern sector. 2) Seven major segment boundaries have been assigned, where the fault changes its strike and has lower tectonic activity. 3) The fault segment between the cities of Huaxian and Huayin characterized by almost pure normal slip has been active during the Holocene. We suggest that these findings would provide a basis for further investigating on the seismic risk in densely-populated Weihe Graben. Table S2. The values and classification of geomorphic indices obtained in this study. Fig. S1. Morphological features of the stream long profiles (Nos. 1-75) and corresponding SLK values. Fig. S2. Comparison of geomorphological parameters acquired from different DEMs (90-m SRTM and 30-m ASTER GDEM): (a) HI values; (b) HI linear regression; (c) mean slope of drainage basin; (d) mean slope linear regression.

  12. Three-Dimensional Shear Wave Velocity Structure of the Peru Flat Slab Subduction Segment

    Science.gov (United States)

    Knezevic Antonijevic, S.; Wagner, L. S.; Beck, S. L.; Zandt, G.; Long, M. D.

    2012-12-01

    Recent studies focused on flat slab subduction segments in central Chile (L. S. Wagner, 2006) and Alaska (B. R. Hacker and G. A. Aber, 2012) suggest significant differences in seismic velocity structures, and hence, composition in the mantle wedge between flat and normal "steep" subducting slabs. Instead of finding the low velocities and high Vp/Vs ratios common in normal subduction zones, these studies find low Vp, high Vs, and very low Vp/Vs above flat slabs. This may indicate the presence of dry, cold material in the mantle wedge. In order to investigate the seismic velocities of the upper mantle above the Peruvian flat segment, we have inverted for 2D Rayleigh wave phase velocity maps using data from the currently deployed 40 station PULSE seismic network and some adjacent stations from the CAUGHT seismic network. We then used the sensitivity of surface waves to shear wave velocity structure with depth to develop a 3D shear wave velocity model. This model will allow us to determine the nature of the mantle lithosphere above the flat slab, and how this may have influenced the development of local topography. For example, dry conditions (high Vs velocities) above the flat slab would imply greater strength of this material, possibly making it capable of causing further inland overthrusting, while wet conditions (low Vs) would imply weaker material. This could provide some insight into the ongoing debate over whether the Fitzcarrald arch (along the northern most flank of the Altiplano) could be a topographical response to the subducted Nazca ridge hundred kilometers away from the trench (N. Espurt, 2012, P. Baby, 2005, V. A. Ramos, 2012) or not (J. Martinod, 2005, M. Wipf, 2008, T. Gerya, 2008).

  13. Complementary SAXS and SANS for structural characteristics of a polyurethethane elastomer of low hard-segment content

    International Nuclear Information System (INIS)

    Sun, Y.-S.; Jeng, U-S.; Huang, Y.-S.; Liang, K.S.; Lin, T.-L.; Tsao, C.-S.

    2006-01-01

    A polyurethane (PU) elastomer film based on segmented poly(tetramethylene oxide) (PTMO) has been studied using wide-angle X-ray scattering (WAXS), and small-angle X-ray and neutron scattering (SAXS and SANS). The broad WAXS peaks measured for the PU elastomer reveal a low crystallinity of the soft segments PTMO and no crystalline domains for the hard segments, methylene bis(4-isocynatobenzene) (MDI), at 20 deg. C. Whereas small-angle scattering indicates the existence of hard-segment-rich aggregates. Using the contrast variation provided by the SANS and SAXS, we have extracted detailed structural information of the aggregates, including the shape, size, and the aggregation numbers

  14. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis

    Science.gov (United States)

    Vilar, Santiago; Harpaz, Rave; Chase, Herbert S; Costanzi, Stefano; Rabadan, Raul

    2011-01-01

    Background Adverse drug events (ADE) cause considerable harm to patients, and consequently their detection is critical for patient safety. The US Food and Drug Administration maintains an adverse event reporting system (AERS) to facilitate the detection of ADE in drugs. Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task. Objective To develop a new methodology that combines existing data mining algorithms with chemical information by analysis of molecular fingerprints to enhance initial ADE signals generated from AERS, and to provide a decision support mechanism to facilitate the identification of novel adverse events. Results The method achieved a significant improvement in precision in identifying known ADE, and a more than twofold signal enhancement when applied to the ADE rhabdomyolysis. The simplicity of the method assists in highlighting the etiology of the ADE by identifying structurally similar drugs. A set of drugs with strong evidence from both AERS and molecular fingerprint-based modeling is constructed for further analysis. Conclusion The results demonstrate that the proposed methodology could be used as a pharmacovigilance decision support tool to facilitate ADE detection. PMID:21946238

  15. Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens

    Directory of Open Access Journals (Sweden)

    Gomez Shawn M

    2010-04-01

    Full Text Available Abstract Background In the course of infection, viruses such as HIV-1 must enter a cell, travel to sites where they can hijack host machinery to transcribe their genes and translate their proteins, assemble, and then leave the cell again, all while evading the host immune system. Thus, successful infection depends on the pathogen's ability to manipulate the biological pathways and processes of the organism it infects. Interactions between HIV-encoded and human proteins provide one means by which HIV-1 can connect into cellular pathways to carry out these survival processes. Results We developed and applied a computational approach to predict interactions between HIV and human proteins based on structural similarity of 9 HIV-1 proteins to human proteins having known interactions. Using functional data from RNAi studies as a filter, we generated over 2000 interaction predictions between HIV proteins and 406 unique human proteins. Additional filtering based on Gene Ontology cellular component annotation reduced the number of predictions to 502 interactions involving 137 human proteins. We find numerous known interactions as well as novel interactions showing significant functional relevance based on supporting Gene Ontology and literature evidence. Conclusions Understanding the interplay between HIV-1 and its human host will help in understanding the viral lifecycle and the ways in which this virus is able to manipulate its host. The results shown here provide a potential set of interactions that are amenable to further experimental manipulation as well as potential targets for therapeutic intervention.

  16. Asymmetry quantification from reflectance images of orthotic patients using structural similarity metrics

    Science.gov (United States)

    Boucher, Marc-Antoine; Watts, Nicolas; Gremillet, Frederic; Legare, Philippe; Kadoury, Samuel

    2018-02-01

    Pathologies like plantar fasciitis, a common soft tissue disorder of the foot, is frequently associated with older age, high BMI and little exercise. Like other pathologies associated with the foot, the knee or hip, foot orthoses can help the patient's posture and recent techniques allow the creation of personalized foot orthoses based on 3D foot model that are fitted with high accuracy to the foot surface. In order to assess the efficacy of the personalized orthoses on the patient's pose and balance, depth images with reflectance camera filters are acquired in order to evaluate the posture of the patient before and after the use of the orthoses. Images are analysed by clinicians to assess the region asymmetry and posture changes. However, this remains a subjective evaluation and a quantifiable measurement is required to follow patient progression. In this paper, we present a novel tool to assess and quantify the asymmetry of body regions using a color-based structural similarity metric calculated from paired regions. This provides a quantitative measure to evaluate the effect of the personalized orthoses on the patient. A user-friendly interface allows the user to select an area of the body and automatically generate a symmetry axis, along with a measure of asymmetry measuring reflectance variations from the skin. The tool was validated on 30 patients, demonstrating an 83% agreement rate compare to clinical observations.

  17. Discrimination and Measurements of Three Flavonols with Similar Structure Using Terahertz Spectroscopy and Chemometrics

    Science.gov (United States)

    Yan, Ling; Liu, Changhong; Qu, Hao; Liu, Wei; Zhang, Yan; Yang, Jianbo; Zheng, Lei

    2018-03-01

    Terahertz (THz) technique, a recently developed spectral method, has been researched and used for the rapid discrimination and measurements of food compositions due to its low-energy and non-ionizing characteristics. In this study, THz spectroscopy combined with chemometrics has been utilized for qualitative and quantitative analysis of myricetin, quercetin, and kaempferol with concentrations of 0.025, 0.05, and 0.1 mg/mL. The qualitative discrimination was achieved by KNN, ELM, and RF models with the spectra pre-treatments. An excellent discrimination (100% CCR in the prediction set) could be achieved using the RF model. Furthermore, the quantitative analyses were performed by partial least square regression (PLSR) and least squares support vector machine (LS-SVM). Comparing to the PLSR models, the LS-SVM yielded better results with low RMSEP (0.0044, 0.0039, and 0.0048), higher Rp (0.9601, 0.9688, and 0.9359), and higher RPD (8.6272, 9.6333, and 7.9083) for myricetin, quercetin, and kaempferol, respectively. Our results demonstrate that THz spectroscopy technique is a powerful tool for identification of three flavonols with similar chemical structures and quantitative determination of their concentrations.

  18. Technical report on semiautomatic segmentation using the Adobe Photoshop.

    Science.gov (United States)

    Park, Jin Seo; Chung, Min Suk; Hwang, Sung Bae; Lee, Yong Sook; Har, Dong-Hwan

    2005-12-01

    The purpose of this research is to enable users to semiautomatically segment the anatomical structures in magnetic resonance images (MRIs), computerized tomographs (CTs), and other medical images on a personal computer. The segmented images are used for making 3D images, which are helpful to medical education and research. To achieve this purpose, the following trials were performed. The entire body of a volunteer was scanned to make 557 MRIs. On Adobe Photoshop, contours of 19 anatomical structures in the MRIs were semiautomatically drawn using MAGNETIC LASSO TOOL and manually corrected using either LASSO TOOL or DIRECT SELECTION TOOL to make 557 segmented images. In a similar manner, 13 anatomical structures in 8,590 anatomical images were segmented. Proper segmentation was verified by making 3D images from the segmented images. Semiautomatic segmentation using Adobe Photoshop is expected to be widely used for segmentation of anatomical structures in various medical images.

  19. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

    Directory of Open Access Journals (Sweden)

    Manzini Giovanni

    2007-07-01

    Full Text Available Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity, NCD (Normalized Compression Dissimilarity and CD (Compression Dissimilarity. Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. Results We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC

  20. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

    Science.gov (United States)

    Ferragina, Paolo; Giancarlo, Raffaele; Greco, Valentina; Manzini, Giovanni; Valiente, Gabriel

    2007-07-13

    Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity), NCD (Normalized Compression Dissimilarity) and CD (Compression Dissimilarity). Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC (Receiver Operating Curve) analysis, aims at

  1. Lung structure and function similarities between primary ciliary dyskinesia and mild cystic fibrosis: a pilot study.

    Science.gov (United States)

    Maglione, Marco; Montella, Silvia; Mollica, Carmine; Carnovale, Vincenzo; Iacotucci, Paola; De Gregorio, Fabiola; Tosco, Antonella; Cervasio, Mariarosaria; Raia, Valeria; Santamaria, Francesca

    2017-04-12

    Primary ciliary dyskinesia (PCD) and cystic fibrosis (CF) are increasingly compared. There are no chest magnetic resonance imaging (MRI) comparative studies of PCD and CF. We assessed clinical, functional, microbiological and MRI findings in PCD and mild CF patients in order to evaluate different expression of lung disease. Twenty PCD (15.1 years) and 20 CF subjects with mild respiratory impairment (16 years, 70% with pancreatic insufficiency) underwent MRI, spirometry, and sputum cultures when clinically stable. MRI was scored using the modified Helbich system. PCD was diagnosed later than CF (9.9 versus 0.6 years, p = 0.03), despite earlier symptoms (0.1 versus 0.6 years, p = 0.02). In the year preceding the study, patients from both groups underwent two systemic antibiotic courses (p = 0.48). MRI total scores were 11.6 ± 0.7 and 9.1 ± 1 in PCD and CF, respectively. FEV 1 and FVC Z-scores were -1.75 (range, -4.6-0.7) and -0.6 (-3.9-1.8) in PCD, and -0.9 (range, -5.4-2.3) and -0.3 (-3.4-2.5) in CF, respectively. No difference was found between lung function or structure, despite a higher MRI subscore of collapse/consolidation in PCD versus CF (1.6 ± 0.1 and 0.6 ± 0.2, p < 0.001). These findings were confirmed after data-control for diagnostic delay. Pseudomonas aeruginosa and Staphylococcus aureus were more frequent in CF than in PCD (p = 0.05 and p = 0.003, respectively). MRI is a valuable radiation-free tool for comparative PCD and CF lung disease assessment. Patients with PCD may exhibit similar MRI and lung function changes as CF subjects with mild pulmonary disease. Delay in PCD diagnosis is unlikely the only determinant of similarities.

  2. Along-Axis Structure and Crustal Construction Processes of Spreading Segments in Iceland: Implications for Magmatic Rifts

    Science.gov (United States)

    Siler, D. L.; Karson, J. A.

    2017-10-01

    Magmatic rift systems are composed of discrete spreading segments defined by morphologic, structural, and volcanic features that vary systematically along strike. In Iceland, structural features mapped in the glaciated and exhumed Miocene age upper crust correlate with analogous features in the seismically and volcanically active neovolcanic zone. Integrating information from both the active rift zones and ancient crust provides a three-dimensional perspective of crustal structure and the volcanic and tectonic processes that construct crust along spreading segments. Crustal exposures in the Skagi region of northern Iceland reveal significant along-strike variations in geologic structure. The upper crust at exhumed magmatic centers (segment centers) is characterized by a variety of intrusive rocks, high-temperature hydrothermal alteration, and geologic evidence for kilometer-scale subsidence. In contrast, the upper crust along segment limbs, which extend along strike from magmatic centers, is characterized by thick sections of gently dipping lava flows, cut by varying proportions of subvertical dikes. This structure implies relatively minor upper crustal subsidence and lateral dike intrusion. The differing modes of subsidence beneath segment centers and segment limbs require along-axis mass redistribution in the underlying upper, middle, and lower crust during crustal construction. This along-axis material transport is accomplished through lateral dike intrusion in the upper crust and by along-axis flow of magmatic to high-temperature solid-state gabbroic material in the middle and lower crust. These processes, inferred from outcrop evidence in Skagi, are consistent with processes inferred to be important during active rifting in Iceland and at analogous magmatic oceanic and continental rifts.

  3. Testing statistical significance scores of sequence comparison methods with structure similarity

    Directory of Open Access Journals (Sweden)

    Leunissen Jack AM

    2006-10-01

    Full Text Available Abstract Background In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. Results All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. Conclusion The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.

  4. Vibration based structural assessment of the rehabilitation intervention in r.c. segmental bridge

    Directory of Open Access Journals (Sweden)

    Franchetti Paolo

    2015-01-01

    Full Text Available A vibration based structural assessment campaign was carried out on a r.c. segmental bridge in North East Italy. The bridge has a cantilever static scheme, fixed at the top of the piers and with a hinge at the centre of the span. The particular configuration of the hinge consists in a couple of steel elements, each one composed by a tongue and groove joint. Since the year 1960, the hinge was subjected to consumption and degradation, that caused a malfunctioning of the device. An intervention of rehabilitation of the bridge led to a reinforcement of the existing hinges with the coupling of new metallic devices: new tongue and groove hinges were applied, that by one side allow the horizontal displacements and rotation, by the other side strongly reduce the relative vertical displacements of the two parts of the bridge. A dynamic test campaign was set up in order to assess the effectiveness of the intervention. The principal dynamic parameters were calculated and analysed with respect to the intervention that was realized. The tests clearly showed the effectiveness of the intervention, and helped the designer to have a better understanding of the structural behaviour of the bridge.

  5. Interleaved 3D-CNNs for joint segmentation of small-volume structures in head and neck CT images.

    Science.gov (United States)

    Ren, Xuhua; Xiang, Lei; Nie, Dong; Shao, Yeqin; Zhang, Huan; Shen, Dinggang; Wang, Qian

    2018-02-26

    Accurate 3D image segmentation is a crucial step in radiation therapy planning of head and neck tumors. These segmentation results are currently obtained by manual outlining of tissues, which is a tedious and time-consuming procedure. Automatic segmentation provides an alternative solution, which, however, is often difficult for small tissues (i.e., chiasm and optic nerves in head and neck CT images) because of their small volumes and highly diverse appearance/shape information. In this work, we propose to interleave multiple 3D Convolutional Neural Networks (3D-CNNs) to attain automatic segmentation of small tissues in head and neck CT images. A 3D-CNN was designed to segment each structure of interest. To make full use of the image appearance information, multiscale patches are extracted to describe the center voxel under consideration and then input to the CNN architecture. Next, as neighboring tissues are often highly related in the physiological and anatomical perspectives, we interleave the CNNs designated for the individual tissues. In this way, the tentative segmentation result of a specific tissue can contribute to refine the segmentations of other neighboring tissues. Finally, as more CNNs are interleaved and cascaded, a complex network of CNNs can be derived, such that all tissues can be jointly segmented and iteratively refined. Our method was validated on a set of 48 CT images, obtained from the Medical Image Computing and Computer Assisted Intervention (MICCAI) Challenge 2015. The Dice coefficient (DC) and the 95% Hausdorff Distance (95HD) are computed to measure the accuracy of the segmentation results. The proposed method achieves higher segmentation accuracy (with the average DC: 0.58 ± 0.17 for optic chiasm, and 0.71 ± 0.08 for optic nerve; 95HD: 2.81 ± 1.56 mm for optic chiasm, and 2.23 ± 0.90 mm for optic nerve) than the MICCAI challenge winner (with the average DC: 0.38 for optic chiasm, and 0.68 for optic nerve; 95HD: 3.48 for

  6. Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment

    Directory of Open Access Journals (Sweden)

    Bruno Aquino

    2017-05-01

    Full Text Available Kinases are primary regulators of plant metabolism and excellent targets for plant breeding. However, most kinases, including the abundant receptor-like kinases (RLK, have no assigned role. SIRK1 is a leucine-rich repeat receptor-like kinase (LRR-RLK, the largest family of RLK. In Arabidopsis thaliana, SIRK1 (AtSIRK1 is phosphorylated after sucrose is resupplied to sucrose-starved seedlings and it modulates the sugar response by phosphorylating several substrates. In maize, the ZmSIRK1 expression is altered in response to drought stress. In neither Arabidopsis nor in maize has the function of SIRK1 been completely elucidated. As a first step toward the biochemical characterization of ZmSIRK1, we obtained its recombinant kinase domain, demonstrated that it binds AMP-PNP, a non-hydrolysable ATP-analog, and solved the structure of ZmSIRK1- AMP-PNP co-crystal. The ZmSIRK1 crystal structure revealed a unique conformation for the activation segment. In an attempt to find inhibitors for ZmSIRK1, we screened a focused small molecule library and identified six compounds that stabilized ZmSIRK1 against thermal melt. ITC analysis confirmed that three of these compounds bound to ZmSIRK1 with low micromolar affinity. Solving the 3D structure of ZmSIRK1-AMP-PNP co-crystal provided information on the molecular mechanism of ZmSIRK1 activity. Furthermore, the identification of small molecules that bind this kinase can serve as initial backbone for development of new potent and selective ZmSIRK1 antagonists.

  7. Segmental isotope labeling of proteins for NMR structural study using a protein S tag for higher expression and solubility

    International Nuclear Information System (INIS)

    Kobayashi, Hiroshi; Swapna, G. V. T.; Wu, Kuen-Phon; Afinogenova, Yuliya; Conover, Kenith; Mao, Binchen; Montelione, Gaetano T.; Inouye, Masayori

    2012-01-01

    A common obstacle to NMR studies of proteins is sample preparation. In many cases, proteins targeted for NMR studies are poorly expressed and/or expressed in insoluble forms. Here, we describe a novel approach to overcome these problems. In the protein S tag-intein (PSTI) technology, two tandem 92-residue N-terminal domains of protein S (PrS 2 ) from Myxococcus xanthus is fused at the N-terminal end of a protein to enhance its expression and solubility. Using intein technology, the isotope-labeled PrS 2 -tag is replaced with non-isotope labeled PrS 2 -tag, silencing the NMR signals from PrS 2 -tag in isotope-filtered 1 H-detected NMR experiments. This method was applied to the E. coli ribosome binding factor A (RbfA), which aggregates and precipitates in the absence of a solubilization tag unless the C-terminal 25-residue segment is deleted (RbfAΔ25). Using the PrS 2 -tag, full-length well-behaved RbfA samples could be successfully prepared for NMR studies. PrS 2 (non-labeled)-tagged RbfA (isotope-labeled) was produced with the use of the intein approach. The well-resolved TROSY-HSQC spectrum of full-length PrS 2 -tagged RbfA superimposes with the TROSY-HSQC spectrum of RbfAΔ25, indicating that PrS 2 -tag does not affect the structure of the protein to which it is fused. Using a smaller PrS-tag, consisting of a single N-terminal domain of protein S, triple resonance experiments were performed, and most of the backbone 1 H, 15 N and 13 C resonance assignments for full-length E. coli RbfA were determined. Analysis of these chemical shift data with the Chemical Shift Index and heteronuclear 1 H– 15 N NOE measurements reveal the dynamic nature of the C-terminal segment of the full-length RbfA protein, which could not be inferred using the truncated RbfAΔ25 construct. CS-Rosetta calculations also demonstrate that the core structure of full-length RbfA is similar to that of the RbfAΔ25 construct.

  8. Associative Interference in Pavlovian Conditioning: A Function of Similarity Between the Interfering and Target Associative Structures

    OpenAIRE

    Amundson, Jeffrey C.; Miller, Ralph R.

    2008-01-01

    Three lever-press suppression studies were conducted with water-deprived rats to investigate the role of similarity in proactive interference within first-order Pavlovian conditioning. Experiments 1a and 1b assessed the influence of stimulus complexity in proactive interference. Both experiments found greater interference when the interfering cue and target cue were composed of the same number of elements. Experiment 2 assessed the influence of context similarity in proactive interference and...

  9. In vivo estimation of normal amygdala volume from structural MRI scans with anatomical-based segmentation.

    Science.gov (United States)

    Siozopoulos, Achilleas; Thomaidis, Vasilios; Prassopoulos, Panos; Fiska, Aliki

    2018-02-01

    Literature includes a number of studies using structural MRI (sMRI) to determine the volume of the amygdala, which is modified in various pathologic conditions. The reported values vary widely mainly because of different anatomical approaches to the complex. This study aims at estimating of the normal amygdala volume from sMRI scans using a recent anatomical definition described in a study based on post-mortem material. The amygdala volume has been calculated in 106 healthy subjects, using sMRI and anatomical-based segmentation. The resulting volumes have been analyzed for differences related to hemisphere, sex, and age. The mean amygdalar volume was estimated at 1.42 cm 3 . The mean right amygdala volume has been found larger than the left, but the difference for the raw values was within the limits of the method error. No intersexual differences or age-related alterations have been observed. The study provides a method for determining the boundaries of the amygdala in sMRI scans based on recent anatomical considerations and an estimation of the mean normal amygdala volume from a quite large number of scans for future use in comparative studies.

  10. Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.

    Science.gov (United States)

    Rizk, Aurélien; Paul, Grégory; Incardona, Pietro; Bugarski, Milica; Mansouri, Maysam; Niemann, Axel; Ziegler, Urs; Berger, Philipp; Sbalzarini, Ivo F

    2014-03-01

    Detection and quantification of fluorescently labeled molecules in subcellular compartments is a key step in the analysis of many cell biological processes. Pixel-wise colocalization analyses, however, are not always suitable, because they do not provide object-specific information, and they are vulnerable to noise and background fluorescence. Here we present a versatile protocol for a method named 'Squassh' (segmentation and quantification of subcellular shapes), which is used for detecting, delineating and quantifying subcellular structures in fluorescence microscopy images. The workflow is implemented in freely available, user-friendly software. It works on both 2D and 3D images, accounts for the microscope optics and for uneven image background, computes cell masks and provides subpixel accuracy. The Squassh software enables both colocalization and shape analyses. The protocol can be applied in batch, on desktop computers or computer clusters, and it usually requires images, respectively. Basic computer-user skills and some experience with fluorescence microscopy are recommended to successfully use the protocol.

  11. The eye of the magellanic penguin (Spheniscus magellanicus): structure of the anterior segment.

    Science.gov (United States)

    Suburo, A M; Scolaro, J A

    1990-11-01

    We undertook a light and scanning electron microscopic study of the eye in the Magellanic penguin (Spheniscus magellanicus). The anatomical peculiarities of the eyeball shape in Sphenisciformes have been previously described by others; here, we show that they are accompanied by several modifications in the organization of the anterior segment of the eye. The main change was found in the portion of opaque sclera extending from the cornea to the anterior border of the scleral ossicles, which was much broader than in other avian eyes. This scleral region was made of a very dense fibrous tissue and was as difficult to cut as the ossicles. The corneo-scleral boundary was also different from that of other birds, since the aqueous humor channel and the pectinate ligament were located 1.0-1.5 mm posterior to the cornea. The osseous ring was formed by 13 bones, including three pairs of over- and underplates. There was a single ciliary muscle, with meridionally oriented striated fibers. They were inserted on a circumference along the boundary between the fibrous sclera and the ossicles, far away from the wall of the aqueous humor channel. On their posterior end, the muscle fibers formed a tendinous structure attached to the inner surface of the sclera and to the outer surface of the ciliary body. Only short zonular fibrils were observed. These anatomical features are probably relevant for the adaptation of penguin eyes to vision on land and in the aquatic environment.

  12. Studies on micro-domain structure in segmented polyether polyurethane-ureas by positron annihilation lifetime and small-angle X-ray scattering

    International Nuclear Information System (INIS)

    Yin Chuanyuan; Gu Qingchao

    1997-01-01

    The micro-domain structure of segmented polyether polyurethane-ureas is investigated by means of positron annihilation lifetime spectroscopy, small-angle X-ray scattering and differential scanning calorimetry. The experimental results show that the decrease in the domain volume and free volume results from the increase in the hard segment (polyurethane-urea segment) contents as the number-average molecular weight M n -bar of the soft segments (polyethylene glycol segments) is the same, and that the increase in domain volume and free volume result from the increase in the M n -bar of the soft segments when the hard segment content is the same or nearly the same. These results demonstrate that positron annihilation lifetime spectroscopy is a sensitive technique to probe the micro-domain structure in polymers

  13. A Comparison of Supervised Machine Learning Algorithms and Feature Vectors for MS Lesion Segmentation Using Multimodal Structural MRI

    Science.gov (United States)

    Sweeney, Elizabeth M.; Vogelstein, Joshua T.; Cuzzocreo, Jennifer L.; Calabresi, Peter A.; Reich, Daniel S.; Crainiceanu, Ciprian M.; Shinohara, Russell T.

    2014-01-01

    Machine learning is a popular method for mining and analyzing large collections of medical data. We focus on a particular problem from medical research, supervised multiple sclerosis (MS) lesion segmentation in structural magnetic resonance imaging (MRI). We examine the extent to which the choice of machine learning or classification algorithm and feature extraction function impacts the performance of lesion segmentation methods. As quantitative measures derived from structural MRI are important clinical tools for research into the pathophysiology and natural history of MS, the development of automated lesion segmentation methods is an active research field. Yet, little is known about what drives performance of these methods. We evaluate the performance of automated MS lesion segmentation methods, which consist of a supervised classification algorithm composed with a feature extraction function. These feature extraction functions act on the observed T1-weighted (T1-w), T2-weighted (T2-w) and fluid-attenuated inversion recovery (FLAIR) MRI voxel intensities. Each MRI study has a manual lesion segmentation that we use to train and validate the supervised classification algorithms. Our main finding is that the differences in predictive performance are due more to differences in the feature vectors, rather than the machine learning or classification algorithms. Features that incorporate information from neighboring voxels in the brain were found to increase performance substantially. For lesion segmentation, we conclude that it is better to use simple, interpretable, and fast algorithms, such as logistic regression, linear discriminant analysis, and quadratic discriminant analysis, and to develop the features to improve performance. PMID:24781953

  14. Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

  15. Spatio-Temporal Video Object Segmentation via Scale-Adaptive 3D Structure Tensor

    Directory of Open Access Journals (Sweden)

    Hai-Yun Wang

    2004-06-01

    Full Text Available To address multiple motions and deformable objects' motions encountered in existing region-based approaches, an automatic video object (VO segmentation methodology is proposed in this paper by exploiting the duality of image segmentation and motion estimation such that spatial and temporal information could assist each other to jointly yield much improved segmentation results. The key novelties of our method are (1 scale-adaptive tensor computation, (2 spatial-constrained motion mask generation without invoking dense motion-field computation, (3 rigidity analysis, (4 motion mask generation and selection, and (5 motion-constrained spatial region merging. Experimental results demonstrate that these novelties jointly contribute much more accurate VO segmentation both in spatial and temporal domains.

  16. Hydrophobic coating of microfluidic chips structured by SU-8 polymer for segmented flow operation

    International Nuclear Information System (INIS)

    Schumacher, J T; Grodrian, A; Metze, J; Kremin, C; Hoffmann, M

    2008-01-01

    We present a hydrophobization procedure for SU-8-based microfluidic chips on borofloat substrates. Different layouts of gold electrodes passivated by the polymer have been investigated. The chips are used for segmented flow in a two-fluid mode that requires a distinct hydrophobicity of the channel walls which is generated by the use of specific silane. In this paper we describe the production and silanization of the chips and demonstrate segmented flow operation

  17. Design of compound libraries based on natural product scaffolds and protein structure similarity clustering (PSSC)

    NARCIS (Netherlands)

    Balamurugan, Rengarajan; Dekker, Frank J; Waldmann, Herbert; Dekker, Frans

    Recent advances in structural biology, bioinformatics and combinatorial chemistry have significantly impacted the discovery of small molecules that modulate protein functions. Natural products which have evolved to bind to proteins may serve as biologically validated starting points for the design

  18. Math Anxiety Questionnaire: Similar Latent Structure in Brazilian and German School Children

    Directory of Open Access Journals (Sweden)

    Guilherme Wood

    2012-01-01

    Full Text Available Math anxiety is a relatively frequent phenomenon often related to low mathematics achievement and dyscalculia. In the present study, the German and the Brazilian versions of the Mathematics Anxiety Questionnaire (MAQ were examined. The two-dimensional structure originally reported for the German MAQ, that includes both affective and cognitive components of math anxiety was reproduced in the Brazilian version. Moreover, mathematics anxiety also was found to increase with age in both populations and was particularly associated with basic numeric competencies and more complex arithmetics. The present results suggest that mathematics anxiety as measured by the MAQ presents the same internal structure in culturally very different populations.

  19. Panarchy: discontinuities reval similarities in the dynamic system structure of ecological and social systems

    Science.gov (United States)

    Debates on the organization, structure and dynamics of ecosystems across scales of space and time have waxed and waned in the literature for a century. From successional theory to ecosystem theories of resilience and robustness, from hierarchy to ascendency to panarchy theory, e...

  20. The potential indirect effects among plants via shared hummingbird pollinators are structured by phenotypic similarity.

    Science.gov (United States)

    Bergamo, Pedro Joaquim; Wolowski, Marina; Maruyama, Pietro Kiyoshi; Vizentin-Bugoni, Jeferson; Carvalheiro, Luísa G; Sazima, Marlies

    2017-07-01

    Plant species within communities may overlap in pollinators' use and influence visitation patterns of shared pollinators, potentially engaging in indirect interactions (e.g., facilitation or competition). While several studies have explored the mechanisms regulating insect-pollination networks, there is a lack of studies on bird-pollination systems, particularly in species-rich tropical areas. Here, we evaluated if phenotypic similarity, resource availability (floral abundance), evolutionary relatedness and flowering phenology affect the potential for indirect effects via shared pollinators in hummingbird-pollinated plant species within four communities in the Brazilian Atlantic forest. Among the evaluated factors, phenotypic similarity (corolla length and anther height) was the most important variable, while resource availability (floral abundance) had a secondary importance. On the other hand, evolutionary relatedness and flowering phenology were less important, which altogether highlights the relevance of convergent evolution and that the contribution of a plant to the diet of the pollinators of another plant is independent of the level of temporal overlap in flowering in this tropical system. Interestingly, our findings contrast with results from multiple insect-pollinated plant communities, mostly from temperate regions, in which floral abundance was the most important driver, followed by evolutionary relatedness and phenotypic similarity. We propose that these contrasting results are due to high level of specialization inherent to tropical hummingbird-pollination systems. Moreover, our results demonstrated that factors defining linkage rules of plant-hummingbird networks also determinate plant-plant potential indirect effects. Future studies are needed to test if these findings can be generalized to other highly specialized systems. Overall, our results have important implications for the understanding of ecological processes due resource sharing in

  1. Automatic Segmenting Structures in MRI's Based on Texture Analysis and Fuzzy Logic

    Science.gov (United States)

    Kaur, Mandeep; Rattan, Munish; Singh, Pushpinder

    2017-12-01

    The purpose of this paper is to present the variational method for geometric contours which helps the level set function remain close to the sign distance function, therefor it remove the need of expensive re-initialization procedure and thus, level set method is applied on magnetic resonance images (MRI) to track the irregularities in them as medical imaging plays a substantial part in the treatment, therapy and diagnosis of various organs, tumors and various abnormalities. It favors the patient with more speedy and decisive disease controlling with lesser side effects. The geometrical shape, the tumor's size and tissue's abnormal growth can be calculated by the segmentation of that particular image. It is still a great challenge for the researchers to tackle with an automatic segmentation in the medical imaging. Based on the texture analysis, different images are processed by optimization of level set segmentation. Traditionally, optimization was manual for every image where each parameter is selected one after another. By applying fuzzy logic, the segmentation of image is correlated based on texture features, to make it automatic and more effective. There is no initialization of parameters and it works like an intelligent system. It segments the different MRI images without tuning the level set parameters and give optimized results for all MRI's.

  2. Different Context but Similar Cognitive Structures: Older Adults in Rural Bangladesh.

    Science.gov (United States)

    Sternäng, Ola; Lövdén, Martin; Kabir, Zarina N; Hamadani, Jena D; Wahlin, Åke

    2016-06-01

    Most research in cognitive aging is based on literate participants from high-income and Western populations. The extent to which findings generalize to low-income and illiterate populations is unknown. The main aim was to examine the structure of between-person differences in cognitive functions among elderly from rural Bangladesh. We used data from the Poverty and Health in Aging (PHA) project in Bangladesh. The participants (n = 452) were in the age range 60-92 years. Structural equation modeling was used to estimate the fit of a five-factor model (episodic recall, episodic recognition, verbal fluency, semantic knowledge, processing speed) and to examine whether the model generalized across age, sex, and literacy. This study demonstrates that an established model of cognition is valid also among older persons from rural Bangladesh. The model demonstrated strong (or scalar) invariance for age, and partial strong invariance for sex and literacy. Semantic knowledge and processing speed showed weak (or metric) sex invariance, and semantic knowledge demonstrated also sensitivity to illiteracy. In general, women performed poorer on all abilities. The structure of individual cognitive differences established in Western populations also fits a population in rural Bangladesh well. This is an important prerequisite for comparisons of cognitive functioning (e.g., declarative memory) across cultures. It is also worth noting that absolute sex differences in cognitive performance among rural elderly in Bangladesh differ from those usually found in Western samples.

  3. Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK.

    Science.gov (United States)

    Machado Benelli, Elaine; Buck, Martin; Polikarpov, Igor; Maltempi de Souza, Emanuel; Cruz, Leonardo M; Pedrosa, Fábio O

    2002-07-01

    PII-like proteins are signal transduction proteins found in bacteria, archaea and eukaryotes. They mediate a variety of cellular responses. A second PII-like protein, called GlnK, has been found in several organisms. In the diazotroph Herbaspirillum seropedicae, PII protein is involved in sensing nitrogen levels and controlling nitrogen fixation genes. In this work, the crystal structure of the unliganded H. seropedicae PII was solved by X-ray diffraction. H. seropedicae PII has a Gly residue, Gly108 preceding Pro109 and the main-chain forms a beta turn. The glycine at position 108 allows a bend in the C-terminal main-chain, thereby modifying the surface of the cleft between monomers and potentially changing function. The structure suggests that the C-terminal region of PII proteins may be involved in specificity of function, and nonenteric diazotrophs are found to have the C-terminal consensus XGXDAX(107-112). We are also proposing binding sites for ATP and 2-oxoglutarate based on the structural alignment of PII with PII-ATP/GlnK-ATP, 5-carboxymethyl-2-hydroxymuconate isomerase and 4-oxalocrotonate tautomerase bound to the inhibitor 2-oxo-3-pentynoate.

  4. Structural similarity causes different category-effects depending on task characteristics

    DEFF Research Database (Denmark)

    Gerlach, Christian

    2001-01-01

    difference was found on easy object decision tasks. In experiment 2 an advantage for natural objects was found during object decisions performed under degraded viewing conditions (lateralized stimulus presentation). It is argued that these findings can be accounted for by assuming that natural objects...... it is in difficult object decision tasks). However, when viewing conditions are degraded and performance tends to depend on global shape information (carried by low spatial frequency components), natural objects may fare better than artefacts because the global shape of natural objects reveals more of their identity......It has been suggested that category-specific impairments for natural objects may reflect that natural objects are more globally visually similar than artefacts and therefore more difficult to recognize following brain damage [Aphasiology 13 (1992) 169]. This account has been challenged...

  5. LIGHT-WEIGHT LOAD-BEARING STRUCTURES REINFORCED BY CORE ELEMENTS MADE OF SEGMENTS AND A METHOD OF CASTING SUCH STRUCTURES

    DEFF Research Database (Denmark)

    2009-01-01

    The invention relates to a light-weight load-bearing structure, reinforced by core elements (2) of a strong material constituting one or more compression or tension zones in the structure to be cast, which core (2) is surrounded by or adjacent to a material of less strength compared to the core (2......), where the core (2) is constructed from segments (1) of core elements (2) assembled by means of one or more prestressing elements (4). The invention further relates to a method of casting of light-weight load-bearing structures, reinforced by core elements (2) of a strong material constituting one...... or more compression or tension zones in the structure to be cast, which core (2) is surrounded by or adjacent to a material of less strength compared to the core (2), where the core (2) is constructed from segments (1) of core elements (2) assembled and hold together by means of one or more prestressing...

  6. Structural Alterations of Segmented Macular Inner Layers in Aquaporin4-Antibody-Positive Optic Neuritis Patients in a Chinese Population.

    Directory of Open Access Journals (Sweden)

    Chunxia Peng

    Full Text Available This study aimed to analyse the structural injury of the peripapillary retinal nerve fibre layer (pRNFL and segmented macular layers in optic neuritis (ON in aquaporin4-antibody (AQP4-Ab seropositivity(AQP4-Ab-positiveON patients and in AQP4-Ab seronegativity (AQP4-Ab-negative ON patients in order to evaluate their correlations with the best-corrected visual acuity (BCVA and the value of the early diagnosis of neuromyelitis optica (NMO.This is a retrospective, cross-sectional and control observational study.In total, 213 ON patients (291 eyes and 50 healthy controls (HC (100 eyes were recruited in this study. According to a serum AQP4-Ab assay, 98 ON patients (132 eyes were grouped as AQP4-Ab-positive ON and 115 ON patients (159 eyes were grouped as AQP4-Ab-negative ON cohorts. All subjects underwent scanning with spectralis optical coherence tomography (OCT and BCVA tests. pRNFL and segmented macular layer measurements were analysed.The pRNFL thickness in AQP4-Ab-positive ON eyes showed a more serious loss during 0-2 months (-27.61μm versus -14.47 μm and ≥6 months (-57.91μm versus -47.19μm when compared with AQP4-Ab-negative ON eyes. AQP4-Ab-positive ON preferentially damaged the nasal lateral pRNFL. The alterations in the macular ganglion cell layer plus the inner plexiform layer (GCIP in AQP4-Ab-positive ON eyes were similar to those in AQP4-Ab-negative ON eyes. AQP4-Ab-positive ON eyes had entirely different injury patterns in the inner nuclear layer (INL compared with AQP4-Ab-negative ON eyes during the first 6 months after the initial ON attack. These differences were as follows: the INL volume of AQP4-Ab-positive ON eyes had a gradual growing trend compared with AQP4-Ab-negative ON eyes, and it increased rapidly during 0-2 months, reached its peak during 2-4 months, and then decreased gradually. The pRNFL and GCIP in AQP4-Ab-positive ON eyes had positive correlations with BCVA. When the pRNFL thickness decreased to 95%CI (50.77

  7. From epidemics to information propagation: Striking differences in structurally similar adaptive network models

    Science.gov (United States)

    Trajanovski, Stojan; Guo, Dongchao; Van Mieghem, Piet

    2015-09-01

    The continuous-time adaptive susceptible-infected-susceptible (ASIS) epidemic model and the adaptive information diffusion (AID) model are two adaptive spreading processes on networks, in which a link in the network changes depending on the infectious state of its end nodes, but in opposite ways: (i) In the ASIS model a link is removed between two nodes if exactly one of the nodes is infected to suppress the epidemic, while a link is created in the AID model to speed up the information diffusion; (ii) a link is created between two susceptible nodes in the ASIS model to strengthen the healthy part of the network, while a link is broken in the AID model due to the lack of interest in informationless nodes. The ASIS and AID models may be considered as first-order models for cascades in real-world networks. While the ASIS model has been exploited in the literature, we show that the AID model is realistic by obtaining a good fit with Facebook data. Contrary to the common belief and intuition for such similar models, we show that the ASIS and AID models exhibit different but not opposite properties. Most remarkably, a unique metastable state always exists in the ASIS model, while there an hourglass-shaped region of instability in the AID model. Moreover, the epidemic threshold is a linear function in the effective link-breaking rate in the AID model, while it is almost constant but noisy in the AID model.

  8. A discriminative structural similarity measure and its application to video-volume registration for endoscope three-dimensional motion tracking.

    Science.gov (United States)

    Luo, Xiongbiao; Mori, Kensaku

    2014-06-01

    Endoscope 3-D motion tracking, which seeks to synchronize pre- and intra-operative images in endoscopic interventions, is usually performed as video-volume registration that optimizes the similarity between endoscopic video and pre-operative images. The tracking performance, in turn, depends significantly on whether a similarity measure can successfully characterize the difference between video sequences and volume rendering images driven by pre-operative images. The paper proposes a discriminative structural similarity measure, which uses the degradation of structural information and takes image correlation or structure, luminance, and contrast into consideration, to boost video-volume registration. By applying the proposed similarity measure to endoscope tracking, it was demonstrated to be more accurate and robust than several available similarity measures, e.g., local normalized cross correlation, normalized mutual information, modified mean square error, or normalized sum squared difference. Based on clinical data evaluation, the tracking error was reduced significantly from at least 14.6 mm to 4.5 mm. The processing time was accelerated more than 30 frames per second using graphics processing unit.

  9. Structural control of the upper plate on the down-dip segmentation of subduction dynamics

    Science.gov (United States)

    Shi, Q.; Barbot, S.; Karato, S. I.; Shibazaki, B.; Matsuzawa, T.; Tapponnier, P.

    2017-12-01

    -sip segmentation of the subduction dynamic is attributed to the upper plate structure that vary with depth. The high pore pressure, grain-size evolution and alternation of the rock physics may explain the existence and the periodicity of different slow earthquakes from shallow to deep regions in the subduction zone.

  10. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    Science.gov (United States)

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-05

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  11. Functional and structural comparison of visual lateralization in birds – similar but still different

    Science.gov (United States)

    Ströckens, Felix

    2014-01-01

    Vertebrate brains display physiological and anatomical left-right differences, which are related to hemispheric dominances for specific functions. Functional lateralizations likely rely on structural left-right differences in intra- and interhemispheric connectivity patterns that develop in tight gene-environment interactions. The visual systems of chickens and pigeons show that asymmetrical light stimulation during ontogeny induces a dominance of the left hemisphere for visuomotor control that is paralleled by projection asymmetries within the ascending visual pathways. But structural asymmetries vary essentially between both species concerning the affected pathway (thalamo- vs. tectofugal system), constancy of effects (transient vs. permanent), and the hemisphere receiving stronger bilateral input (right vs. left). These discrepancies suggest that at least two aspects of visual processes are influenced by asymmetric light stimulation: (1) visuomotor dominance develops within the ontogenetically stronger stimulated hemisphere but not necessarily in the one receiving stronger bottom-up input. As a secondary consequence of asymmetrical light experience, lateralized top-down mechanisms play a critical role in the emergence of hemispheric dominance. (2) Ontogenetic light experiences may affect the dominant use of left- and right-hemispheric strategies. Evidences from social and spatial cognition tasks indicate that chickens rely more on a right-hemispheric global strategy whereas pigeons display a dominance of the left hemisphere. Thus, behavioral asymmetries are linked to a stronger bilateral input to the right hemisphere in chickens but to the left one in pigeons. The degree of bilateral visual input may determine the dominant visual processing strategy when redundant encoding is possible. This analysis supports that environmental stimulation affects the balance between hemispheric-specific processing by lateralized interactions of bottom-up and top-down systems

  12. Functional and structural comparison of visual lateralization in birds – similar but still different

    Directory of Open Access Journals (Sweden)

    Martina eManns

    2014-03-01

    Full Text Available Vertebrate brains display physiological and anatomical left-right differences, which are related to hemispheric dominances for specific functions. Functional lateralizations likely rely on structural left-right differences in intra- and interhemispheric connectivity patterns that develop in tight gene-environment interactions. The visual systems of chickens and pigeons show that asymmetrical light stimulation during ontogeny induces a dominance of the left hemisphere for visuomotor control that is paralleled by projection asymmetries within the ascending visual pathways. But structural asymmetries vary essentially between both species concerning the affected pathway (thalamo- vs. tectofugal system, constancy of effects (transient vs. permanent, and the hemisphere receiving stronger bilateral input (right vs. left. These discrepancies suggest that at least two aspects of visual processes are influenced by asymmetric light stimulation: 1. Visuomotor dominance develops within the ontogenetically stronger stimulated hemisphere but not necessarily in the one receiving stronger bottom-up input. As a secondary consequence of asymmetrical light experience, lateralized top-down mechanisms play a critical role in the emergence of hemispheric dominance. 2. Ontogenetic light experiences may affect the dominant use of left- and right-hemispheric strategies. Evidences from social and spatial cognition tasks indicate that chickens rely more on a right-hemispheric global strategy whereas pigeons display a dominance of the left hemisphere. Thus, behavioural asymmetries are linked to a stronger bilateral input to the right hemisphere in chickens but to the left one in pigeons. The degree of bilateral visual input may determine the dominant visual processing strategy when redundant encoding is possible. This analysis supports that environmental stimulation affects the balance between hemispheric-specific processing by lateralized interactions of bottom-up and top

  13. A tale of two pectins: Diverse fine structures can result from identical processive PME treatments on similar high DM subtrates

    Science.gov (United States)

    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...

  14. Solid-support Electron Paramagnetic Resonance (EPR) Studies of Aβ40 Monomers Reveal a Structured State with Three Ordered Segments*

    Science.gov (United States)

    Gu, Lei; Ngo, Sam; Guo, Zhefeng

    2012-01-01

    Alzheimer disease is associated with the pathological accumulation of amyloid-β peptide (Aβ) in the brain. Soluble Aβ oligomers formed during early aggregation process are believed to be neurotoxins and causative agents in Alzheimer disease. Aβ monomer is the building block for amyloid assemblies. A comprehensive understanding of the structural features of Aβ monomer is crucial for delineating the mechanism of Aβ oligomerization. Here we investigated the structures of Aβ40 monomer using a solid-support approach, in which Aβ40 monomers are tethered on the solid support via an N-terminal His tag to prevent further aggregation. EPR spectra of tethered Aβ40 with spin labels at 18 different positions show that Aβ40 monomers adopt a completely disordered structure under denaturing conditions. Under native conditions, however, EPR spectra suggest that Aβ40 monomers adopt both a disordered state and a structured state. The structured state of Aβ40 monomer has three more ordered segments at 14–18, 29–30, and 38–40. Interactions between these segments may stabilize the structured state, which likely plays an important role in Aβ aggregation. PMID:22277652

  15. A Semiautomatic Segmentation Algorithm for Extracting the Complete Structure of Acini from Synchrotron Micro-CT Images

    Directory of Open Access Journals (Sweden)

    Luosha Xiao

    2013-01-01

    Full Text Available Pulmonary acinus is the largest airway unit provided with alveoli where blood/gas exchange takes place. Understanding the complete structure of acinus is necessary to measure the pathway of gas exchange and to simulate various mechanical phenomena in the lungs. The usual manual segmentation of a complete acinus structure from their experimentally obtained images is difficult and extremely time-consuming, which hampers the statistical analysis. In this study, we develop a semiautomatic segmentation algorithm for extracting the complete structure of acinus from synchrotron micro-CT images of the closed chest of mouse lungs. The algorithm uses a combination of conventional binary image processing techniques based on the multiscale and hierarchical nature of lung structures. Specifically, larger structures are removed, while smaller structures are isolated from the image by repeatedly applying erosion and dilation operators in order, adjusting the parameter referencing to previously obtained morphometric data. A cluster of isolated acini belonging to the same terminal bronchiole is obtained without floating voxels. The extracted acinar models above 98% agree well with those extracted manually. The run time is drastically shortened compared with manual methods. These findings suggest that our method may be useful for taking samples used in the statistical analysis of acinus.

  16. Fast automatic segmentation of anatomical structures in x-ray computed tomography images to improve fluorescence molecular tomography reconstruction.

    Science.gov (United States)

    Freyer, Marcus; Ale, Angelique; Schulz, Ralf B; Zientkowska, Marta; Ntziachristos, Vasilis; Englmeier, Karl-Hans

    2010-01-01

    The recent development of hybrid imaging scanners that integrate fluorescence molecular tomography (FMT) and x-ray computed tomography (XCT) allows the utilization of x-ray information as image priors for improving optical tomography reconstruction. To fully capitalize on this capacity, we consider a framework for the automatic and fast detection of different anatomic structures in murine XCT images. To accurately differentiate between different structures such as bone, lung, and heart, a combination of image processing steps including thresholding, seed growing, and signal detection are found to offer optimal segmentation performance. The algorithm and its utilization in an inverse FMT scheme that uses priors is demonstrated on mouse images.

  17. The small angle neutron scattering study on the segmented polyurethane

    International Nuclear Information System (INIS)

    Sudirman; Gunawan; Prasetyo, S.M.; Karo Karo, A.; Lahagu, I.M.; Darwinto, Tri

    1999-01-01

    The distance between hard segment (HS) and soft segment (SS) of segmented polyurethane have been determined using the Small Angle Neutron Scattering (SANS) technique. The segmented Polyurethanes (SPU) are linear multiblock copolymers, which include elastomer thermoplastic. SPU consist of hard segment and soft segment, each has tendency to make a group with similar type to form a domain. The soft segments used were polypropylene glycol (PPG) and 4,4 diphenylmethane diisocyanate (MDI), while l,4 butanediol (BD) was used as hard segment. The characteristic of SPU depends on its phase structure which is affected by several factors, such as type of chemical formula and the composition of the HS and SS, solvent as well as the synthesizing process. The samples used in this study were SPU56 and SPU68. Based on the appearance of SANS profile, it was obtained that domain distances are 12.32 nm for the SPU56 and 19 nm for the SPU68. (author)

  18. Structural design of an in-line bolted joint for the space shuttle solid rocket motor case segments

    Science.gov (United States)

    Dorsey, John T.; Stein, Peter A.; Bush, Harold G.

    1987-01-01

    Results of a structural design study of an in-line bolted joint concept which can be used to assemble Space Shuttle Solid Rocket Motor (SRM) case segments are presented. Numerous parametric studies are performed to characterize the in-line bolted joint behavior as major design variables are altered, with the primary objective always being to keep the inside of the joint (where the O-rings are located) closed during the SRM firing. The resulting design has 180 1-inch studs, an eccentricity of -0.5 inch, a flange thickness of 3/4 inch, a bearing plate thickness of 1/4 inch, and the studs are subjected to a preload which is 70% of ultimate. The mass penalty per case segment joint for the in-line design is 346 lbm more than the weight penalty for the proposed capture tang fix.

  19. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics

    NARCIS (Netherlands)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert; Dekker, Frans

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain

  20. Thermoplastic polyurethanes from undecylenic acid-based soft segments: structural features and release properties.

    Science.gov (United States)

    Lluch, Cristina; Lligadas, Gerard; Ronda, Joan C; Galià, Marina; Cádiz, Virginia

    2013-05-01

    A set of thermoplastic polyurethanes is synthesized, combining undecylenic acid-derived telechelic diols as soft segments and 1,4-butanediol/4,4'-methylenebis(phenylisocyanate) as a hard segment (HS). These polymers are fully chemically and physically characterized by means of NMR and Fourier transform IR (FTIR) spectroscopy, size-exclusion chromatography (SEC), DSC, thermogravimetric analysis (TGA), tensile testing, and contact angle measurements. The obtained results reveal that both the molecular weight of the diol and the HS content greatly influence the physical and mechanical properties of these polymers. In addition, given the potential use of these materials for biomedical applications, hydrolytic degradation, their biocompatibility using a human fibroblast cell line, and performance as drug delivery carriers are evaluated. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Concept project of joining segment, connecting two folding bridge structures MS-54 and widened DMS-65

    Directory of Open Access Journals (Sweden)

    Jan Marszałek

    2015-09-01

    Full Text Available The article includes the concept project of truss segment enabling the constructions of MS-54 and DMS-65 bridges to joint. At the beginning, the basic technical and exploitative characteristics of joined constructions are introduced. On the basis of this data, geometrical analysis of the component is carried out. As a result, the concept project of fitting, enabling the crossing from two types of foldable constructions to be built, is developed. Sequentially, the computer calculations of the bridge including the part of the designed fitting are carried out.The article contains the fragments of M.A. dissertation awarded by the rector of Military University of Technology as the best from the Faculty of Civil Engineering in 2014. The article is summarized with the conclusions.[b]Keywords[/b]: construction, folding bridges, truss segment

  2. Volutin granules of Eimeria parasites are acidic compartments and have physiological and structural characteristics similar to acidocalcisomes

    Science.gov (United States)

    Medeiros, Lia Carolina Soares; Gomes, Fabio; Maciel, Luis Renato Maia; Seabra, Sergio Henrique; Docampo, Roberto; Moreno, Silvia; Plattner, Helmut; Hentschel, Joachim; Kawazoe, Urara; Barrabin, Hector; de Souza, Wanderley; DaMatta, Renato Augusto; Miranda, Kildare

    2012-01-01

    The structural organization of parasites has been the subject of investigation by many groups and has lead to the identification of structures and metabolic pathways that may represent targets for anti-parasitic drugs. A specific group of organelles named acidocalcisomes has been identified in a number of organisms, including the apicomplexan parasites such as Toxoplasma and Plasmodium, where they have been shown to be involved in cation homeostasis, polyphosphate metabolism, and osmoregulation. Their structural counterparts in the apicomplexan parasite Eimeria have not been fully characterized. In this work, the ultrastructural and chemical properties of acidocalcisomes in Eimeria were characterized. Electron microscopy analysis of Eimeria parasites showed the dense organelles called volutin granules similar to acidocalcisomes. Immunolocalization of the vacuolar proton pyrophosphatase, considered as a marker for acidocalcisomes, showed labeling in vesicles of size and distribution similar to the dense organelles seen by electron microscopy. Spectrophotometric measurements of the kinetics of proton uptake showed a vacuolar proton pyrophosphatase activity. X-ray mapping revealed significant amounts of Na, Mg, P, K, Ca, and Zn in their matrix. The results suggest that volutin granules of Eimeria parasites are acidic, dense organelles and possess structural and chemical properties analogous to those of other acidocalcisomes, suggesting a similar functional role in these parasites. PMID:21699625

  3. Psychometrics Of Hotel Service Quality: Comparative Factor Structures Of Alternative Market Segments

    OpenAIRE

    Mark I. Alpert; Rajagopal Raghunathan

    2011-01-01

    When different market segments are encountered, can the same instrument be used to understand and predict the determinants of customer perceptions of service quality, satisfaction and retention? This paper analyzes a national sample of over 18,000 U.S. customer surveys regarding hotel experiences in a range of properties from budget to near-luxury accommodations. Its purpose is to examine the dimensionality of customer satisfaction for business vs. pleasure travelers, and male vs. female gues...

  4. Adapting Active Shape Models for 3D segmentation of tubular structures in medical images.

    Science.gov (United States)

    de Bruijne, Marleen; van Ginneken, Bram; Viergever, Max A; Niessen, Wiro J

    2003-07-01

    Active Shape Models (ASM) have proven to be an effective approach for image segmentation. In some applications, however, the linear model of gray level appearance around a contour that is used in ASM is not sufficient for accurate boundary localization. Furthermore, the statistical shape model may be too restricted if the training set is limited. This paper describes modifications to both the shape and the appearance model of the original ASM formulation. Shape model flexibility is increased, for tubular objects, by modeling the axis deformation independent of the cross-sectional deformation, and by adding supplementary cylindrical deformation modes. Furthermore, a novel appearance modeling scheme that effectively deals with a highly varying background is developed. In contrast with the conventional ASM approach, the new appearance model is trained on both boundary and non-boundary points, and the probability that a given point belongs to the boundary is estimated non-parametrically. The methods are evaluated on the complex task of segmenting thrombus in abdominal aortic aneurysms (AAA). Shape approximation errors were successfully reduced using the two shape model extensions. Segmentation using the new appearance model significantly outperformed the original ASM scheme; average volume errors are 5.1% and 45% respectively.

  5. MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

    Science.gov (United States)

    Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele; Andreini, Claudia

    2014-08-01

    We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.

  6. Deep learning of the sectional appearances of 3D CT images for anatomical structure segmentation based on an FCN voting method.

    Science.gov (United States)

    Zhou, Xiangrong; Takayama, Ryosuke; Wang, Song; Hara, Takeshi; Fujita, Hiroshi

    2017-10-01

    We propose a single network trained by pixel-to-label deep learning to address the general issue of automatic multiple organ segmentation in three-dimensional (3D) computed tomography (CT) images. Our method can be described as a voxel-wise multiple-class classification scheme for automatically assigning labels to each pixel/voxel in a 2D/3D CT image. We simplify the segmentation algorithms of anatomical structures (including multiple organs) in a CT image (generally in 3D) to a majority voting scheme over the semantic segmentation of multiple 2D slices drawn from different viewpoints with redundancy. The proposed method inherits the spirit of fully convolutional networks (FCNs) that consist of "convolution" and "deconvolution" layers for 2D semantic image segmentation, and expands the core structure with 3D-2D-3D transformations to adapt to 3D CT image segmentation. All parameters in the proposed network are trained pixel-to-label from a small number of CT cases with human annotations as the ground truth. The proposed network naturally fulfills the requirements of multiple organ segmentations in CT cases of different sizes that cover arbitrary scan regions without any adjustment. The proposed network was trained and validated using the simultaneous segmentation of 19 anatomical structures in the human torso, including 17 major organs and two special regions (lumen and content inside of stomach). Some of these structures have never been reported in previous research on CT segmentation. A database consisting of 240 (95% for training and 5% for testing) 3D CT scans, together with their manually annotated ground-truth segmentations, was used in our experiments. The results show that the 19 structures of interest were segmented with acceptable accuracy (88.1% and 87.9% voxels in the training and testing datasets, respectively, were labeled correctly) against the ground truth. We propose a single network based on pixel-to-label deep learning to address the challenging

  7. Predicting drug?drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge

    OpenAIRE

    Takeda, Takako; Hao, Ming; Cheng, Tiejun; Bryant, Stephen H.; Wang, Yanli

    2017-01-01

    Drug?drug interactions (DDIs) may lead to adverse effects and potentially result in drug withdrawal from the market. Predicting DDIs during drug development would help reduce development costs and time by rigorous evaluation of drug candidates. The primary mechanisms of DDIs are based on pharmacokinetics (PK) and pharmacodynamics (PD). This study examines the effects of 2D structural similarities of drugs on DDI prediction through interaction networks including both PD and PK knowledge. Our a...

  8. Ectopic osteogenesis and angiogenesis regulated by porous architecture of hydroxyapatite scaffolds with similar interconnecting structure in vivo

    Science.gov (United States)

    Li, Jinyu; Zhi, Wei; Xu, Taotao; Shi, Feng; Duan, Ke; Wang, Jianxin; Mu, Yandong; Weng, Jie

    2016-01-01

    The macro-pore sizes of porous scaffold play a key role for regulating ectopic osteogenesis and angiogenesis but many researches ignored the influence of interconnection between macro-pores with different sizes. In order to accurately reveal the relationship between ectopic osteogenesis and macro-pore sizes in dorsal muscle and abdominal cavities of dogs, hydroxyapatite (HA) scaffolds with three different macro-pore sizes of 500–650, 750–900 and 1100–1250 µm were prepared via sugar spheres-leaching process, which also had similar interconnecting structure determined by keeping the d/s ratio of interconnecting window diameter to macro-pore size constant. The permeability test showed that the seepage flow of fluid through the porous scaffolds increased with the increase of macro-pore sizes. The cell growth in three scaffolds was not affected by the macro-pore sizes. The in vivo ectopic implantation results indicated that the macro-pore sizes of HA scaffolds with the similar interconnecting structure have impact not only the speed of osteogenesis and angiogenesis but also the space distribution of newly formed bone. The scaffold with macro-pore sizes of 750–900 µm exhibited much faster angiogenesis and osteogenesis, and much more uniformly distribution of new bone than those with other macro-pore sizes. This work illustrates the importance of a suitable macro-pore sizes in HA scaffolds with the similar interconnecting structure which provides the environment for ectopic osteogenesis and angiogenesis. PMID:27699059

  9. Primary structure of segment 7 of the RNA of the influenza virus A/USSR/90/77 (HlNl)

    International Nuclear Information System (INIS)

    Samokhvalov, E.I.; Karginov, V.A.; Chizhikov, V.E.; Blinov, V.M.; Yuferov, V.P.; Vasilenko, S.K.; Uryvaev, L.V.; Zhdanov, V.M.

    1986-01-01

    The nucleotide sequence of segment 7 of the RNA of the influenza virus A/USSR/90/77 (HlNl) has been determined, and an analysis has been given of the nucleotide substitutions in comparison with known primary structures of segment 7 of other strains of the influenza virus. A hypothetical model of the secondary structure of segment 7 of the RNA of the influenza virus and a direct repeat both at the nucleotide level and at the amino acid level found in the center of the M 1 protein are discussed

  10. Structural similarity between β(3)-peptides synthesized from β(3)-homo-amino acids and aspartic acid monomers.

    Science.gov (United States)

    Ahmed, Sahar; Sprules, Tara; Kaur, Kamaljit

    2014-07-01

    Formation of stable secondary structures by oligomers that mimic natural peptides is a key asset for enhanced biological response. Here we show that oligomeric β(3)-hexapeptides synthesized from L-aspartic acid monomers (β(3)-peptides 1, 5a, and 6) or homologated β(3)-amino acids (β(3)-peptide 2), fold into similar stable 14-helical secondary structures in solution, except that the former form right-handed 14-helix and the later form left-handed 14-helix. β(3)-Peptides from L-Asp monomers contain an additional amide bond in the side chains that provides opportunities for more hydrogen bonding. However, based on the NMR solution structures, we found that β(3)-peptide from L-Asp monomers (1) and from homologated amino acids (2) form similar structures with no additional side-chain interactions. These results suggest that the β(3)-peptides derived from L-Asp are promising peptide-mimetics that can be readily synthesized using L-Asp monomers as well as the right-handed 14-helical conformation of these β(3)-peptides (such as 1 and 6) may prove beneficial in the design of mimics for right-handed α-helix of α-peptides. © 2014 Wiley Periodicals, Inc.

  11. Segmentation pattern and structural complexities in seismogenic extensional settings: The North Matese Fault System (Central Italy)

    Science.gov (United States)

    Ferrarini, Federica; Boncio, Paolo; de Nardis, Rita; Pappone, Gerardo; Cesarano, Massimo; Aucelli, Pietro P. C.; Lavecchia, Giusy

    2017-02-01

    We investigated the northern slope of the Matese Mts. (Molise, Central Italy) with the aim of characterizing the N- to NE-dipping active normal fault system in the Bojano basin, a sector of primary importance from a seismic hazard perspective. We collected field data to define the geometry and segmentation pattern of two sub-systems (Patalecchia-Colle di Mezzo and Bojano-Campochiaro). New evidence of late Quaternary faulting was obtained by exploiting well log interpretations. Kinematic analysis revealed the interaction of pre-Quaternary inherited (mainly E-W-striking) and newly formed (NW-SE-striking) normal faults. Slip accommodation through linkage was clearly noted in the case of the Patalecchia-Colle di Mezzo sub-system. Detailed topographic profiles across the active fault segments provided post-LGM (15 ± 3 kyr) slip rates up to ∼2 mm/yr which agree with the high deformation rates based on different approaches in the literature. Finally, the instrumental seismicity analysis constrained the bottom of the seismogenic layer to depths of 13-14 km, and the gathered information allowed us to reconstruct the North Matese seismogenic source. Its 3D geometry and dimensions agree with both the dimension-magnitude relationships and macroseismic information available for the 1805 earthquake (Mw 6.6), the main historical earthquake to have struck the Bojano basin.

  12. Solenopsis invicta virus 3: mapping of structural proteins, ribosomal frameshifting, and similarities to Acyrthosiphon pisum virus and Kelp fly virus.

    Directory of Open Access Journals (Sweden)

    Steven M Valles

    Full Text Available Solenopsis invicta virus 3 (SINV-3 is a positive-sense single-stranded RNA virus that infects the red imported fire ant, Solenopsis invicta. We show that the second open reading frame (ORF of the dicistronic genome is expressed via a frameshifting mechanism and that the sequences encoding the structural proteins map to both ORF2 and the 3' end of ORF1, downstream of the sequence that encodes the RNA-dependent RNA polymerase. The genome organization and structural protein expression strategy resemble those of Acyrthosiphon pisum virus (APV, an aphid virus. The capsid protein that is encoded by the 3' end of ORF1 in SINV-3 and APV is predicted to have a jelly-roll fold similar to the capsid proteins of picornaviruses and caliciviruses. The capsid-extension protein that is produced by frameshifting, includes the jelly-roll fold domain encoded by ORF1 as its N-terminus, while the C-terminus encoded by the 5' half of ORF2 has no clear homology with other viral structural proteins. A third protein, encoded by the 3' half of ORF2, is associated with purified virions at sub-stoichiometric ratios. Although the structural proteins can be translated from the genomic RNA, we show that SINV-3 also produces a subgenomic RNA encoding the structural proteins. Circumstantial evidence suggests that APV may also produce such a subgenomic RNA. Both SINV-3 and APV are unclassified picorna-like viruses distantly related to members of the order Picornavirales and the family Caliciviridae. Within this grouping, features of the genome organization and capsid domain structure of SINV-3 and APV appear more similar to caliciviruses, perhaps suggesting the basis for a "Calicivirales" order.

  13. CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

    Directory of Open Access Journals (Sweden)

    Li Gong-Hua

    2010-08-01

    Full Text Available Abstract Background The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB, thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been developed to predict protein function, but these methods need to be improved further, such as, enhancing the accuracy, sensitivity, and the computational speed. Here, an accurate algorithm, the CMASA (Contact MAtrix based local Structural Alignment algorithm, has been developed to predict unknown functions of proteins based on the local protein structural similarity. This algorithm has been evaluated by building a test set including 164 enzyme families, and also been compared to other methods. Results The evaluation of CMASA shows that the CMASA is highly accurate (0.96, sensitive (0.86, and fast enough to be used in the large-scale functional annotation. Comparing to both sequence-based and global structure-based methods, not only the CMASA can find remote homologous proteins, but also can find the active site convergence. Comparing to other local structure comparison-based methods, the CMASA can obtain the better performance than both FFF (a method using geometry to predict protein function and SPASM (a local structure alignment method; and the CMASA is more sensitive than PINTS and is more accurate than JESS (both are local structure alignment methods. The CMASA was applied to annotate the enzyme catalytic sites of the non-redundant PDB, and at least 166 putative catalytic sites have been suggested, these sites can not be observed by the Catalytic Site Atlas (CSA. Conclusions The CMASA is an accurate algorithm for detecting local protein structural similarity, and it holds several advantages in predicting enzyme active sites. The CMASA can be used in large-scale enzyme active site annotation. The CMASA can be available by the

  14. Segmented block copolymers with monodisperse aramide end-segments

    NARCIS (Netherlands)

    Araichimani, A.; Gaymans, R.J.

    2008-01-01

    Segmented block copolymers were synthesized using monodisperse diaramide (TT) as hard segments and PTMO with a molecular weight of 2 900 g · mol-1 as soft segments. The aramide: PTMO segment ratio was increased from 1:1 to 2:1 thereby changing the structure from a high molecular weight multi-block

  15. Reynolds stress structures in a self-similar adverse pressure gradient turbulent boundary layer at the verge of separation.

    Science.gov (United States)

    Atkinson, C.; Sekimoto, A.; Jiménez, J.; Soria, J.

    2018-04-01

    Mean Reynolds stress profiles and instantaneous Reynolds stress structures are investigated in a self-similar adverse pressure gradient turbulent boundary layer (APG-TBL) at the verge of separation using data from direct numerical simulations. The use of a self-similar APG-TBL provides a flow domain in which the flow gradually approaches a constant non-dimensional pressure gradient, resulting in a flow in which the relative contribution of each term in the governing equations is independent of streamwise position over a domain larger than two boundary layer thickness. This allows the flow structures to undergo a development that is less dependent on the upstream flow history when compared to more rapidly decelerated boundary layers. This APG-TBL maintains an almost constant shape factor of H = 2.3 to 2.35 over a momentum thickness based Reynolds number range of Re δ 2 = 8420 to 12400. In the APG-TBL the production of turbulent kinetic energy is still mostly due to the correlation of streamwise and wall-normal fluctuations, 〈uv〉, however the contribution form the other components of the Reynolds stress tensor are no longer negligible. Statistical properties associated with the scale and location of sweeps and ejections in this APG-TBL are compared with those of a zero pressure gradient turbulent boundary layer developing from the same inlet profile, resulting in momentum thickness based range of Re δ 2 = 3400 to 3770. In the APG-TBL the peak in both the mean Reynolds stress and the production of turbulent kinetic energy move from the near wall region out to a point consistent with the displacement thickness height. This is associated with a narrower distribution of the Reynolds stress and a 1.6 times higher relative number of wall-detached negative uv structures. These structures occupy 5 times less of the boundary layer volume and show a similar reduction in their streamwise extent with respect to the boundary layer thickness. A significantly lower percentage

  16. ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.

    Science.gov (United States)

    Konc, Janez; Janezic, Dusanka

    2012-07-01

    The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si.

  17. On the nature of structural disorder in calcium silicate hydrates with a calcium/silicon ratio similar to tobermorite

    Energy Technology Data Exchange (ETDEWEB)

    Grangeon, Sylvain, E-mail: S.Grangeon@brgm.fr [BRGM, 3, Avenue Claude Guillemin, 45060 Orléans Cedex 2 (France); Claret, Francis; Lerouge, Catherine [BRGM, 3, Avenue Claude Guillemin, 45060 Orléans Cedex 2 (France); Warmont, Fabienne [CRMD, UMR 6619 – CNRS, 1b rue de la férollerie, 45071 Orléans Cedex 2 (France); Sato, Tsutomu; Anraku, Sohtaro [Laboratory of Environmental Geology, Research Group of Geoenvironmental/Engineering Division of Solid Waste, Resources and Geoenvironmental/Engineering Graduate School of Engineering, Hokkaido University, Kita 13 Nishi 8, Sapporo 060-8628 (Japan); Numako, Chiya [Faculty of Integrated Arts and Sciences, The University of Tokushima, 1-1, Minami-Josanjima, Tokushima, 770-8502 (Japan); Linard, Yannick [ANDRA, Centre de Meuse/Haute Marne, 55290 Bure (France); Lanson, Bruno [ISTerre, Grenoble University, CNRS, F-38041 Grenoble (France)

    2013-10-15

    Four calcium silicate hydrates (C-S-H) with structural calcium/silicon (Ca/Si) ratios ranging from 0.82 ± 0.02 to 0.87 ± 0.02 were synthesized at room temperature, 50, 80, and 110 °C. Their structure was elucidated by collating information from electron probe micro-analysis, transmission electron microscopy, extended X-ray absorption fine structure spectroscopy, and powder X-ray diffraction (XRD). A modeling approach specific to defective minerals was used because sample turbostratism prevented analysis using usual XRD refinement techniques (e.g. Rietveld analysis). It is shown that C-S-H with Ca/Si ratio of ∼ 0.8 are structurally similar to nano-crystalline turbostratic tobermorite, a naturally occurring mineral. Their structure thus consists of sheets of calcium atoms in 7-fold coordination, covered by ribbons of silicon tetrahedra with a dreierketten (wollastonite-like) organization. In these silicate ribbons, 0.42 Si per bridging tetrahedron are missing. Random stacking faults occur systematically between successive layers (turbostratic stacking). Layer-to-layer distance is equal to 11.34 Å. Crystallites have a mean size of 10 nm in the a–b plane, and a mean number of 2.6–2.9 layers stacked coherently along the c* axis.

  18. Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta-community.

    Science.gov (United States)

    Chalmandrier, L; Münkemüller, T; Lavergne, S; Thuiller, W

    2015-01-01

    Different assembly processes drive the spatial structure of meta-communities (beta-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high beta-diversity along environmental gradients should be the result of environmental filtering while low beta-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting beta-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf-height-seed spectrum) and phylogenetic facets of beta-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional beta-diversity, was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic beta-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs

  19. Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

    Directory of Open Access Journals (Sweden)

    Eric Venner

    Full Text Available High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks.

  20. Large-scale structural and textual similarity-based mining of knowledge graph to predict drug-drug interactions

    KAUST Repository

    Abdelaziz, Ibrahim; Fokoue, Achille; Hassanzadeh, Oktie; Zhang, Ping; Sadoghi, Mohammad

    2017-01-01

    Drug-Drug Interactions (DDIs) are a major cause of preventable Adverse Drug Reactions (ADRs), causing a significant burden on the patients’ health and the healthcare system. It is widely known that clinical studies cannot sufficiently and accurately identify DDIs for new drugs before they are made available on the market. In addition, existing public and proprietary sources of DDI information are known to be incomplete and/or inaccurate and so not reliable. As a result, there is an emerging body of research on in-silico prediction of drug-drug interactions. In this paper, we present Tiresias, a large-scale similarity-based framework that predicts DDIs through link prediction. Tiresias takes in various sources of drug-related data and knowledge as inputs, and provides DDI predictions as outputs. The process starts with semantic integration of the input data that results in a knowledge graph describing drug attributes and relationships with various related entities such as enzymes, chemical structures, and pathways. The knowledge graph is then used to compute several similarity measures between all the drugs in a scalable and distributed framework. In particular, Tiresias utilizes two classes of features in a knowledge graph: local and global features. Local features are derived from the information directly associated to each drug (i.e., one hop away) while global features are learnt by minimizing a global loss function that considers the complete structure of the knowledge graph. The resulting similarity metrics are used to build features for a large-scale logistic regression model to predict potential DDIs. We highlight the novelty of our proposed Tiresias and perform thorough evaluation of the quality of the predictions. The results show the effectiveness of Tiresias in both predicting new interactions among existing drugs as well as newly developed drugs.

  1. Large-scale structural and textual similarity-based mining of knowledge graph to predict drug-drug interactions

    KAUST Repository

    Abdelaziz, Ibrahim

    2017-06-12

    Drug-Drug Interactions (DDIs) are a major cause of preventable Adverse Drug Reactions (ADRs), causing a significant burden on the patients’ health and the healthcare system. It is widely known that clinical studies cannot sufficiently and accurately identify DDIs for new drugs before they are made available on the market. In addition, existing public and proprietary sources of DDI information are known to be incomplete and/or inaccurate and so not reliable. As a result, there is an emerging body of research on in-silico prediction of drug-drug interactions. In this paper, we present Tiresias, a large-scale similarity-based framework that predicts DDIs through link prediction. Tiresias takes in various sources of drug-related data and knowledge as inputs, and provides DDI predictions as outputs. The process starts with semantic integration of the input data that results in a knowledge graph describing drug attributes and relationships with various related entities such as enzymes, chemical structures, and pathways. The knowledge graph is then used to compute several similarity measures between all the drugs in a scalable and distributed framework. In particular, Tiresias utilizes two classes of features in a knowledge graph: local and global features. Local features are derived from the information directly associated to each drug (i.e., one hop away) while global features are learnt by minimizing a global loss function that considers the complete structure of the knowledge graph. The resulting similarity metrics are used to build features for a large-scale logistic regression model to predict potential DDIs. We highlight the novelty of our proposed Tiresias and perform thorough evaluation of the quality of the predictions. The results show the effectiveness of Tiresias in both predicting new interactions among existing drugs as well as newly developed drugs.

  2. Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain.

    Science.gov (United States)

    Tao, Y; Strelkov, S V; Mesyanzhinov, V V; Rossmann, M G

    1997-06-15

    Oligomeric coiled-coil motifs are found in numerous protein structures; among them is fibritin, a structural protein of bacteriophage T4, which belongs to a class of chaperones that catalyze a specific phage-assembly process. Fibritin promotes the assembly of the long tail fibers and their subsequent attachment to the tail baseplate; it is also a sensing device that controls the retraction of the long tail fibers in adverse environments and, thus, prevents infection. The structure of fibritin had been predicted from sequence and biochemical analyses to be mainly a triple-helical coiled coil. The determination of its structure at atomic resolution was expected to give insights into the assembly process and biological function of fibritin, and the properties of modified coiled-coil structures in general. The three-dimensional structure of fibritin E, a deletion mutant of wild-type fibritin, was determined to 2.2 A resolution by X-ray crystallography. Three identical subunits of 119 amino acid residues form a trimeric parallel coiled-coil domain and a small globular C-terminal domain about a crystallographic threefold axis. The coiled-coil domain is divided into three segments that are separated by insertion loops. The C-terminal domain, which consists of 30 residues from each subunit, contains a beta-propeller-like structure with a hydrophobic interior. The residues within the C-terminal domain make extensive hydrophobic and some polar intersubunit interactions. This is consistent with the C-terminal domain being important for the correct assembly of fibritin, as shown earlier by mutational studies. Tight interactions between the C-terminal residues of adjacent subunits counteract the latent instability that is suggested by the structural properties of the coiled-coil segments. Trimerization is likely to begin with the formation of the C-terminal domain which subsequently initiates the assembly of the coiled coil. The interplay between the stabilizing effect of the C

  3. Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase.

    Science.gov (United States)

    Muruganandam, Gopinath; Raasakka, Arne; Myllykoski, Matti; Kursula, Inari; Kursula, Petri

    2017-05-16

    Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5'-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase). We employed different biophysical and biochemical methods to elucidate the overall structural and functional features of the tRNA healing enzymes yeast Trl1 PNK/CPDase and lancelet PNK/CPDase and compared them with vertebrate CNPase. The yeast and the lancelet enzymes have cyclic phosphodiesterase and polynucleotide kinase activity, while vertebrate CNPase lacks PNK activity. In addition, we also show that the healing enzymes are structurally similar to the vertebrate CNPase by applying synchrotron radiation circular dichroism spectroscopy and small-angle X-ray scattering. We provide a structural analysis of the tRNA healing enzyme PNK and CPDase domains together. Our results support evolution of vertebrate CNPase from tRNA healing enzymes with a loss of function at its N-terminal PNK-like domain.

  4. Multidimensional Riemann problem with self-similar internal structure. Part II - Application to hyperbolic conservation laws on unstructured meshes

    Science.gov (United States)

    Balsara, Dinshaw S.; Dumbser, Michael

    2015-04-01

    Multidimensional Riemann solvers that have internal sub-structure in the strongly-interacting state have been formulated recently (D.S. Balsara (2012, 2014) [5,16]). Any multidimensional Riemann solver operates at the grid vertices and takes as its input all the states from its surrounding elements. It yields as its output an approximation of the strongly interacting state, as well as the numerical fluxes. The multidimensional Riemann problem produces a self-similar strongly-interacting state which is the result of several one-dimensional Riemann problems interacting with each other. To compute this strongly interacting state and its higher order moments we propose the use of a Galerkin-type formulation to compute the strongly interacting state and its higher order moments in terms of similarity variables. The use of substructure in the Riemann problem reduces numerical dissipation and, therefore, allows a better preservation of flow structures, like contact and shear waves. In this second part of a series of papers we describe how this technique is extended to unstructured triangular meshes. All necessary details for a practical computer code implementation are discussed. In particular, we explicitly present all the issues related to computational geometry. Because these Riemann solvers are Multidimensional and have Self-similar strongly-Interacting states that are obtained by Consistency with the conservation law, we call them MuSIC Riemann solvers. (A video introduction to multidimensional Riemann solvers is available on http://www.elsevier.com/xml/linking-roles/text/html". The MuSIC framework is sufficiently general to handle general nonlinear systems of hyperbolic conservation laws in multiple space dimensions. It can also accommodate all self-similar one-dimensional Riemann solvers and subsequently produces a multidimensional version of the same. In this paper we focus on unstructured triangular meshes. As examples of different systems of conservation laws we

  5. Automated quantification of renal interstitial fibrosis for computer-aided diagnosis: A comprehensive tissue structure segmentation method.

    Science.gov (United States)

    Tey, Wei Keat; Kuang, Ye Chow; Ooi, Melanie Po-Leen; Khoo, Joon Joon

    2018-03-01

    Interstitial fibrosis in renal biopsy samples is a scarring tissue structure that may be visually quantified by pathologists as an indicator to the presence and extent of chronic kidney disease. The standard method of quantification by visual evaluation presents reproducibility issues in the diagnoses. This study proposes an automated quantification system for measuring the amount of interstitial fibrosis in renal biopsy images as a consistent basis of comparison among pathologists. The system extracts and segments the renal tissue structures based on colour information and structural assumptions of the tissue structures. The regions in the biopsy representing the interstitial fibrosis are deduced through the elimination of non-interstitial fibrosis structures from the biopsy area and quantified as a percentage of the total area of the biopsy sample. A ground truth image dataset has been manually prepared by consulting an experienced pathologist for the validation of the segmentation algorithms. The results from experiments involving experienced pathologists have demonstrated a good correlation in quantification result between the automated system and the pathologists' visual evaluation. Experiments investigating the variability in pathologists also proved the automated quantification error rate to be on par with the average intra-observer variability in pathologists' quantification. Interstitial fibrosis in renal biopsy samples is a scarring tissue structure that may be visually quantified by pathologists as an indicator to the presence and extent of chronic kidney disease. The standard method of quantification by visual evaluation presents reproducibility issues in the diagnoses due to the uncertainties in human judgement. An automated quantification system for accurately measuring the amount of interstitial fibrosis in renal biopsy images is presented as a consistent basis of comparison among pathologists. The system identifies the renal tissue structures

  6. Structural character of the northern segment of the Paintbrush Canyon fault, Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Dickerson, R.P.; Spengler, R.W.

    1994-01-01

    Detailed mapping of exposed features along the northern part of the Paintbrush Canyon fault was initiated to aid in construction of the computer-assisted three-dimensional lithostratigraphic model of Yucca Mountain, to contribute to kinematic reconstruction of the tectonic history of the Paintbrush Canyon fault, and to assist in the interpretation of geophysical data from Midway Valley. Yucca Mountain is segmented into relatively intact blocks of east-dipping Miocene volcanic strata, bounded by north-striking, west-dipping high-angle normal faults. The Paintbrush Canyon fault, representing the easternmost block-bounding normal fault, separates Fran Ridge from Midway Valley and continues northward across Yucca Wash to at least the southern margin of the Timber Mountain Caldera complex. South of Yucca Wash, the Paintbrush Canyon Fault is largely concealed beneath thick Quaternary deposits. Bedrock exposures to the north reveal a complex fault, zone, displaying local north- and west-trending grabens, and rhombic pull-apart features. The fault scarp, discontinuously exposed along a mapped length of 8 km north of Yucca Wash, dips westward by 41 degrees to 74 degrees. Maximum vertical offset of the Rhyolite of Comb Peak along the fault measures about 210 m in Paintbrush Canyon and, on the basis of drill hole information, vertical offset of the Topopoah Spring Tuff is about 360 m near the northern part of Fran Ridge. Observed displacement along the fault in Paintbrush Canyon is down to the west with a component of left-lateral oblique slip. Unlike previously proposed tectonic models, strata adjacent to the fault dip to the east. Quaternary deposits do not appear displaced along the fault scarp north of Yucca Wash, but are displaced in trenches south of Yucca Wash

  7. An Automated Fluid-Structural Interaction Analysis of a Large Segmented Solid Rocket Motor

    National Research Council Canada - National Science Library

    Rex, Brian

    2003-01-01

    ... couple the ABAQUS structural solver with FLUENT, the computational fluid dynamics (CFD) solver. This iterative process automatically used the results of one solver as the inputs to the other solver until convergence to a solution was obtained...

  8. An Automated Fluid-Structural Interaction Analysis of a Large Segmented Solid Rocket Motor

    National Research Council Canada - National Science Library

    Rex, Brian

    2003-01-01

    .... The fluid-structural interaction (FSI) analysis of the ETM-3 motor used PYTHON, a powerful programming language, and FEM BUILDER, a pre- and post processor developed by ATK Thiokol Propulsion under contract to the AFRL, to automatically...

  9. Segmentation of liver tumors on CT images

    International Nuclear Information System (INIS)

    Pescia, D.

    2011-01-01

    This thesis is dedicated to 3D segmentation of liver tumors in CT images. This is a task of great clinical interest since it allows physicians benefiting from reproducible and reliable methods for segmenting such lesions. Accurate segmentation would indeed help them during the evaluation of the lesions, the choice of treatment and treatment planning. Such a complex segmentation task should cope with three main scientific challenges: (i) the highly variable shape of the structures being sought, (ii) their similarity of appearance compared with their surrounding medium and finally (iii) the low signal to noise ratio being observed in these images. This problem is addressed in a clinical context through a two step approach, consisting of the segmentation of the entire liver envelope, before segmenting the tumors which are present within the envelope. We begin by proposing an atlas-based approach for computing pathological liver envelopes. Initially images are pre-processed to compute the envelopes that wrap around binary masks in an attempt to obtain liver envelopes from estimated segmentation of healthy liver parenchyma. A new statistical atlas is then introduced and used to segmentation through its diffeomorphic registration to the new image. This segmentation is achieved through the combination of image matching costs as well as spatial and appearance prior using a multi-scale approach with MRF. The second step of our approach is dedicated to lesions segmentation contained within the envelopes using a combination of machine learning techniques and graph based methods. First, an appropriate feature space is considered that involves texture descriptors being determined through filtering using various scales and orientations. Then, state of the art machine learning techniques are used to determine the most relevant features, as well as the hyper plane that separates the feature space of tumoral voxels to the ones corresponding to healthy tissues. Segmentation is then

  10. The growth of vegetative and reproductive structures (leaves and silks) respond similarly to hydraulic cues in maize.

    Science.gov (United States)

    Turc, Olivier; Bouteillé, Marie; Fuad-Hassan, Avan; Welcker, Claude; Tardieu, François

    2016-10-01

    The elongation of styles and stigma (silks) of maize (Zea mays) flowers is rapid (1-3 mm h(-1) ), occurs over a short period and plays a pivotal role in reproductive success in adverse environments. Silk elongation rate was measured using displacement transducers in 350 plants of eight genotypes during eight experiments with varying evaporative demand and soil water status. Measured time courses revealed that silk elongation rate closely followed changes in soil water status and evaporative demand, with day-night alternations similar to those in leaves. Day-night alternations were steeper with high than with low plant transpiration rate, manipulated via evaporative demand or by covering part of the leaf area. Half times of changes in silk elongation rate upon changes in evaporative demand or soil water status were 10-30 min, similar to those in leaves. The sensitivity of silk elongation rate to xylem water potential was genetically linked to that of leaf elongation rate. Lines greatly differed for these sensitivities. These results are consistent with a common hydraulic control of expansive growth in vegetative and reproductive structures upon changes in environmental conditions via a close connection with the xylem water potential. They have important implications for breeding, modelling and phenotyping. © 2016 INRA. New Phytologist © 2016 New Phytologist Trust.

  11. STRUCTURE OF MAIN ARBOREAL SPECIES IN CRUCE CABALLERO PARK AND ITS FLORISTIC SIMILARITY WITH AREAS FROM ARGENTINE AND BRAZIL

    Directory of Open Access Journals (Sweden)

    Román Carlos Ríos

    2010-08-01

    Full Text Available The present work aimed to study the fitossociologic structure and floristic similarity among seasonal and mixed forests of Argentina and Brazil. Cruce Caballero Park with 522 hectares where the method of multiple plots was adopted with (20 x 10 m. In each plot all individual tree of size equal or heigher than 5 cm diameter were registered, being measured the stem diameter and height into three environmental compartments, Haplorthox, Ustorthent and Udorthent. In Haplorthox, Araucaria angustifolia (Bertol. Kuntze prevail at higher stratum and Sorocea bonplandii (Baill. W.C.Burger, Lanj. & Boer, Cabralea canjerana (Vell. Mart., Ocotea lancifolia Mez and Apuleia leiocarpa J.F.Macbr. follow it. In Ustorthent araucaria is absent and Gymnanthes concolor Müll.Arg., Trichilia claussenii C.DC., Apuleia leiocarpa, Pilocarpus pennatifolius Lem. and Sorocea bonplandii prevail. Aracuaria is scarce in Udorthent where Parapiptadenia rigida (Benth. Brenan, Alchornea triplinervia Müll.Arg., Luehea divaricata Mart., Erythrina falcata Benth. and Myrsine gardneriana A.DC. prevail. A comparative analysis shown Cruce Caballero more similar to seasonal forests than mixed araucaria forest from Brazil.

  12. Analysis of the structural behaviour of colonic segments by inflation tests: Experimental activity and physio-mechanical model.

    Science.gov (United States)

    Carniel, Emanuele L; Mencattelli, Margherita; Bonsignori, Gabriella; Fontanella, Chiara G; Frigo, Alessandro; Rubini, Alessandro; Stefanini, Cesare; Natali, Arturo N

    2015-11-01

    A coupled experimental and computational approach is provided for the identification of the structural behaviour of gastrointestinal regions, accounting for both elastic and visco-elastic properties. The developed procedure is applied to characterize the mechanics of gastrointestinal samples from pig colons. Experimental data about the structural behaviour of colonic segments are provided by inflation tests. Different inflation processes are performed according to progressively increasing top pressure conditions. Each inflation test consists of an air in-flow, according to an almost constant increasing pressure rate, such as 3.5 mmHg/s, up to a prescribed top pressure, which is held constant for about 300 s to allow the development of creep phenomena. Different tests are interspersed by 600 s of rest to allow the recovery of the tissues' mechanical condition. Data from structural tests are post-processed by a physio-mechanical model in order to identify the mechanical parameters that interpret both the non-linear elastic behaviour of the sample, as the instantaneous pressure-stretch trend, and the time-dependent response, as the stretch increase during the creep processes. The parameters are identified by minimizing the discrepancy between experimental and model results. Different sets of parameters are evaluated for different specimens from different pigs. A statistical analysis is performed to evaluate the distribution of the parameters and to assess the reliability of the experimental and computational activities. © IMechE 2015.

  13. ON THE STRUCTURE OF THE MEDIAN SEGMENT OF THE DIGESTIVE TUBE AND ON THE ACTIVITY OF ALPHA-AMYLASE AT ARISTICHTHYS NOBILIS, IN VARIOUS STAGES OF DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Gabriela Vasile

    2007-12-01

    Full Text Available The investigations have been dedicated to the structure of the median segment of the digestive tube, on Aristichthys nobilis individuals of various ages (i.e., one summer- and, respectively, four summer-old, correlated, on one side, with the main feeding regime and, on the other, with the amylasic activity present in this part of the digestive tract. As to the structural aspects, higher values of the thickness of the mucous tunic have been recorded in the four summer-old bighead carp individuals, to be possibly associated with the high values of the α-amylase activity in this segment of the digestive tube.

  14. Surfaces of Minimal Paths from Topological Structures and Applications to 3D Object Segmentation

    KAUST Repository

    Algarni, Marei

    2017-10-24

    Extracting surfaces, representing boundaries of objects of interest, from volumetric images, has important applications in various scientific domains, from medicine to geology. In this thesis, I introduce novel mathematical, computational, and algorithmic machinery for extraction of sheet-like surfaces (with boundary), whose boundary is unknown a-priori, a particularly important case in applications that has no convenient methods. This case of a surface with boundaries has applications in extracting faults (among other geological structures) from seismic images in geological applications. Another application domain is in the extraction of structures in the lung from computed tomography (CT) images. Although many methods have been developed in computer vision for extraction of surfaces, including level sets, convex optimization approaches, and graph cut methods, none of these methods appear to be applicable to the case of surfaces with boundary. The novel methods for surface extraction, derived in this thesis, are built on the theory of Minimal Paths, which has been used primarily to extract curves in noisy or corrupted images and have had wide applicability in 2D computer vision. This thesis extends such methods to surfaces, and it is based on novel observations that surfaces can be determined by extracting topological structures from the solution of the eikonal partial differential equation (PDE), which is the basis of Minimal Path theory. Although topological structures are known to be difficult to extract from images, which are both noisy and discrete, this thesis builds robust methods based on Morse theory and computational topology to address such issues. The algorithms have run-time complexity O(NlogN), less complex than existing approaches. The thesis details the algorithms, theory, and shows an extensive experimental evaluation on seismic images and medical images. Experiments show out-performance in accuracy, computational speed, and user convenience

  15. Molecular-dynamics simulations of crosslinking and confinement effects on structure, segmental mobility and mechanics of filled elastomers

    Science.gov (United States)

    Davris, Theodoros; Lyulin, Alexey V.

    2016-05-01

    The significant drop of the storage modulus under uniaxial deformation (Payne effect) restrains the performance of the elastomer-based composites and the development of possible new applications. In this paper molecular-dynamics (MD) computer simulations using LAMMPS MD package have been performed to study the mechanical properties of a coarse-grained model of this family of nanocomposite materials. Our goal is to provide simulational insights into the viscoelastic properties of filled elastomers, and try to connect the macroscopic mechanics with composite microstructure, the strength of the polymer-filler interactions and the polymer mobility at different scales. To this end we simulate random copolymer films capped between two infinite solid (filler aggregate) walls. We systematically vary the strength of the polymer-substrate adhesion interactions, degree of polymer confinement (film thickness), polymer crosslinking density, and study their influence on the equilibrium and non-equilibrium structure, segmental dynamics, and the mechanical properties of the simulated systems. The glass-transition temperature increases once the mesh size became smaller than the chain radius of gyration; otherwise it remained invariant to mesh-size variations. This increase in the glass-transition temperature was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls.

  16. Direct Patlak Reconstruction From Dynamic PET Data Using the Kernel Method With MRI Information Based on Structural Similarity.

    Science.gov (United States)

    Gong, Kuang; Cheng-Liao, Jinxiu; Wang, Guobao; Chen, Kevin T; Catana, Ciprian; Qi, Jinyi

    2018-04-01

    Positron emission tomography (PET) is a functional imaging modality widely used in oncology, cardiology, and neuroscience. It is highly sensitive, but suffers from relatively poor spatial resolution, as compared with anatomical imaging modalities, such as magnetic resonance imaging (MRI). With the recent development of combined PET/MR systems, we can improve the PET image quality by incorporating MR information into image reconstruction. Previously, kernel learning has been successfully embedded into static and dynamic PET image reconstruction using either PET temporal or MRI information. Here, we combine both PET temporal and MRI information adaptively to improve the quality of direct Patlak reconstruction. We examined different approaches to combine the PET and MRI information in kernel learning to address the issue of potential mismatches between MRI and PET signals. Computer simulations and hybrid real-patient data acquired on a simultaneous PET/MR scanner were used to evaluate the proposed methods. Results show that the method that combines PET temporal information and MRI spatial information adaptively based on the structure similarity index has the best performance in terms of noise reduction and resolution improvement.

  17. Relative transmembrane segment rearrangements during BK channel activation resolved by structurally assigned fluorophore–quencher pairing

    Science.gov (United States)

    Pantazis, Antonios

    2012-01-01

    Voltage-activated proteins can sense, and respond to, changes in the electric field pervading the cell membrane by virtue of a transmembrane helix bundle, the voltage-sensing domain (VSD). Canonical VSDs consist of four transmembrane helices (S1–S4) of which S4 is considered a principal component because it possesses charged residues immersed in the electric field. Membrane depolarization compels the charges, and by extension S4, to rearrange with respect to the field. The VSD of large-conductance voltage- and Ca-activated K+ (BK) channels exhibits two salient inconsistencies from the canonical VSD model: (1) the BK channel VSD possesses an additional nonconserved transmembrane helix (S0); and (2) it exhibits a “decentralized” distribution of voltage-sensing charges, in helices S2 and S3, in addition to S4. Considering these unique features, the voltage-dependent rearrangements of the BK VSD could differ significantly from the standard model of VSD operation. To understand the mode of operation of this unique VSD, we have optically tracked the relative motions of the BK VSD transmembrane helices during activation, by manipulating the quenching environment of site-directed fluorescent labels with native and introduced Trp residues. Having previously reported that S0 and S4 diverge during activation, in this work we demonstrate that S4 also diverges from S1 and S2, whereas S2, compelled by its voltage-sensing charged residues, moves closer to S1. This information contributes spatial constraints for understanding the BK channel voltage-sensing process, revealing the structural rearrangements in a non-canonical VSD. PMID:22802360

  18. Automatic detection and segmentation of vascular structures in dermoscopy images using a novel vesselness measure based on pixel redness and tubularness

    Science.gov (United States)

    Kharazmi, Pegah; Lui, Harvey; Stoecker, William V.; Lee, Tim

    2015-03-01

    Vascular structures are one of the most important features in the diagnosis and assessment of skin disorders. The presence and clinical appearance of vascular structures in skin lesions is a discriminating factor among different skin diseases. In this paper, we address the problem of segmentation of vascular patterns in dermoscopy images. Our proposed method is composed of three parts. First, based on biological properties of human skin, we decompose the skin to melanin and hemoglobin component using independent component analysis of skin color images. The relative quantities and pure color densities of each component were then estimated. Subsequently, we obtain three reference vectors of the mean RGB values for normal skin, pigmented skin and blood vessels from the hemoglobin component by averaging over 100000 pixels of each group outlined by an expert. Based on the Euclidean distance thresholding, we generate a mask image that extracts the red regions of the skin. Finally, Frangi measure was applied to the extracted red areas to segment the tubular structures. Finally, Otsu's thresholding was applied to segment the vascular structures and get a binary vessel mask image. The algorithm was implemented on a set of 50 dermoscopy images. In order to evaluate the performance of our method, we have artificially extended some of the existing vessels in our dermoscopy data set and evaluated the performance of the algorithm to segment the newly added vessel pixels. A sensitivity of 95% and specificity of 87% were achieved.

  19. PREVENTION OF POLYURETHANE OXIDATIVE DEGRADATION WITH PHENOLIC-ANTIOXIDANTS COVALENTLY ATTACHED TO THE HARD SEGMENTS: STRUCTURE FUNCTION RELATIONSHIPS

    Science.gov (United States)

    Stachelek, Stanley J; Alferiev, Ivan; Ueda, Masako; Eckels, Edward C.; Gleason, Kevin T.; Levy, Robert J

    2010-01-01

    Oxidative degradation of the polyurethane elastomeric (PU) components greatly reduces the efficacy of PU containing cardiovascular devices. Covalently appending the phenol-based antioxidant, 4-substituted 2,6-di-tert-butylphenol (DBP), to PU hard segments effectively reduced oxidative degradation of the PU in vivo and in vitro in prior studies by our group. In these experiments we analyze the contribution of the tethering molecule to the antioxidant capabilities of the DBP modified PU. Bromoalkylation chemistry was used to link DBP to the hard segment of the polyether polyurethane, Tecothane, via our original linker (PU-DBP), or variants containing side chains with 1 (PU-C-DBP) or 3 (PU-3C-DBP) carbons. Two additional DBP variants were fabricated in which the DBP group was appended to the alkyl chain via an oxygen atom (PU-O-DBP) or an amide linkage in the middle of the tether (PU-NHCO-DBP). All DBP variant films and unmodified control films were subject to oxidative degradation via 15 day immersion in a solution of 20% H2O2 + 0.1 M CoCl2. At the end of the oxidation protocol films were analyzed for the presence of oxidation related endpoints via scanning electron microscopy, contact angle measurements and Fourier transformation infrared spectroscopy (FTIR). All DBP containing variants resisted oxidation damage significantly better than the unmodified control PU. SEM analysis of oxidized PU-C-DBP and PU-O-DBP showed evidence of surface cracking consistent with oxidative degradation of the PU surfaces. Similarly there was a trend in increased ether cross-linking, a marker for oxidative degradation, in PU-C-DBP and PU-NHCO-DBP films. Consistent with these FTIR results, both PU-C-DBP and PU-NHCO-DBP had significant reductions in measured surface hydrophobicity as a result of oxidation. These data show for the first time that the choice of linker molecule significantly affects the efficiency of the linked phenolic antioxidant. PMID:20306526

  20. An objective evaluation framework for segmentation techniques of functional positron emission tomography studies

    CERN Document Server

    Kim, J; Eberl, S; Feng, D

    2004-01-01

    Segmentation of multi-dimensional functional positron emission tomography (PET) studies into regions of interest (ROI) exhibiting similar temporal behavior is useful in diagnosis and evaluation of neurological images. Quantitative evaluation plays a crucial role in measuring the segmentation algorithm's performance. Due to the lack of "ground truth" available for evaluating segmentation of clinical images, automated segmentation results are usually compared with manual delineation of structures which is, however, subjective, and is difficult to perform. Alternatively, segmentation of co-registered anatomical images such as magnetic resonance imaging (MRI) can be used as the ground truth to the PET segmentation. However, this is limited to PET studies which have corresponding MRI. In this study, we introduce a framework for the objective and quantitative evaluation of functional PET study segmentation without the need for manual delineation or registration to anatomical images of the patient. The segmentation ...

  1. Active Segmentation.

    Science.gov (United States)

    Mishra, Ajay; Aloimonos, Yiannis

    2009-01-01

    The human visual system observes and understands a scene/image by making a series of fixations. Every fixation point lies inside a particular region of arbitrary shape and size in the scene which can either be an object or just a part of it. We define as a basic segmentation problem the task of segmenting that region containing the fixation point. Segmenting the region containing the fixation is equivalent to finding the enclosing contour- a connected set of boundary edge fragments in the edge map of the scene - around the fixation. This enclosing contour should be a depth boundary.We present here a novel algorithm that finds this bounding contour and achieves the segmentation of one object, given the fixation. The proposed segmentation framework combines monocular cues (color/intensity/texture) with stereo and/or motion, in a cue independent manner. The semantic robots of the immediate future will be able to use this algorithm to automatically find objects in any environment. The capability of automatically segmenting objects in their visual field can bring the visual processing to the next level. Our approach is different from current approaches. While existing work attempts to segment the whole scene at once into many areas, we segment only one image region, specifically the one containing the fixation point. Experiments with real imagery collected by our active robot and from the known databases 1 demonstrate the promise of the approach.

  2. Segmentation: Identification of consumer segments

    DEFF Research Database (Denmark)

    Høg, Esben

    2005-01-01

    It is very common to categorise people, especially in the advertising business. Also traditional marketing theory has taken in consumer segments as a favorite topic. Segmentation is closely related to the broader concept of classification. From a historical point of view, classification has its...... origin in other sciences as for example biology, anthropology etc. From an economic point of view, it is called segmentation when specific scientific techniques are used to classify consumers to different characteristic groupings. What is the purpose of segmentation? For example, to be able to obtain...... a basic understanding of grouping people. Advertising agencies may use segmentation totarget advertisements, while food companies may usesegmentation to develop products to various groups of consumers. MAPP has for example investigated the positioning of fish in relation to other food products...

  3. Structural Behavior of a Long-Span Partially Earth-Anchored Cable-Stayed Bridge during Installation of a Key Segment by Thermal Prestressing

    Directory of Open Access Journals (Sweden)

    Sang-Hyo Kim

    2016-08-01

    Full Text Available This study investigated structural behavior of long-span partially earth-anchored cable-stayed bridges with a main span length of 810 m that use a new key segment closing method based on a thermal prestressing technique. A detailed construction sequence analysis matched with the free cantilever method (FCM was performed using a three-dimensional finite element (FE model of a partially earth-anchored cable-stayed bridge. The new method offers an effective way of connecting key segments by avoiding large movements resulting from the removal of the longitudinal restraint owing to the asymmetry of axial forces in the girders near the pylons. The new method develops new member forces through the process of heating the cantilever system before installing the key segment and cooling the system continuously after installing key segments. The resulting forces developed by the thermal process enhance the structural behavior of partially earth-anchored cable-stayed bridges owing to decreased axial forces in the girders.

  4. Segmental Vitiligo.

    Science.gov (United States)

    van Geel, Nanja; Speeckaert, Reinhart

    2017-04-01

    Segmental vitiligo is characterized by its early onset, rapid stabilization, and unilateral distribution. Recent evidence suggests that segmental and nonsegmental vitiligo could represent variants of the same disease spectrum. Observational studies with respect to its distribution pattern point to a possible role of cutaneous mosaicism, whereas the original stated dermatomal distribution seems to be a misnomer. Although the exact pathogenic mechanism behind the melanocyte destruction is still unknown, increasing evidence has been published on the autoimmune/inflammatory theory of segmental vitiligo. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. On the use of the fictitious wave steepness and related surf-similarity parameters in methods that describe the hydraulic and structural response to waves

    NARCIS (Netherlands)

    Heineke, D.; Verhagen, H.J.

    2007-01-01

    To assess the hydraulic performance of coastal structures - viz. wave run-up, overtopping and reflection - and to evaluate the stability of the armour layers, use is made of the dimensionless surf similarity parameter, as introduced by Battjes (1974). The front side slope of the structure and the

  6. On the role of salt formation and structural similarity of co-formers in co-amorphous drug delivery systems

    DEFF Research Database (Denmark)

    Wu, Wenqi; Löbmann, Korbinian; Rades, Thomas

    2018-01-01

    solubility. However, little is known about the importance of the overall structure of the co-former. In this study, the structurally related amino acids arginine (basic) and citrulline (neutral) were chosen together with four model drugs (acidic furosemide and nitrofurantoin; basic cimetidine and mebendazole...

  7. Chromosome condensation and segmentation

    International Nuclear Information System (INIS)

    Viegas-Pequignot, E.M.

    1981-01-01

    Some aspects of chromosome condensation in mammalians -humans especially- were studied by means of cytogenetic techniques of chromosome banding. Two further approaches were adopted: a study of normal condensation as early as prophase, and an analysis of chromosome segmentation induced by physical (temperature and γ-rays) or chemical agents (base analogues, antibiotics, ...) in order to show out the factors liable to affect condensation. Here 'segmentation' means an abnormal chromosome condensation appearing systematically and being reproducible. The study of normal condensation was made possible by the development of a technique based on cell synchronization by thymidine and giving prophasic and prometaphasic cells. Besides, the possibility of inducing R-banding segmentations on these cells by BrdU (5-bromodeoxyuridine) allowed a much finer analysis of karyotypes. Another technique was developed using 5-ACR (5-azacytidine), it allowed to induce a segmentation similar to the one obtained using BrdU and identify heterochromatic areas rich in G-C bases pairs [fr

  8. Heparan sulfate chains from glypican and syndecans bind the Hep II domain of fibronectin similarly despite minor structural differences

    DEFF Research Database (Denmark)

    Tumova, S; Woods, A; Couchman, J R

    2000-01-01

    syndecan-4. Despite distinct molecular masses of glypican and syndecan glycosaminoglycans and minor differences in disaccharide composition and sulfation pattern, the overall proportion and distribution of sulfated regions and the affinity for the Hep II domain were similar. Therefore, adhesion regulation...

  9. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

    Directory of Open Access Journals (Sweden)

    Xu Wanhong

    2008-12-01

    Full Text Available Abstract Background The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses. Results We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode λB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV and aquareovirus (AqRV genome segment and protein sequences. There was ~55% amino acid identity between ARV λB and MRV λ3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was ~28% identity between ARV λB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV λ3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces. Conclusion The ARV λB and MRV λ3 proteins showed the highest ARV:MRV identity values (~55% amongst all currently known ARV and MRV

  10. Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota.

    Directory of Open Access Journals (Sweden)

    Tatsuki Ogura

    Full Text Available Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an "ECOMICS" web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation.

  11. Revisiting the dose-effect correlations in irradiated head and neck cancer using automatic segmentation tools of the dental structures, mandible and maxilla

    International Nuclear Information System (INIS)

    Thariat, J.; Ramus, L.; Odin, G.; Vincent, S.; Orlanducci, M.H.; Dassonville, O.; Darcourt, V.; Lacout, A.; Marcy, P.Y.; Cagnol, G.; Malandain, G.

    2011-01-01

    Purpose. - Manual delineation of dental structures is too time-consuming to be feasible in routine practice. Information on dose risk levels is crucial for dentists following irradiation of the head and neck to avoid post-extraction osteoradionecrosis based on empirical dose-effects data established on bidimensional radiation therapy plans. Material and methods. - We present an automatic atlas-based segmentation framework of the dental structures, called Dentalmaps, constructed from a patient image-segmentation database. Results. - This framework is accurate (within 2 Gy accuracy) and relevant for the routine use. It has the potential to guide dental care in the context of new irradiation techniques. Conclusion. - This tool provides a user-friendly interface for dentists and radiation oncologists in the context of irradiated head and neck cancer patients. It will likely improve the knowledge of dose-effect correlations for dental complications and osteoradionecrosis. (authors)

  12. Acquired degenerative changes of the intervertebral segments at and suprajacent to the lumbosacral junction. A radioanatomic analysis of the nondiskal structures of the spinal column and perispinal soft tissues.

    Science.gov (United States)

    Jinkins, J R

    2001-01-01

    In earlier evolutionary times, mammals were primarily quadrupeds. However, other bipeds have also been represented during the course of the Earth's several billion year history. In many cases, either the bipedal stance yielded a large tail and hypoplastic upper extremities (e.g., Tyrannosaurus rex and the kangaroo), or it culminated in hypoplasia of the tail and further development and specialization of the upper extremities (e.g., nonhuman primates and human beings). In the human species this relatively recently acquired posture resulted in a more or less pronounced lumbosacral kyphosis. In turn, certain compensatory anatomic features have since occurred. These include the normal characteristic posteriorly directed wedge-shape of the L5 vertebral body and the L5-S1 intervertebral disk; the L4 vertebral body and the L4-L5 disk may be similarly visibly affected. These compensatory mechanisms, however, have proved to be functionally inadequate over the long term of the human life span. Upright posture also leads to increased weight bearing in humans that progressively causes excess stresses at and suprajacent to the lumbosacral junction. These combined factors result in accelerated aging and degenerative changes and a predisposition to frank biomechanical failure of the subcomponents of the spinal column in these spinal segments. One other specific problem that occurs at the lumbosacral junction that predisposes toward premature degeneration is the singular relationship that exists between a normally mobile segment of spine (i.e., the lumbar spine) and a normally immobile one (i.e., the sacrum). It is well known that mobile spinal segments adjacent to congenitally or acquired fused segments have a predilection toward accelerated degenerative changes. The only segment of the spine in which this is invariably normally true is at the lumbosacral junction (i.e., the unfused lumbar spine adjoining the fused sacrum). Nevertheless, biomechanical failures of the human spine

  13. International EUREKA: Initialization Segment

    International Nuclear Information System (INIS)

    1982-02-01

    The Initialization Segment creates the starting description of the uranium market. The starting description includes the international boundaries of trade, the geologic provinces, resources, reserves, production, uranium demand forecasts, and existing market transactions. The Initialization Segment is designed to accept information of various degrees of detail, depending on what is known about each region. It must transform this information into a specific data structure required by the Market Segment of the model, filling in gaps in the information through a predetermined sequence of defaults and built in assumptions. A principal function of the Initialization Segment is to create diagnostic messages indicating any inconsistencies in data and explaining which assumptions were used to organize the data base. This permits the user to manipulate the data base until such time the user is satisfied that all the assumptions used are reasonable and that any inconsistencies are resolved in a satisfactory manner

  14. Structural and sequence variants in patients with Silver-Russell syndrome or similar features-Curation of a disease database

    DEFF Research Database (Denmark)

    Tümer, Zeynep; López-Hernández, Julia Angélica; Netchine, Irène

    2018-01-01

    data of these patients. The clinical features are scored according to the Netchine-Harbison clinical scoring system (NH-CSS), which has recently been accepted as standard by consensus. The structural and sequence variations are reviewed and where necessary redescribed according to recent...

  15. In Vitro-Assembled Alphavirus Core-Like Particles Maintain a Structure Similar to That of Nucleocapsid Cores in Mature Virus

    OpenAIRE

    Mukhopadhyay, Suchetana; Chipman, Paul R.; Hong, Eunmee M.; Kuhn, Richard J.; Rossmann, Michael G.

    2002-01-01

    In vitro-assembled core-like particles produced from alphavirus capsid protein and nucleic acid were studied by cryoelectron microscopy. These particles were found to have a diameter of 420 Å with 240 copies of the capsid protein arranged in a T=4 icosahedral surface lattice, similar to the nucleocapsid core in mature virions. However, when the particles were subjected to gentle purification procedures, they were damaged, preventing generation of reliable structural information. Similarly, pu...

  16. Dictionary Based Image Segmentation

    DEFF Research Database (Denmark)

    Dahl, Anders Bjorholm; Dahl, Vedrana Andersen

    2015-01-01

    We propose a method for weakly supervised segmentation of natural images, which may contain both textured or non-textured regions. Our texture representation is based on a dictionary of image patches. To divide an image into separated regions with similar texture we use an implicit level sets...

  17. Structural and Sequence Similarities of Hydra Xeroderma Pigmentosum A Protein to Human Homolog Suggest Early Evolution and Conservation

    Directory of Open Access Journals (Sweden)

    Apurva Barve

    2013-01-01

    Full Text Available Xeroderma pigmentosum group A (XPA is a protein that binds to damaged DNA, verifies presence of a lesion, and recruits other proteins of the nucleotide excision repair (NER pathway to the site. Though its homologs from yeast, Drosophila, humans, and so forth are well studied, XPA has not so far been reported from protozoa and lower animal phyla. Hydra is a fresh-water cnidarian with a remarkable capacity for regeneration and apparent lack of organismal ageing. Cnidarians are among the first metazoa with a defined body axis, tissue grade organisation, and nervous system. We report here for the first time presence of XPA gene in hydra. Putative protein sequence of hydra XPA contains nuclear localization signal and bears the zinc-finger motif. It contains two conserved Pfam domains and various characterized features of XPA proteins like regions for binding to excision repair cross-complementing protein-1 (ERCC1 and replication protein A 70 kDa subunit (RPA70 proteins. Hydra XPA shows a high degree of similarity with vertebrate homologs and clusters with deuterostomes in phylogenetic analysis. Homology modelling corroborates the very close similarity between hydra and human XPA. The protein thus most likely functions in hydra in the same manner as in other animals, indicating that it arose early in evolution and has been conserved across animal phyla.

  18. Segmentation of anatomical structures in chest radiographs using supervised methods: a comparative study on a public database

    DEFF Research Database (Denmark)

    van Ginneken, Bram; Stegmann, Mikkel Bille; Loog, Marco

    2006-01-01

    classification method that employs a multi-scale filter bank of Gaussian derivatives and a k-nearest-neighbors classifier. The methods have been tested on a publicly available database of 247 chest radiographs, in which all objects have been manually segmented by two human observers. A parameter optimization...

  19. Intrinsic structural differences in the N-terminal segment of pulmonary surfactant protein SP-C from different species

    DEFF Research Database (Denmark)

    Plasencia, I; Rivas, L; Casals, C

    2001-01-01

    Predictive studies suggest that the known sequences of the N-terminal segment of surfactant protein SP-C from animal species have an intrinsic tendency to form beta-turns, but there are important differences on the probable location of these motifs in different SP-C species. Our hypothesis...

  20. StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A; Lang, D; Kostova, T; Andino, R; Zhou, C

    2010-11-29

    Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected

  1. Unsupervised motion-based object segmentation refined by color

    Science.gov (United States)

    Piek, Matthijs C.; Braspenning, Ralph; Varekamp, Chris

    2003-06-01

    For various applications, such as data compression, structure from motion, medical imaging and video enhancement, there is a need for an algorithm that divides video sequences into independently moving objects. Because our focus is on video enhancement and structure from motion for consumer electronics, we strive for a low complexity solution. For still images, several approaches exist based on colour, but these lack in both speed and segmentation quality. For instance, colour-based watershed algorithms produce a so-called oversegmentation with many segments covering each single physical object. Other colour segmentation approaches exist which somehow limit the number of segments to reduce this oversegmentation problem. However, this often results in inaccurate edges or even missed objects. Most likely, colour is an inherently insufficient cue for real world object segmentation, because real world objects can display complex combinations of colours. For video sequences, however, an additional cue is available, namely the motion of objects. When different objects in a scene have different motion, the motion cue alone is often enough to reliably distinguish objects from one another and the background. However, because of the lack of sufficient resolution of efficient motion estimators, like the 3DRS block matcher, the resulting segmentation is not at pixel resolution, but at block resolution. Existing pixel resolution motion estimators are more sensitive to noise, suffer more from aperture problems or have less correspondence to the true motion of objects when compared to block-based approaches or are too computationally expensive. From its tendency to oversegmentation it is apparent that colour segmentation is particularly effective near edges of homogeneously coloured areas. On the other hand, block-based true motion estimation is particularly effective in heterogeneous areas, because heterogeneous areas improve the chance a block is unique and thus decrease the

  2. Probing multi-scale self-similarity of tissue structures using light scattering spectroscopy: prospects in pre-cancer detection

    Science.gov (United States)

    Chatterjee, Subhasri; Das, Nandan K.; Kumar, Satish; Mohapatra, Sonali; Pradhan, Asima; Panigrahi, Prasanta K.; Ghosh, Nirmalya

    2013-02-01

    Multi-resolution analysis on the spatial refractive index inhomogeneities in the connective tissue regions of human cervix reveals clear signature of multifractality. We have thus developed an inverse analysis strategy for extraction and quantification of the multifractality of spatial refractive index fluctuations from the recorded light scattering signal. The method is based on Fourier domain pre-processing of light scattering data using Born approximation, and its subsequent analysis through Multifractal Detrended Fluctuation Analysis model. The method has been validated on several mono- and multi-fractal scattering objects whose self-similar properties are user controlled and known a-priori. Following successful validation, this approach has initially been explored for differentiating between different grades of precancerous human cervical tissues.

  3. Malignant pleural mesothelioma segmentation for photodynamic therapy planning.

    Science.gov (United States)

    Brahim, Wael; Mestiri, Makram; Betrouni, Nacim; Hamrouni, Kamel

    2018-04-01

    Medical imaging modalities such as computed tomography (CT) combined with computer-aided diagnostic processing have already become important part of clinical routine specially for pleural diseases. The segmentation of the thoracic cavity represents an extremely important task in medical imaging for different reasons. Multiple features can be extracted by analyzing the thoracic cavity space and these features are signs of pleural diseases including the malignant pleural mesothelioma (MPM) which is the main focus of our research. This paper presents a method that detects the MPM in the thoracic cavity and plans the photodynamic therapy in the preoperative phase. This is achieved by using a texture analysis of the MPM region combined with a thoracic cavity segmentation method. The algorithm to segment the thoracic cavity consists of multiple stages. First, the rib cage structure is segmented using various image processing techniques. We used the segmented rib cage to detect feature points which represent the thoracic cavity boundaries. Next, the proposed method segments the structures of the inner thoracic cage and fits 2D closed curves to the detected pleural cavity features in each slice. The missing bone structures are interpolated using a prior knowledge from manual segmentation performed by an expert. Next, the tumor region is segmented inside the thoracic cavity using a texture analysis approach. Finally, the contact surface between the tumor region and the thoracic cavity curves is reconstructed in order to plan the photodynamic therapy. Using the adjusted output of the thoracic cavity segmentation method and the MPM segmentation method, we evaluated the contact surface generated from these two steps by comparing it to the ground truth. For this evaluation, we used 10 CT scans with pathologically confirmed MPM at stages 1 and 2. We obtained a high similarity rate between the manually planned surface and our proposed method. The average value of Jaccard index

  4. Using sparse LU factorisation to precondition GMRES for a family of similarly structured matrices arising from process modelling

    Energy Technology Data Exchange (ETDEWEB)

    Brooking, C. [Univ. of Bath (United Kingdom)

    1996-12-31

    Process engineering software is used to simulate the operation of large chemical plants. Such simulations are used for a variety of tasks, including operator training. For the software to be of practical use for this, dynamic simulations need to run in real-time. The models that the simulation is based upon are written in terms of Differential Algebraic Equations (DAE`s). In the numerical time-integration of systems of DAE`s using an implicit method such as backward Euler, the solution of nonlinear systems is required at each integration point. When solved using Newton`s method, this leads to the repeated solution of nonsymmetric sparse linear systems. These systems range in size from 500 to 20,000 variables. A typical integration may require around 3000 timesteps, and if 4 Newton iterates were needed on each time step, then this means approximately 12,000 linear systems must be solved. The matrices produced by the simulations have a similar sparsity pattern throughout the integration. They are also severely ill-conditioned, and have widely-scattered spectra.

  5. Monin-Obukhov Similarity Functions of the Structure Parameter of Temperature and Turbulent Kinetic Energy Dissipation Rate in the Stable Boundary Layer

    NARCIS (Netherlands)

    Hartogensis, O.K.; Debruin, H.A.R.

    2005-01-01

    The Monin-Obukhov similarity theory (MOST) functions fepsi; and fT, of the dissipation rate of turbulent kinetic energy (TKE), ¿, and the structure parameter of temperature, CT2, were determined for the stable atmospheric surface layer using data gathered in the context of CASES-99. These data cover

  6. Mixed segmentation

    DEFF Research Database (Denmark)

    Hansen, Allan Grutt; Bonde, Anders; Aagaard, Morten

    content analysis and audience segmentation in a single-source perspective. The aim is to explain and understand target groups in relation to, on the one hand, emotional response to commercials or other forms of audio-visual communication and, on the other hand, living preferences and personality traits...

  7. Leisure market segmentation : an integrated preferences/constraints-based approach

    NARCIS (Netherlands)

    Stemerding, M.P.; Oppewal, H.; Beckers, T.A.M.; Timmermans, H.J.P.

    1996-01-01

    Traditional segmentation schemes are often based on a grouping of consumers with similar preference functions. The research steps, ultimately leading to such segmentation schemes, are typically independent. In the present article, a new integrated approach to segmentation is introduced, which

  8. Processes of Similarity Judgment

    Science.gov (United States)

    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…

  9. Segmentation of DTI based on tensorial morphological gradient

    Science.gov (United States)

    Rittner, Leticia; de Alencar Lotufo, Roberto

    2009-02-01

    This paper presents a segmentation technique for diffusion tensor imaging (DTI). This technique is based on a tensorial morphological gradient (TMG), defined as the maximum dissimilarity over the neighborhood. Once this gradient is computed, the tensorial segmentation problem becomes an scalar one, which can be solved by conventional techniques, such as watershed transform and thresholding. Similarity functions, namely the dot product, the tensorial dot product, the J-divergence and the Frobenius norm, were compared, in order to understand their differences regarding the measurement of tensor dissimilarities. The study showed that the dot product and the tensorial dot product turned out to be inappropriate for computation of the TMG, while the Frobenius norm and the J-divergence were both capable of measuring tensor dissimilarities, despite the distortion of Frobenius norm, since it is not an affine invariant measure. In order to validate the TMG as a solution for DTI segmentation, its computation was performed using distinct similarity measures and structuring elements. TMG results were also compared to fractional anisotropy. Finally, synthetic and real DTI were used in the method validation. Experiments showed that the TMG enables the segmentation of DTI by watershed transform or by a simple choice of a threshold. The strength of the proposed segmentation method is its simplicity and robustness, consequences of TMG computation. It enables the use, not only of well-known algorithms and tools from the mathematical morphology, but also of any other segmentation method to segment DTI, since TMG computation transforms tensorial images in scalar ones.

  10. Exploratory analysis of genomic segmentations with Segtools

    Directory of Open Access Journals (Sweden)

    Buske Orion J

    2011-10-01

    Full Text Available Abstract Background As genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations. Results We present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and Plasmodium falciparum local chromatin structure data sets. Conclusions Segtools provides a convenient, powerful means of interpreting a genomic segmentation.

  11. Cytotoxic and Apoptotic Effect of Structurally Similar Flavonoids on Parental and Drug-Resistant Cells of a Human Cervical Carcinoma

    Directory of Open Access Journals (Sweden)

    Ksenija Durgo

    2009-01-01

    Full Text Available Flavonoids are phytochemicals characterized by a wide range of biological activities, including antioxidant activity, the ability to modulate enzyme or cell receptor activity patterns, and to interfere with essential biochemical pathways. Using HeLa cells of a human cervical carcinoma, and their drug-resistant HeLa CK subline, the effects of three structurally related flavonoids (quercetin, fisetin and luteolin have been examined, in terms of their: (i cytotoxicity, (ii influence on intracellular glutathione (GSH level, (iii influence on glutathione S-transferase (GST activity, and (iv influence on the expression of apoptosis-related genes (PARP, Bcl-2, survivin. Fisetin was more toxic to resistant HeLa CK cell line than to parental cell line, causing decreased expression of survivin in the same cell line. Concentrations of 5 μM of the examined flavonoids caused PARP degradation in parental cell line, leading HeLa cell line into apoptotic cell death. The same event was not determined in the resistant cell line. Fisetin and luteolin induce glutathione and GST in the resistant cell line, pointing to complex cellular effects which could be responsible for higher sensitivity of the resistant cell line in comparison with the parental cell line. Prooxidative nature of the investigated flavonoids was not detected, so free radical formation is not responsible for the induction of GSH, GST and proapoptotic enzymes.

  12. UPF201 Archaeal Specific Family Members Reveals Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

    Energy Technology Data Exchange (ETDEWEB)

    Rao, K.N.; Swaminathan, S.; Burley, S. K.

    2008-12-11

    We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10-40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel {beta}-sheet and five {alpha}-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.

  13. Molecular similarity measures.

    Science.gov (United States)

    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.

  14. Relations between segmental and motor variability in prosodically complex nonword sequences.

    Science.gov (United States)

    Goffman, Lisa; Gerken, Louann; Lucchesi, Julie

    2007-04-01

    To assess how prosodic prominence and hierarchical foot structure influence segmental and articulatory aspects of speech production, specifically segmental accuracy and variability, and oral movement trajectory variability. Thirty individuals participated: 10 young adults, 10 children who are normally developing, and 10 children diagnosed with specific language impairment. Segmental error and segmental variability and movement trajectory variability were compared in low and high prosodic prominence conditions (i.e., strong and weak syllables) and in different prosodic foot structures. Between-participants findings were that both groups of children showed more segmental error and segmental variability and more movement trajectory variability than did adults. A similar within-participant pattern of results was observed for all 3 groups. Prosodic prominence influenced both segmental and motor levels of analysis, with weak syllables produced less accurately and with more lip and jaw movement trajectory variability than strong syllables. However, hierarchical foot structure affected segmental but not motor measures of speech production accuracy and variability. Motor and segmental variables were not consistently aligned. This pattern of results has clinical implications because inferences about motor variability may not directly follow from observations of segmental variability.

  15. On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

    Directory of Open Access Journals (Sweden)

    Theobald Douglas L

    2011-11-01

    Full Text Available Abstract Background The universal common ancestry (UCA of all known life is a fundamental component of modern evolutionary theory, supported by a wide range of qualitative molecular evidence. Nevertheless, recently both the status and nature of UCA has been questioned. In earlier work I presented a formal, quantitative test of UCA in which model selection criteria overwhelmingly choose common ancestry over independent ancestry, based on a dataset of universally conserved proteins. These model-based tests are founded in likelihoodist and Bayesian probability theory, in opposition to classical frequentist null hypothesis tests such as Karlin-Altschul E-values for sequence similarity. In a recent comment, Koonin and Wolf (K&W claim that the model preference for UCA is "a trivial consequence of significant sequence similarity". They support this claim with a computational simulation, derived from universally conserved proteins, which produces similar sequences lacking phylogenetic structure. The model selection tests prefer common ancestry for this artificial data set. Results For the real universal protein sequences, hierarchical phylogenetic structure (induced by genealogical history is the overriding reason for why the tests choose UCA; sequence similarity is a relatively minor factor. First, for cases of conflicting phylogenetic structure, the tests choose independent ancestry even with highly similar sequences. Second, certain models, like star trees and K&W's profile model (corresponding to their simulation, readily explain sequence similarity yet lack phylogenetic structure. However, these are extremely poor models for the real proteins, even worse than independent ancestry models, though they explain K&W's artificial data well. Finally, K&W's simulation is an implementation of a well-known phylogenetic model, and it produces sequences that mimic homologous proteins. Therefore the model selection tests work appropriately with the artificial

  16. Schizosaccharomyces pombe Rad22A and Rad22B have similar biochemical properties and form multimeric structures

    Energy Technology Data Exchange (ETDEWEB)

    Vries, Femke A.T. de [Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden (Netherlands); Zonneveld, Jose B.M. [Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden (Netherlands); Groot, Anton J. de [Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden (Netherlands); Koning, Roman I. [Department of Molecular Cell Biology, Leiden University Medical Center, Leiden (Netherlands); Zeeland, Albert A. van [Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden (Netherlands); Pastink, Albert [Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden (Netherlands)]. E-mail: A.Pastink@lumc.nl

    2007-02-03

    The Saccharomyces cerevisiae Rad52 protein has a crucial role in the repair of DNA double-strand breaks by homologous recombination. In vitro, Rad52 displays DNA binding and strand annealing activities and promotes Rad51-mediated strand exchange. Schizosaccharomyces pombe has two Rad52 homologues, Rad22A and Rad22B. Whereas rad22A deficient strains exhibit severe defects in repair and recombination, rad22B mutants have a much less severe phenotype. To better understand the role of Rad22A and Rad22B in double-strand break repair, both proteins were purified to near homogeneity. Using gel retardation and filter binding assays, binding of Rad22A and Rad22B to short single-stranded DNAs was demonstrated. Binding of Rad22A to double-stranded oligonucleotides or linearized plasmid molecules containing blunt ends or short single-stranded overhangs could not be detected. Rad22B also does not bind efficiently to short duplex oligonucleotides but binds readily to DNA fragments containing 3'-overhangs. Rad22A as well as Rad22B efficiently promote annealing of complementary single-stranded DNAs. In the presence of Rad22A annealing of complementary DNAs is almost 90%. Whereas in reactions containing Rad22B the maximum level of annealing is 60%, most likely due to inhibition of the reaction by duplex DNA. Gel-filtration experiments and electron microscopic analyses indicate self-association of Rad22A and Rad22B and the formation of multimeric structures as has been observed for Rad52 in yeast and man.

  17. SU-E-J-230: Evaluation of ViewRay 0.35 T MRI Normal Structure Segmentation

    International Nuclear Information System (INIS)

    Paliwal, B; Asprey, W; Yan, Y; Saenz, D; Bayouth, J

    2015-01-01

    Purpose: In order to take advantage of the high resolution soft tissue imaging available in MR images, we investigated 3D images obtained with the low field 0.35 T MR in ViewRay to serve as an alternative to CT scans for radiotherapy treatment planning. In these images, normal and target structure delineation can be visualized. Assessment is based upon comparison with the CT images and the ability to produce comparable contours. Methods: Routine radiation oncology CT scans were acquired on five patients. Contours of brain, brainstem, esophagus, heart, lungs, spinal cord, and the external body were drawn. The same five patients were then scanned on the ViewRay TrueFISP-based imaging pulse sequence. The same organs were selected on the MR images and compared to those from the CT scan. Physical volume and the Dice Similarity Coefficient (DSC) were used to assess the contours from the two systems. Image quality stability was quantitatively ensured throughout the study following the recommendations of the ACR MR accreditation procedure. Results: The highest DSC of 0.985, 0.863, and 0.843 were observed for brain, lungs, and heart respectively. On the other hand, the brainstem, spinal cord, and esophagus had the lowest DSC. Volume agreement was most satisfied for the heart (within 5%) and the brain (within 2%). Contour volume for the brainstem and lung (a widely dynamic organ) varied the most (27% and 19%). Conclusion: The DSC and volume measurements suggest that the results obtained from ViewRay images are quantitatively consistent and comparable to those obtained from CT scans for the brain, heart, and lungs. MR images from ViewRay are well-suited for treatment planning and for adaptive MRI-guided radiotherapy. The physical data from 0.35 T MR imaging is consistent with our geometrical understanding of normal structures

  18. Segmentation in cinema perception.

    Science.gov (United States)

    Carroll, J M; Bever, T G

    1976-03-12

    Viewers perceptually segment moving picture sequences into their cinematically defined units: excerpts that follow short film sequences are recognized faster when the excerpt originally came after a structural cinematic break (a cut or change in the action) than when it originally came before the break.

  19. New robust algorithm for tracking cells in videos of Drosophila morphogenesis based on finding an ideal path in segmented spatio-temporal cellular structures.

    Science.gov (United States)

    Bellaïche, Yohanns; Bosveld, Floris; Graner, François; Mikula, Karol; Remesíková, Mariana; Smísek, Michal

    2011-01-01

    In this paper, we present a novel algorithm for tracking cells in time lapse confocal microscopy movie of a Drosophila epithelial tissue during pupal morphogenesis. We consider a 2D + time video as a 3D static image, where frames are stacked atop each other, and using a spatio-temporal segmentation algorithm we obtain information about spatio-temporal 3D tubes representing evolutions of cells. The main idea for tracking is the usage of two distance functions--first one from the cells in the initial frame and second one from segmented boundaries. We track the cells backwards in time. The first distance function attracts the subsequently constructed cell trajectories to the cells in the initial frame and the second one forces them to be close to centerlines of the segmented tubular structures. This makes our tracking algorithm robust against noise and missing spatio-temporal boundaries. This approach can be generalized to a 3D + time video analysis, where spatio-temporal tubes are 4D objects.

  20. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field......-shaped relation exists between expenditure strategy isomorphism and structure isomorphism in a longitudinal quantitative study of Danish municipalities....

  1. Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Balaji Petety V

    2006-04-01

    Full Text Available Abstract Background The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. Results Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. Conclusion The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate

  2. Segmentation of complex document

    Directory of Open Access Journals (Sweden)

    Souad Oudjemia

    2014-06-01

    Full Text Available In this paper we present a method for segmentation of documents image with complex structure. This technique based on GLCM (Grey Level Co-occurrence Matrix used to segment this type of document in three regions namely, 'graphics', 'background' and 'text'. Very briefly, this method is to divide the document image, in block size chosen after a series of tests and then applying the co-occurrence matrix to each block in order to extract five textural parameters which are energy, entropy, the sum entropy, difference entropy and standard deviation. These parameters are then used to classify the image into three regions using the k-means algorithm; the last step of segmentation is obtained by grouping connected pixels. Two performance measurements are performed for both graphics and text zones; we have obtained a classification rate of 98.3% and a Misclassification rate of 1.79%.

  3. Material Characterization and Geometric Segmentation of a Composite Structure Using Microfocus X-Ray Computed Tomography Image-Based Finite Element Modeling

    Science.gov (United States)

    Abdul-Aziz, Ali; Roth, D. J.; Cotton, R.; Studor, George F.; Christiansen, Eric; Young, P. C.

    2011-01-01

    This study utilizes microfocus x-ray computed tomography (CT) slice sets to model and characterize the damage locations and sizes in thermal protection system materials that underwent impact testing. ScanIP/FE software is used to visualize and process the slice sets, followed by mesh generation on the segmented volumetric rendering. Then, the local stress fields around several of the damaged regions are calculated for realistic mission profiles that subject the sample to extreme temperature and other severe environmental conditions. The resulting stress fields are used to quantify damage severity and make an assessment as to whether damage that did not penetrate to the base material can still result in catastrophic failure of the structure. It is expected that this study will demonstrate that finite element modeling based on an accurate three-dimensional rendered model from a series of CT slices is an essential tool to quantify the internal macroscopic defects and damage of a complex system made out of thermal protection material. Results obtained showing details of segmented images; three-dimensional volume-rendered models, finite element meshes generated, and the resulting thermomechanical stress state due to impact loading for the material are presented and discussed. Further, this study is conducted to exhibit certain high-caliber capabilities that the nondestructive evaluation (NDE) group at NASA Glenn Research Center can offer to assist in assessing the structural durability of such highly specialized materials so improvements in their performance and capacities to handle harsh operating conditions can be made.

  4. Multidimensional Riemann problem with self-similar internal structure - part III - a multidimensional analogue of the HLLI Riemann solver for conservative hyperbolic systems

    Science.gov (United States)

    Balsara, Dinshaw S.; Nkonga, Boniface

    2017-10-01

    Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The fastest way of endowing such sub-structure consists of making a multidimensional extension of the HLLI Riemann solver for hyperbolic conservation laws. Presenting such a multidimensional analogue of the HLLI Riemann solver with linear sub-structure for use on structured meshes is the goal of this work. The multidimensional MuSIC Riemann solver documented here is universal in the sense that it can be applied to any hyperbolic conservation law. The multidimensional Riemann solver is made to be consistent with constraints that emerge naturally from the Galerkin projection of the self-similar states within the wave model. When the full eigenstructure in both directions is used in the present Riemann solver, it becomes a complete Riemann solver in a multidimensional sense. I.e., all the intermediate waves are represented in the multidimensional wave model. The work also presents, for the very first time, an important analysis of the dissipation characteristics of multidimensional Riemann solvers. The present Riemann solver results in the most efficient implementation of a multidimensional Riemann solver with sub-structure. Because it preserves stationary linearly degenerate waves, it might also help with well-balancing. Implementation-related details are presented in pointwise fashion for the one-dimensional HLLI Riemann solver as well as the multidimensional MuSIC Riemann solver.

  5. Brookhaven segment interconnect

    International Nuclear Information System (INIS)

    Morse, W.M.; Benenson, G.; Leipuner, L.B.

    1983-01-01

    We have performed a high energy physics experiment using a multisegment Brookhaven FASTBUS system. The system was composed of three crate segments and two cable segments. We discuss the segment interconnect module which permits communication between the various segments

  6. Detection of structurally similar adulterants in botanical dietary supplements by thin-layer chromatography and surface enhanced Raman spectroscopy combined with two-dimensional correlation spectroscopy.

    Science.gov (United States)

    Li, Hao; Zhu, Qing xia; Chwee, Tsz sian; Wu, Lin; Chai, Yi feng; Lu, Feng; Yuan, Yong fang

    2015-07-09

    Thin-layer chromatography (TLC) coupled with surface enhanced Raman spectroscopy (SERS) has been widely used for the study of various complex systems, especially for the detection of adulterants in botanical dietary supplements (BDS). However, this method is not sufficient to distinguish structurally similar adulterants in BDS since the analogs have highly similar chromatographic and/or spectroscopic behaviors. Taking into account the fact that higher cost and more time will be required for comprehensive chromatographic separation, more efforts with respect to spectroscopy are now focused on analyzing the overlapped SERS peaks. In this paper, the combination of a TLC-SERS method with two-dimensional correlation spectroscopy (2DCOS), with duration of exposure to laser as the perturbation, is applied to solve this problem. Besides the usual advantages of the TLC-SERS method, such as its simplicity, rapidness, and sensitivity, more advantages are presented here, such as enhanced selectivity and good reproducibility, which are obtained by 2DCOS. Two chemicals with similar structures are successfully differentiated from the complex BDS matrices. The study provides a more accurate qualitative screening method for detection of BDS with adulterants, and offers a new universal approach for the analysis of highly overlapped SERS peaks. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

    Science.gov (United States)

    Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

    2017-01-21

    RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA

  8. The Hierarchy of Segment Reports

    Directory of Open Access Journals (Sweden)

    Danilo Dorović

    2015-05-01

    Full Text Available The article presents an attempt to find the connection between reports created for managers responsible for different business segments. With this purpose, the hierarchy of the business reporting segments is proposed. This can lead to better understanding of the expenses under common responsibility of more than one manager since these expenses should be in more than one report. The structure of cost defined per business segment hierarchy with the aim of new, unusual but relevant cost structure for management can be established. Both could potentially bring new information benefits for management in the context of profit reporting.

  9. Vaccinia protein F12 has structural similarity to kinesin light chain and contains a motor binding motif required for virion export.

    Directory of Open Access Journals (Sweden)

    Gareth W Morgan

    2010-02-01

    Full Text Available Vaccinia virus (VACV uses microtubules for export of virions to the cell surface and this process requires the viral protein F12. Here we show that F12 has structural similarity to kinesin light chain (KLC, a subunit of the kinesin-1 motor that binds cargo. F12 and KLC share similar size, pI, hydropathy and cargo-binding tetratricopeptide repeats (TPRs. Moreover, molecular modeling of F12 TPRs upon the crystal structure of KLC2 TPRs showed a striking conservation of structure. We also identified multiple TPRs in VACV proteins E2 and A36. Data presented demonstrate that F12 is critical for recruitment of kinesin-1 to virions and that a conserved tryptophan and aspartic acid (WD motif, which is conserved in the kinesin-1-binding sequence (KBS of the neuronal protein calsyntenin/alcadein and several other cellular kinesin-1 binding proteins, is essential for kinesin-1 recruitment and virion transport. In contrast, mutation of WD motifs in protein A36 revealed they were not required for kinesin-1 recruitment or IEV transport. This report of a viral KLC-like protein containing a KBS that is conserved in several cellular proteins advances our understanding of how VACV recruits the kinesin motor to virions, and exemplifies how viruses use molecular mimicry of cellular components to their advantage.

  10. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

    International Nuclear Information System (INIS)

    He, Yuan; Roth, Christian; Turkenburg, Johan P.; Davies, Gideon J.

    2013-01-01

    The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily. The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP-05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain

  11. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

    Energy Technology Data Exchange (ETDEWEB)

    He, Yuan [Northwest University, Xi’an 710069 (China); The University of York, York YO10 5DD (United Kingdom); Roth, Christian; Turkenburg, Johan P.; Davies, Gideon J., E-mail: gideon.davies@york.ac.uk [The University of York, York YO10 5DD (United Kingdom); Northwest University, Xi’an 710069 (China)

    2014-01-01

    The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily. The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP-05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain.

  12. Nuclear magnetic resonance and relaxation studies of the structure and segmental motions of 4-vinyl-pyridinic polymers in solution

    International Nuclear Information System (INIS)

    Ghesquiere, Denis

    1978-01-01

    The poly 4-vinylpyridine, its quaternized products from HBr and n-alkyl-bromides, and its N-oxide form have been investigated by nuclear magnetic resonance of proton at 100 and 250 MHz and carbon-13 at 25.15 MHz, The 1 H and 13 C relaxation data of poly-vinylpyridine and its ionized form have been correlated with conformational calculations. They have been interpreted in terms of an isotropic motion of the macromolecular segments introducing a correlation times distribution and of an oscillation motion of the pyridyl groups. The same treatment have been used for the 13 C relaxation data of the poly 4- vinyl-pyridines quaternized at various rates by n-alkyl-bromides. The 13 C relaxation times in the side-chains have been interpreted first by semi-empirical equations assuming an exponential gradient of the diffusion coefficients along them, and also by a Monte Carlo simulation of the motions. The results have shown that the quaternization induces a strong rigidity of the macromolecular backbone and that the dominant effect is the electrostatic interactions. On the other hand it seems that the motion of pyridyl rings is not affected. Moreover we have found a range of oscillation amplitudes in agreement with conformational energy calculations and the results obtained from a conformational study of the poly 4-vinylpyridine N-oxide by 1 H and 13 C NMR contact shifts induced by Ni II paramagnetic ions. (author) [fr

  13. Head segmentation in vertebrates

    OpenAIRE

    Kuratani, Shigeru; Schilling, Thomas

    2008-01-01

    Classic theories of vertebrate head segmentation clearly exemplify the idealistic nature of comparative embryology prior to the 20th century. Comparative embryology aimed at recognizing the basic, primary structure that is shared by all vertebrates, either as an archetype or an ancestral developmental pattern. Modern evolutionary developmental (Evo-Devo) studies are also based on comparison, and therefore have a tendency to reduce complex embryonic anatomy into overly simplified patterns. Her...

  14. Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles.

    Science.gov (United States)

    Price, Charles A; Symonova, Olga; Mileyko, Yuriy; Hilley, Troy; Weitz, Joshua S

    2011-01-01

    Interest in the structure and function of physical biological networks has spurred the development of a number of theoretical models that predict optimal network structures across a broad array of taxonomic groups, from mammals to plants. In many cases, direct tests of predicted network structure are impossible given the lack of suitable empirical methods to quantify physical network geometry with sufficient scope and resolution. There is a long history of empirical methods to quantify the network structure of plants, from roots, to xylem networks in shoots and within leaves. However, with few exceptions, current methods emphasize the analysis of portions of, rather than entire networks. Here, we introduce the Leaf Extraction and Analysis Framework Graphical User Interface (LEAF GUI), a user-assisted software tool that facilitates improved empirical understanding of leaf network structure. LEAF GUI takes images of leaves where veins have been enhanced relative to the background, and following a series of interactive thresholding and cleaning steps, returns a suite of statistics and information on the structure of leaf venation networks and areoles. Metrics include the dimensions, position, and connectivity of all network veins, and the dimensions, shape, and position of the areoles they surround. Available for free download, the LEAF GUI software promises to facilitate improved understanding of the adaptive and ecological significance of leaf vein network structure.

  15. Study of the morphology exhibited by linear segmented polyurethanes

    International Nuclear Information System (INIS)

    Pereira, I.M.; Orefice, R.L.

    2009-01-01

    Five series of segmented polyurethanes with different hard segment content were prepared by the prepolymer mixing method. The nano-morphology of the obtained polyurethanes and their microphase separation were investigated by infrared spectroscopy, modulated differential scanning calorimetry and small-angle X-ray scattering. Although highly hydrogen bonded hard segments were formed, high hard segment contents promoted phase mixture and decreased the chain mobility, decreasing the hard segment domain precipitation and the soft segments crystallization. The applied techniques were able to show that the hard-segment content and the hard-segment interactions were the two controlling factors for determining the structure of segmented polyurethanes. (author)

  16. Determination of the complex refractive index segments of turbid sample with multispectral spatially modulated structured light and models approximation

    Science.gov (United States)

    Meitav, Omri; Shaul, Oren; Abookasis, David

    2017-09-01

    Spectral data enabling the derivation of a biological tissue sample's complex refractive index (CRI) can provide a range of valuable information in the clinical and research contexts. Specifically, changes in the CRI reflect alterations in tissue morphology and chemical composition, enabling its use as an optical marker during diagnosis and treatment. In the present work, we report a method for estimating the real and imaginary parts of the CRI of a biological sample using Kramers-Kronig (KK) relations in the spatial frequency domain. In this method, phase-shifted sinusoidal patterns at single high spatial frequency are serially projected onto the sample surface at different near-infrared wavelengths while a camera mounted normal to the sample surface acquires the reflected diffuse light. In the offline analysis pipeline, recorded images at each wavelength are converted to spatial phase maps using KK analysis and are then calibrated against phase-models derived from diffusion approximation. The amplitude of the reflected light, together with phase data, is then introduced into Fresnel equations to resolve both real and imaginary segments of the CRI at each wavelength. The technique was validated in tissue-mimicking phantoms with known optical parameters and in mouse models of ischemic injury and heat stress. Experimental data obtained indicate variations in the CRI among brain tissue suffering from injury. CRI fluctuations correlated with alterations in the scattering and absorption coefficients of the injured tissue are demonstrated. This technique for deriving dynamic changes in the CRI of tissue may be further developed as a clinical diagnostic tool and for biomedical research applications. To the best of our knowledge, this is the first report of the estimation of the spectral CRI of a mouse head following injury obtained in the spatial frequency domain.

  17. The Impact of Protein Structure and Sequence Similarity on the Accuracy of Machine-Learning Scoring Functions for Binding Affinity Prediction.

    Science.gov (United States)

    Li, Hongjian; Peng, Jiangjun; Leung, Yee; Leung, Kwong-Sak; Wong, Man-Hon; Lu, Gang; Ballester, Pedro J

    2018-03-14

    It has recently been claimed that the outstanding performance of machine-learning scoring functions (SFs) is exclusively due to the presence of training complexes with highly similar proteins to those in the test set. Here, we revisit this question using 24 similarity-based training sets, a widely used test set, and four SFs. Three of these SFs employ machine learning instead of the classical linear regression approach of the fourth SF (X-Score which has the best test set performance out of 16 classical SFs). We have found that random forest (RF)-based RF-Score-v3 outperforms X-Score even when 68% of the most similar proteins are removed from the training set. In addition, unlike X-Score, RF-Score-v3 is able to keep learning with an increasing training set size, becoming substantially more predictive than X-Score when the full 1105 complexes are used for training. These results show that machine-learning SFs owe a substantial part of their performance to training on complexes with dissimilar proteins to those in the test set, against what has been previously concluded using the same data. Given that a growing amount of structural and interaction data will be available from academic and industrial sources, this performance gap between machine-learning SFs and classical SFs is expected to enlarge in the future.

  18. Development of a NIR-based blend uniformity method for a drug product containing multiple structurally similar actives by using the quality by design principles.

    Science.gov (United States)

    Lin, Yiqing; Li, Weiyong; Xu, Jin; Boulas, Pierre

    2015-07-05

    The aim of this study is to develop an at-line near infrared (NIR) method for the rapid and simultaneous determination of four structurally similar active pharmaceutical ingredients (APIs) in powder blends intended for the manufacturing of tablets. Two of the four APIs in the formula are present in relatively small amounts, one at 0.95% and the other at 0.57%. Such small amounts in addition to the similarity in structures add significant complexity to the blend uniformity analysis. The NIR method is developed using spectra from six laboratory-created calibration samples augmented by a small set of spectra from a large-scale blending sample. Applying the quality by design (QbD) principles, the calibration design included concentration variations of the four APIs and a main excipient, microcrystalline cellulose. A bench-top FT-NIR instrument was used to acquire the spectra. The obtained NIR spectra were analyzed by applying principal component analysis (PCA) before calibration model development. Score patterns from the PCA were analyzed to reveal relationship between latent variables and concentration variations of the APIs. In calibration model development, both PLS-1 and PLS-2 models were created and evaluated for their effectiveness in predicting API concentrations in the blending samples. The final NIR method shows satisfactory specificity and accuracy. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Vessel-guided airway segmentation based on voxel classification

    DEFF Research Database (Denmark)

    Lo, Pechin Chien Pau; Sporring, Jon; Ashraf, Haseem

    2008-01-01

    This paper presents a method for improving airway tree segmentation using vessel orientation information. We use the fact that an airway branch is always accompanied by an artery, with both structures having similar orientations. This work is based on a  voxel classification airway segmentation...... method proposed previously. The probability of a voxel belonging to the airway, from the voxel classification method, is augmented with an orientation similarity measure as a criterion for region growing. The orientation similarity measure of a voxel indicates how similar is the orientation...... of the surroundings of a voxel, estimated based on a tube model, is to that of a neighboring vessel. The proposed method is tested on 20 CT images from different subjects selected randomly from a lung cancer screening study. Length of the airway branches from the results of the proposed method are significantly...

  20. Efficient graph-cut tattoo segmentation

    Science.gov (United States)

    Kim, Joonsoo; Parra, Albert; Li, He; Delp, Edward J.

    2015-03-01

    Law enforcement is interested in exploiting tattoos as an information source to identify, track and prevent gang-related crimes. Many tattoo image retrieval systems have been described. In a retrieval system tattoo segmentation is an important step for retrieval accuracy since segmentation removes background information in a tattoo image. Existing segmentation methods do not extract the tattoo very well when the background includes textures and color similar to skin tones. In this paper we describe a tattoo segmentation approach by determining skin pixels in regions near the tattoo. In these regions graph-cut segmentation using a skin color model and a visual saliency map is used to find skin pixels. After segmentation we determine which set of skin pixels are connected with each other that form a closed contour including a tattoo. The regions surrounded by the closed contours are considered tattoo regions. Our method segments tattoos well when the background includes textures and color similar to skin.

  1. Metric Learning for Hyperspectral Image Segmentation

    Science.gov (United States)

    Bue, Brian D.; Thompson, David R.; Gilmore, Martha S.; Castano, Rebecca

    2011-01-01

    We present a metric learning approach to improve the performance of unsupervised hyperspectral image segmentation. Unsupervised spatial segmentation can assist both user visualization and automatic recognition of surface features. Analysts can use spatially-continuous segments to decrease noise levels and/or localize feature boundaries. However, existing segmentation methods use tasks-agnostic measures of similarity. Here we learn task-specific similarity measures from training data, improving segment fidelity to classes of interest. Multiclass Linear Discriminate Analysis produces a linear transform that optimally separates a labeled set of training classes. The defines a distance metric that generalized to a new scenes, enabling graph-based segmentation that emphasizes key spectral features. We describe tests based on data from the Compact Reconnaissance Imaging Spectrometer (CRISM) in which learned metrics improve segment homogeneity with respect to mineralogical classes.

  2. The nonenzymatic subunit of pseutarin C, a prothrombin activator from eastern brown snake (Pseudonaja textilis) venom, shows structural similarity to mammalian coagulation factor V.

    Science.gov (United States)

    Rao, Veena S; Swarup, Sanjay; Kini, R Manjunatha

    2003-08-15

    Pseutarin C is a group C prothrombin activator from the venom of the eastern brown snake Pseudonaja textilis. It is a multi-subunit protein complex consisting of catalytic and nonenzymatic subunits similar to coagulation factor Xa and factor Va, respectively. Here we describe the complete sequence of the nonenzymatic subunit. Based on the partial amino acid sequence of the nonenzymatic subunit, degenerate primers were designed. Using a "walking" strategy based on sequentially designed primers, we determined the complete cDNA sequence of the nonenzymatic subunit. The cDNA encodes a protein of 1461 amino acid residues, which includes a 30-residue signal peptide, a mature protein of 1430 amino acid residues, and a stop codon. cDNA blot analysis showed a single transcript of approximately 4.6 kb. The deduced amino acid sequence shows approximately 50% identity to mammalian factor V and by homology has a similar domain structure consisting of domains A1-A2-B-A3-C1-C2. Interestingly, the B domain of pseutarin C is shorter than that of mammalian factor V (FV). Although most of the proteolytic activation sites are conserved, 2 of 3 proteolytic sites cleaved by activated protein C are mutated, and thus activated protein C is not able to inactivate this procoagulant toxin. The predicted posttranslational modifications, including disulfide bonds, N-glycosylation, phosphorylation, and sulfation, in pseutarin C are significantly different compared with bovine factor V. Thus, our data demonstrate that the nonenzymatic subunit of group C prothrombin activators is structurally similar to mammalian FV.

  3. Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core.

    Directory of Open Access Journals (Sweden)

    Franziska Weirich

    Full Text Available Amyloid deposits formed from islet amyloid polypeptide (IAPP are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism.

  4. Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core

    Science.gov (United States)

    Weirich, Franziska; Gremer, Lothar; Mirecka, Ewa A.; Schiefer, Stephanie; Hoyer, Wolfgang; Heise, Henrike

    2016-01-01

    Amyloid deposits formed from islet amyloid polypeptide (IAPP) are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism. PMID:27607147

  5. Hemiptera Mitochondrial Control Region: New Sights into the Structural Organization, Phylogenetic Utility, and Roles of Tandem Repetitions of the Noncoding Segment

    Directory of Open Access Journals (Sweden)

    Kui Li

    2018-04-01

    Full Text Available As a major noncoding fragment, the control region (CR of mtDNA is responsible for the initiation of mitogenome transcription and replication. Several structural features of CR sequences have been reported in many insects. However, comprehensive analyses on the structural organization and phylogenetic utility, as well as the role of tandem replications (TRs on length variation, high A+T content, and shift of base skew of CR sequences are poorly investigated in hemipteran insects. In this study, we conducted a series of comparative analyses, using 116 samples covering all 11 infraorders of the five currently recognized monophyletic groups in the Hemiptera. Several structural elements (mononucleotide stretches containing conserved sequence blocks (CSBs, TRs, and GA-rich region were identified in the mitochondrial control region in hemipteran insects, without showing a consistent location. The presence and absence of certain specific structural elements in CR sequences show the various structural organizations of that segment among the five monophyletic groups, which indicates the diversification of the control region’s structural organization in Hemiptera. Among the many groups within Hemiptera, eight monophyletic groups and three consistent phylogenetic trees were recovered, using CSBs datasets by maximum likelihood and Bayesian methods, which suggests the possible utility of CR sequences for phylogenetic reconstruction in certain groups of Hemiptera. Statistical analyses showed that TRs may contribute to the length variation, high AT content, and the shift of base skewing of CR sequences toward high AT content in the Hemiptera. Our findings enrich the knowledge of structural organization, phylogenetic utility, and roles of tandem replication of hemipteran CR, and provide a possible framework for mitochondrial control region analyses in hemimetabolous insects.

  6. Automatic segmentation of the glenohumeral cartilages from magnetic resonance images

    International Nuclear Information System (INIS)

    Neubert, A.; Yang, Z.; Engstrom, C.; Xia, Y.; Strudwick, M. W.; Chandra, S. S.; Crozier, S.; Fripp, J.

    2016-01-01

    Purpose: Magnetic resonance (MR) imaging plays a key role in investigating early degenerative disorders and traumatic injuries of the glenohumeral cartilages. Subtle morphometric and biochemical changes of potential relevance to clinical diagnosis, treatment planning, and evaluation can be assessed from measurements derived from in vivo MR segmentation of the cartilages. However, segmentation of the glenohumeral cartilages, using approaches spanning manual to automated methods, is technically challenging, due to their thin, curved structure and overlapping intensities of surrounding tissues. Automatic segmentation of the glenohumeral cartilages from MR imaging is not at the same level compared to the weight-bearing knee and hip joint cartilages despite the potential applications with respect to clinical investigation of shoulder disorders. In this work, the authors present a fully automated segmentation method for the glenohumeral cartilages using MR images of healthy shoulders. Methods: The method involves automated segmentation of the humerus and scapula bones using 3D active shape models, the extraction of the expected bone–cartilage interface, and cartilage segmentation using a graph-based method. The cartilage segmentation uses localization, patient specific tissue estimation, and a model of the cartilage thickness variation. The accuracy of this method was experimentally validated using a leave-one-out scheme on a database of MR images acquired from 44 asymptomatic subjects with a true fast imaging with steady state precession sequence on a 3 T scanner (Siemens Trio) using a dedicated shoulder coil. The automated results were compared to manual segmentations from two experts (an experienced radiographer and an experienced musculoskeletal anatomist) using the Dice similarity coefficient (DSC) and mean absolute surface distance (MASD) metrics. Results: Accurate and precise bone segmentations were achieved with mean DSC of 0.98 and 0.93 for the humeral head

  7. Automatic segmentation of the glenohumeral cartilages from magnetic resonance images

    Energy Technology Data Exchange (ETDEWEB)

    Neubert, A., E-mail: ales.neubert@csiro.au [School of Information Technology and Electrical Engineering, University of Queensland, Brisbane 4072, Australia and The Australian E-Health Research Centre, CSIRO Health and Biosecurity, Brisbane 4029 (Australia); Yang, Z. [School of Information Technology and Electrical Engineering, University of Queensland, Brisbane 4072, Australia and Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing 100190 (China); Engstrom, C. [School of Human Movement Studies, University of Queensland, Brisbane 4072 (Australia); Xia, Y.; Strudwick, M. W.; Chandra, S. S.; Crozier, S. [School of Information Technology and Electrical Engineering, University of Queensland, Brisbane 4072 (Australia); Fripp, J. [The Australian E-Health Research Centre, CSIRO Health and Biosecurity, Brisbane, 4029 (Australia)

    2016-10-15

    Purpose: Magnetic resonance (MR) imaging plays a key role in investigating early degenerative disorders and traumatic injuries of the glenohumeral cartilages. Subtle morphometric and biochemical changes of potential relevance to clinical diagnosis, treatment planning, and evaluation can be assessed from measurements derived from in vivo MR segmentation of the cartilages. However, segmentation of the glenohumeral cartilages, using approaches spanning manual to automated methods, is technically challenging, due to their thin, curved structure and overlapping intensities of surrounding tissues. Automatic segmentation of the glenohumeral cartilages from MR imaging is not at the same level compared to the weight-bearing knee and hip joint cartilages despite the potential applications with respect to clinical investigation of shoulder disorders. In this work, the authors present a fully automated segmentation method for the glenohumeral cartilages using MR images of healthy shoulders. Methods: The method involves automated segmentation of the humerus and scapula bones using 3D active shape models, the extraction of the expected bone–cartilage interface, and cartilage segmentation using a graph-based method. The cartilage segmentation uses localization, patient specific tissue estimation, and a model of the cartilage thickness variation. The accuracy of this method was experimentally validated using a leave-one-out scheme on a database of MR images acquired from 44 asymptomatic subjects with a true fast imaging with steady state precession sequence on a 3 T scanner (Siemens Trio) using a dedicated shoulder coil. The automated results were compared to manual segmentations from two experts (an experienced radiographer and an experienced musculoskeletal anatomist) using the Dice similarity coefficient (DSC) and mean absolute surface distance (MASD) metrics. Results: Accurate and precise bone segmentations were achieved with mean DSC of 0.98 and 0.93 for the humeral head

  8. Interactive lung segmentation in abnormal human and animal chest CT scans

    International Nuclear Information System (INIS)

    Kockelkorn, Thessa T. J. P.; Viergever, Max A.; Schaefer-Prokop, Cornelia M.; Bozovic, Gracijela; Muñoz-Barrutia, Arrate; Rikxoort, Eva M. van; Brown, Matthew S.; Jong, Pim A. de; Ginneken, Bram van

    2014-01-01

    Purpose: Many medical image analysis systems require segmentation of the structures of interest as a first step. For scans with gross pathology, automatic segmentation methods may fail. The authors’ aim is to develop a versatile, fast, and reliable interactive system to segment anatomical structures. In this study, this system was used for segmenting lungs in challenging thoracic computed tomography (CT) scans. Methods: In volumetric thoracic CT scans, the chest is segmented and divided into 3D volumes of interest (VOIs), containing voxels with similar densities. These VOIs are automatically labeled as either lung tissue or nonlung tissue. The automatic labeling results can be corrected using an interactive or a supervised interactive approach. When using the supervised interactive system, the user is shown the classification results per slice, whereupon he/she can adjust incorrect labels. The system is retrained continuously, taking the corrections and approvals of the user into account. In this way, the system learns to make a better distinction between lung tissue and nonlung tissue. When using the interactive framework without supervised learning, the user corrects all incorrectly labeled VOIs manually. Both interactive segmentation tools were tested on 32 volumetric CT scans of pigs, mice and humans, containing pulmonary abnormalities. Results: On average, supervised interactive lung segmentation took under 9 min of user interaction. Algorithm computing time was 2 min on average, but can easily be reduced. On average, 2.0% of all VOIs in a scan had to be relabeled. Lung segmentation using the interactive segmentation method took on average 13 min and involved relabeling 3.0% of all VOIs on average. The resulting segmentations correspond well to manual delineations of eight axial slices per scan, with an average Dice similarity coefficient of 0.933. Conclusions: The authors have developed two fast and reliable methods for interactive lung segmentation in

  9. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Wu, Ruiying; Adkins, Joshua N.; Joachimiak, Andrzej; Glover, Mark

    2014-09-16

    In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

  10. A C-terminal segment of the V{sub 1}R vasopressin receptor is unstructured in the crystal structure of its chimera with the maltose-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Adikesavan, Nallini Vijayarangan; Mahmood, Syed Saad; Stanley, Nithianantham; Xu, Zhen; Wu, Nan [Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4935 (United States); Thibonnier, Marc [Department of Medicine, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4935 (United States); Shoham, Menachem, E-mail: mxs10@case.edu [Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4935 (United States)

    2005-04-01

    The 1.8 Å crystal structure of an MBP-fusion protein with the C-terminal cytoplasmic segment of the V1 vasopressin receptor reveals that the receptor segment is unstructured. The V{sub 1} vascular vasopressin receptor (V{sub 1}R) is a G-protein-coupled receptor (GPCR) involved in the regulation of body-fluid osmolality, blood volume and blood pressure. Signal transduction is mediated by the third intracellular loop of this seven-transmembrane protein as well as by the C-terminal cytoplasmic segment. A chimera of the maltose-binding protein (MBP) and the C-terminal segment of V{sub 1}R has been cloned, expressed, purified and crystallized. The crystals belong to space group P2{sub 1}, with unit-cell parameters a = 51.10, b = 66.56, c = 115.72 Å, β = 95.99°. The 1.8 Å crystal structure reveals the conformation of MBP and part of the linker region of this chimera, with the C-terminal segment being unstructured. This may reflect a conformational plasticity in the C-terminal segment that may be necessary for proper function of V{sub 1}R.

  11. SU-E-J-134: Optimizing Technical Parameters for Using Atlas Based Automatic Segmentation for Evaluation of Contour Accuracy Experience with Cardiac Structures From NRG Oncology/RTOG 0617

    Energy Technology Data Exchange (ETDEWEB)

    Yu, J; Gong, Y; Bar-Ad, V; Giaddui, T; Galvin, J; Xiao, Y [Thomas Jefferson University, Philadelphia, PA (United States); Hu, C [NRG oncology, Philadelphia, PA (United States); Gore, E; Wheatley, M [Medical College of Wisconsin, Milwaukee, WI (United States); Witt, J; Robinson, C; Bradley, J [Washington University in St. Louis School of Medicine, St. Louis, MO (United States); Kong, F [Georgia Regents University, Augusta, GA (Georgia)

    2015-06-15

    Purpose: Accurate contour delineation is crucial for radiotherapy. Atlas based automatic segmentation tools can be used to increase the efficiency of contour accuracy evaluation. This study aims to optimize technical parameters utilized in the tool by exploring the impact of library size and atlas number on the accuracy of cardiac contour evaluation. Methods: Patient CT DICOMs from RTOG 0617 were used for this study. Five experienced physicians delineated the cardiac structures including pericardium, atria and ventricles following an atlas guideline. The consistency of cardiac structured delineation using the atlas guideline was verified by a study with four observers and seventeen patients. The CT and cardiac structure DICOM files were then used for the ABAS technique.To study the impact of library size (LS) and atlas number (AN) on automatic contour accuracy, automatic contours were generated with varied technique parameters for five randomly selected patients. Three LS (20, 60, and 100) were studied using commercially available software. The AN was four, recommended by the manufacturer. Using the manual contour as the gold standard, Dice Similarity Coefficient (DSC) was calculated between the manual and automatic contours. Five-patient averaged DSCs were calculated for comparison for each cardiac structure.In order to study the impact of AN, the LS was set 100, and AN was tested from one to five. The five-patient averaged DSCs were also calculated for each cardiac structure. Results: DSC values are highest when LS is 100 and AN is four. The DSC is 0.90±0.02 for pericardium, 0.75±0.06 for atria, and 0.86±0.02 for ventricles. Conclusion: By comparing DSC values, the combination AN=4 and LS=100 gives the best performance. This project was supported by NCI grants U24CA12014, U24CA180803, U10CA180868, U10CA180822, PA CURE grant and Bristol-Myers Squibb and Eli Lilly.

  12. Molecular structural differences between low methoxy pectins induced by pectin methyl esterase II: effects on texture, release and perception of aroma in gels of similar modulus of elasticity.

    Science.gov (United States)

    Kim, Yang; Kim, Young-Suk; Yoo, Sang-Ho; Kim, Kwang-Ok

    2014-02-15

    Six low-methoxy pectins with different degrees of methylesterification and amidation, and molecular weights were used to prepare gels with similar moduli of elasticity by varying the concentrations of pectin and calcium phosphate. Five aroma compounds were added to the gels and their sensory textural properties, release and perception of aromas were investigated. Sensory firmness, springiness, adhesiveness, chewiness and cohesiveness differed according to the gel type, even though the moduli of elasticity were not significantly different (ppectin exhibited the lowest release and perception for all the aroma compounds, while pectin-methylesterase-treated pectin gels exhibited relatively higher aroma release and perception. These results showed that the structural properties of pectins and gelling factors that increase the non-polar character of the gel matrices could decrease the release and perception of aromas in pectin gel systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Lung tumor segmentation in PET images using graph cuts.

    Science.gov (United States)

    Ballangan, Cherry; Wang, Xiuying; Fulham, Michael; Eberl, Stefan; Feng, David Dagan

    2013-03-01

    The aim of segmentation of tumor regions in positron emission tomography (PET) is to provide more accurate measurements of tumor size and extension into adjacent structures, than is possible with visual assessment alone and hence improve patient management decisions. We propose a segmentation energy function for the graph cuts technique to improve lung tumor segmentation with PET. Our segmentation energy is based on an analysis of the tumor voxels in PET images combined with a standardized uptake value (SUV) cost function and a monotonic downhill SUV feature. The monotonic downhill feature avoids segmentation leakage into surrounding tissues with similar or higher PET tracer uptake than the tumor and the SUV cost function improves the boundary definition and also addresses situations where the lung tumor is heterogeneous. We evaluated the method in 42 clinical PET volumes from patients with non-small cell lung cancer (NSCLC). Our method improves segmentation and performs better than region growing approaches, the watershed technique, fuzzy-c-means, region-based active contour and tumor customized downhill. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  14. Structure-function similarities between a plant receptor-like kinase and the human interleukin-1 receptor-associated kinase-4.

    Science.gov (United States)

    Klaus-Heisen, Dörte; Nurisso, Alessandra; Pietraszewska-Bogiel, Anna; Mbengue, Malick; Camut, Sylvie; Timmers, Ton; Pichereaux, Carole; Rossignol, Michel; Gadella, Theodorus W J; Imberty, Anne; Lefebvre, Benoit; Cullimore, Julie V

    2011-04-01

    Phylogenetic analysis has previously shown that plant receptor-like kinases (RLKs) are monophyletic with respect to the kinase domain and share an evolutionary origin with the animal interleukin-1 receptor-associated kinase/Pelle-soluble kinases. The lysin motif domain-containing receptor-like kinase-3 (LYK3) of the legume Medicago truncatula shows 33% amino acid sequence identity with human IRAK-4 over the kinase domain. Using the structure of this animal kinase as a template, homology modeling revealed that the plant RLK contains structural features particular to this group of kinases, including the tyrosine gatekeeper and the N-terminal extension α-helix B. Functional analysis revealed the importance of these conserved features for kinase activity and suggests that kinase activity is essential for the biological role of LYK3 in the establishment of the root nodule nitrogen-fixing symbiosis with rhizobia bacteria. The kinase domain of LYK3 has dual serine/threonine and tyrosine specificity, and mass spectrometry analysis identified seven serine, eight threonine, and one tyrosine residue as autophosphorylation sites in vitro. Three activation loop serine/threonine residues are required for biological activity, and molecular dynamics simulations suggest that Thr-475 is the prototypical phosphorylated residue that interacts with the conserved arginine in the catalytic loop, whereas Ser-471 and Thr-472 may be secondary sites. A threonine in the juxtamembrane region and two threonines in the C-terminal lobe of the kinase domain are important for biological but not kinase activity. We present evidence that the structure-function similarities that we have identified between LYK3 and IRAK-4 may be more widely applicable to plant RLKs in general.

  15. Comparison of atlas-based techniques for whole-body bone segmentation

    DEFF Research Database (Denmark)

    Arabi, Hossein; Zaidi, Habib

    2017-01-01

    out in terms of estimating bone extraction accuracy from whole-body MRI using standard metrics, such as Dice similarity (DSC) and relative volume difference (RVD) considering bony structures obtained from intensity thresholding of the reference CT images as the ground truth. Considering the Dice....../MRI. To this end, a variety of atlas-based segmentation strategies commonly used in medical image segmentation and pseudo-CT generation were implemented and evaluated in terms of whole-body bone segmentation accuracy. Bone segmentation was performed on 23 whole-body CT/MR image pairs via leave-one-out cross...... validation procedure. The evaluated segmentation techniques include: (i) intensity averaging (IA), (ii) majority voting (MV), (iii) global and (iv) local (voxel-wise) weighting atlas fusion frameworks implemented utilizing normalized mutual information (NMI), normalized cross-correlation (NCC) and mean...

  16. SPECIFIC VELOCITY STRUCTURE OF THE UPPER MANTLE IN THE TRANSBAIKALIA SEGMENT OF THE MONGOLIA-OKHOTSK OROGENIC BELT

    Directory of Open Access Journals (Sweden)

    V. M. Soloviev

    2017-01-01

    Full Text Available The paper presents the results of deep seismic studies on Geophysical Reference Profile 1-SB (Sredneargunsk – Ust-Karenga – Taksimo – Vitim in East Transbaikalia,Russia. The1200 kmlong profile crosses the major tectonic structures of the Central Asian fold belt: the Argun median massif, the Selenga-Stanovoy and Transbaikalia folded regions, and the Baikal rift zone. Its northwestern fragment extends into the Angara-Lena monocline of the Siberian platform. The southeastern (Transbaikalia and northwestern (Baikal-Patom fragments of the profile are based on the spot (differential seismic sounding technique using explosions and 40-tonne vibrators. The south­eastern (Transbaikalia fragment shows small crustal thickness values (~40 km, an almost horizontal position of the Moho, and high velocities of longitudinal waves (~8.4 km/sec beneath the Moho. The analysis of parallelism graphs and the dynamic expression of the wave refracted from the Moho suggests a less than 5–10 km thick layer of high velocities and low gradients below Moho. The database on theterritoryofTransbaikaliaincludes ~200 wave arrival times from large earthquakes, which were refracted at the Moho at distances of ~200–1400 km. As part of the tomographic interpretation, using additional DSS data on the Moho, theterritoryofTransbaikaliahas been mapped to show the patterns of the threshold velocity values at the Moho. The seismic data was used to contour an area with high velocity values in the mantle in the central part of the Mongolia-Okhotsk orogenic belt and the neighboring fold structures of Transbaikalia. According to the analysis of the seismic and geologic data on the study area, the mantle layer with high velocity values in the Mongolian-Okhotsk orogenic belt may be represented by the eclogitic rock plates.

  17. Image segmentation by hierarchial agglomeration of polygons using ecological statistics

    Science.gov (United States)

    Prasad, Lakshman; Swaminarayan, Sriram

    2013-04-23

    A method for rapid hierarchical image segmentation based on perceptually driven contour completion and scene statistics is disclosed. The method begins with an initial fine-scale segmentation of an image, such as obtained by perceptual completion of partial contours into polygonal regions using region-contour correspondences established by Delaunay triangulation of edge pixels as implemented in VISTA. The resulting polygons are analyzed with respect to their size and color/intensity distributions and the structural properties of their boundaries. Statistical estimates of granularity of size, similarity of color, texture, and saliency of intervening boundaries are computed and formulated into logical (Boolean) predicates. The combined satisfiability of these Boolean predicates by a pair of adjacent polygons at a given segmentation level qualifies them for merging into a larger polygon representing a coarser, larger-scale feature of the pixel image and collectively obtains the next level of polygonal segments in a hierarchy of fine-to-coarse segmentations. The iterative application of this process precipitates textured regions as polygons with highly convolved boundaries and helps distinguish them from objects which typically have more regular boundaries. The method yields a multiscale decomposition of an image into constituent features that enjoy a hierarchical relationship with features at finer and coarser scales. This provides a traversable graph structure from which feature content and context in terms of other features can be derived, aiding in automated image understanding tasks. The method disclosed is highly efficient and can be used to decompose and analyze large images.

  18. An Automatic Cognitive Graph-Based Segmentation for Detection of Blood Vessels in Retinal Images

    Directory of Open Access Journals (Sweden)

    Rasha Al Shehhi

    2016-01-01

    Full Text Available This paper presents a hierarchical graph-based segmentation for blood vessel detection in digital retinal images. This segmentation employs some of perceptual Gestalt principles: similarity, closure, continuity, and proximity to merge segments into coherent connected vessel-like patterns. The integration of Gestalt principles is based on object-based features (e.g., color and black top-hat (BTH morphology and context and graph-analysis algorithms (e.g., Dijkstra path. The segmentation framework consists of two main steps: preprocessing and multiscale graph-based segmentation. Preprocessing is to enhance lighting condition, due to low illumination contrast, and to construct necessary features to enhance vessel structure due to sensitivity of vessel patterns to multiscale/multiorientation structure. Graph-based segmentation is to decrease computational processing required for region of interest into most semantic objects. The segmentation was evaluated on three publicly available datasets. Experimental results show that preprocessing stage achieves better results compared to state-of-the-art enhancement methods. The performance of the proposed graph-based segmentation is found to be consistent and comparable to other existing methods, with improved capability of detecting small/thin vessels.

  19. Adaptation of the Maracas algorithm for carotid artery segmentation and stenosis quantification on CT images

    International Nuclear Information System (INIS)

    Maria A Zuluaga; Maciej Orkisz; Edgar J F Delgado; Vincent Dore; Alfredo Morales Pinzon; Marcela Hernandez Hoyos

    2010-01-01

    This paper describes the adaptations of Maracas algorithm to the segmentation and quantification of vascular structures in CTA images of the carotid artery. The maracas algorithm, which is based on an elastic model and on a multi-scale Eigen-analysis of the inertia matrix, was originally designed to segment a single artery in MRA images. The modifications are primarily aimed at addressing the specificities of CT images and the bifurcations. The algorithms implemented in this new version are classified into two levels. 1. The low-level processing (filtering of noise and directional artifacts, enhancement and pre-segmentation) to improve the quality of the image and to pre-segment it. These techniques are based on a priori information about noise, artifacts and typical gray levels ranges of lumen, background and calcifications. 2. The high-level processing to extract the centerline of the artery, to segment the lumen and to quantify the stenosis. At this level, we apply a priori knowledge of shape and anatomy of vascular structures. The method was evaluated on 31 datasets from the carotid lumen segmentation and stenosis grading grand challenge 2009. The segmentation results obtained an average of 80:4% dice similarity score, compared to reference segmentation, and the mean stenosis quantification error was 14.4%.

  20. Emphasis of spatial cues in the temporal fine structure during the rising segments of amplitude-modulated sounds

    Science.gov (United States)

    Dietz, Mathias; Marquardt, Torsten; Salminen, Nelli H.; McAlpine, David

    2013-01-01

    The ability to locate the direction of a target sound in a background of competing sources is critical to the survival of many species and important for human communication. Nevertheless, brain mechanisms that provide for such accurate localization abilities remain poorly understood. In particular, it remains unclear how the auditory brain is able to extract reliable spatial information directly from the source when competing sounds and reflections dominate all but the earliest moments of the sound wave reaching each ear. We developed a stimulus mimicking the mutual relationship of sound amplitude and binaural cues, characteristic to reverberant speech. This stimulus, named amplitude modulated binaural beat, allows for a parametric and isolated change of modulation frequency and phase relations. Employing magnetoencephalography and psychoacoustics it is demonstrated that the auditory brain uses binaural information in the stimulus fine structure only during the rising portion of each modulation cycle, rendering spatial information recoverable in an otherwise unlocalizable sound. The data suggest that amplitude modulation provides a means of “glimpsing” low-frequency spatial cues in a manner that benefits listening in noisy or reverberant environments. PMID:23980161

  1. On the Development and Use of Large Chemical Similarity Networks, Informatics Best Practices and Novel Chemical Descriptors Towards Materials Quantitative Structure Property Relationships

    Science.gov (United States)

    Krein, Michael

    After decades of development and use in a variety of application areas, Quantitative Structure Property Relationships (QSPRs) and related descriptor-based statistical learning methods have achieved a level of infamy due to their misuse. The field is rife with past examples of overtrained models, overoptimistic performance assessment, and outright cheating in the form of explicitly removing data to fit models. These actions do not serve the community well, nor are they beneficial to future predictions based on established models. In practice, in order to select combinations of descriptors and machine learning methods that might work best, one must consider the nature and size of the training and test datasets, be aware of existing hypotheses about the data, and resist the temptation to bias structure representation and modeling to explicitly fit the hypotheses. The definition and application of these best practices is important for obtaining actionable modeling outcomes, and for setting user expectations of modeling accuracy when predicting the endpoint values of unknowns. A wide variety of statistical learning approaches, descriptor types, and model validation strategies are explored herein, with the goals of helping end users understand the factors involved in creating and using QSPR models effectively, and to better understand relationships within the data, especially by looking at the problem space from multiple perspectives. Molecular relationships are commonly envisioned in a continuous high-dimensional space of numerical descriptors, referred to as chemistry space. Descriptor and similarity metric choice influence the partitioning of this space into regions corresponding to local structural similarity. These regions, known as domains of applicability, are most likely to be successfully modeled by a QSPR. In Chapter 2, the network topology and scaling relationships of several chemistry spaces are thoroughly investigated. Chemistry spaces studied include the

  2. Automatic segmentation of mandible in panoramic x-ray.

    Science.gov (United States)

    Abdi, Amir Hossein; Kasaei, Shohreh; Mehdizadeh, Mojdeh

    2015-10-01

    As the panoramic x-ray is the most common extraoral radiography in dentistry, segmentation of its anatomical structures facilitates diagnosis and registration of dental records. This study presents a fast and accurate method for automatic segmentation of mandible in panoramic x-rays. In the proposed four-step algorithm, a superior border is extracted through horizontal integral projections. A modified Canny edge detector accompanied by morphological operators extracts the inferior border of the mandible body. The exterior borders of ramuses are extracted through a contour tracing method based on the average model of mandible. The best-matched template is fetched from the atlas of mandibles to complete the contour of left and right processes. The algorithm was tested on a set of 95 panoramic x-rays. Evaluating the results against manual segmentations of three expert dentists showed that the method is robust. It achieved an average performance of [Formula: see text] in Dice similarity, specificity, and sensitivity.

  3. Construction of patient specific atlases from locally most similar anatomical pieces

    Science.gov (United States)

    Ramus, Liliane; Commowick, Olivier; Malandain, Grégoire

    2010-01-01

    Radiotherapy planning requires accurate delineations of the critical structures. To avoid manual contouring, atlas-based segmentation can be used to get automatic delineations. However, the results strongly depend on the chosen atlas, especially for the head and neck region where the anatomical variability is high. To address this problem, atlases adapted to the patient’s anatomy may allow for a better registration, and already showed an improvement in segmentation accuracy. However, building such atlases requires the definition of a criterion to select among a database the images that are the most similar to the patient. Moreover, the inter-expert variability of manual contouring may be high, and therefore bias the segmentation if selecting only one image for each region. To tackle these issues, we present an original method to design a piecewise most similar atlas. Given a query image, we propose an efficient criterion to select for each anatomical region the K most similar images among a database by considering local volume variations possibly induced by the tumor. Then, we present a new approach to combine the K images selected for each region into a piecewise most similar template. Our results obtained with 105 CT images of the head and neck show that our method reduces the over-segmentation seen with an average atlas while being robust to inter-expert manual segmentation variability. PMID:20879395

  4. Amplified DNAs in laboratory stocks of Leishmania tarentolae: extrachromosomal circles structurally and functionally similar to the inverted-H-region amplification of methotrexate-resistant Leishmania major

    International Nuclear Information System (INIS)

    Petrillo-Peixoto, M.L.; Beverley, S.M.

    1988-01-01

    We describe the structure of amplified DNA that was discovered in two laboratory stocks of the protozoan parasite Leishmania tarentolae. Restriction mapping and molecular cloning revealed that a region of 42 kilobases was amplified 8- to 30-fold in these lines. Southern blot analyses of digested DNAs or chromosomes separated by pulsed-field electrophoresis showed that the amplified DNA corresponded to the H region, a locus defined originally by its amplification in methotrexate-resistant Leishmania major. Similarities between the amplified DNA of the two species included (i) extensive cross-hybridization; (ii) approximate conservation of sequence order; (iii) extrachromosomal localization; (iv) an overall inverted, head-to-head configuration as a circular 140-kilobase tetrameric molecule; (v) two regions of DNA sequence rearrangement, each of which was closely associated with the two centers of the inverted repeats; (vi) association with methotrexate resistance; and (vii) phenotypically conservative amplification, in which the wild-type chromosomal arrangement was retained without apparent modification. Our data showed that amplified DNA mediating drug resistance arose in unselected L. tarentolae, although the pressures leading to apparently spontaneous amplification and maintenance of the H region are not known. The simple structure and limited extent of DNA amplified in these and other Leishmania lines suggests that the study of gene amplification in Leishmania spp. offers an attractive model system for the study of amplification in cultured mammalian cells and tumors. We also introduced a method for measuring the size of large circular DNAs, using gamma-irradiation to introduce limited double-strand breaks followed by sizing of the linear DNAs by pulsed-field electrophoresis

  5. Handwriting segmentation of unconstrained Oriya text

    Indian Academy of Sciences (India)

    Based on vertical projection profiles and structural features of Oriya characters, text lines are segmented into words. For character segmentation, at first, the isolated and connected (touching) characters in a word are detected. Using structural, topological and water reservoir concept-based features, characters of the word ...

  6. Segmental Colitis Complicating Diverticular Disease

    Directory of Open Access Journals (Sweden)

    Guido Ma Van Rosendaal

    1996-01-01

    Full Text Available Two cases of idiopathic colitis affecting the sigmoid colon in elderly patients with underlying diverticulosis are presented. Segmental resection has permitted close review of the histopathology in this syndrome which demonstrates considerable similarity to changes seen in idiopathic ulcerative colitis. The reported experience with this syndrome and its clinical features are reviewed.

  7. Extended local similarity analysis (eLSA) reveals unique associations between bacterial community structure and odor emission during pig carcasses decomposition.

    Science.gov (United States)

    Ki, Bo-Min; Ryu, Hee Wook; Cho, Kyung-Suk

    2018-02-22

    Soil burial and composting methods have been widely used for the disposal of pig carcasses. The relationship between bacterial community structure and odor emission was examined using extended local similarity analysis (eLSA) during the degradation of pig carcasses in soil and compost. In soil, Hyphomicrobium, Niastella, Rhodanobacter, Polaromonas, Dokdonella and Mesorhizobium were associated with the emission of sulfur-containing odors such as hydrogen sulfide, methyl mercaptan and dimethyl disulfide. Sphingomonas, Rhodanobacter, Mesorhizobium, Dokdonella, Leucobacter and Truepera were associated with the emission of nitrogen-containing odors including ammonia and trimetylamine. In compost, however, Carnobacteriaceae, Lachnospiaceae and Clostridiales were highly correlated with the emission of sulfur-containing odors, while Rumincoccaceae was associated with the emission of nitrogen-containing odors. The emission of organic acids was closely related to Massilia, Sphaerobacter and Bradyrhizobiaceae in soil, but to Actinobacteria, Sporacetigenium, Micromonosporaceae and Solirubrobacteriales in compost. This study suggests that network analysis using eLSA is a useful strategy for exploring the mechanisms of odor emission during biodegradation of pig carcasses.

  8. RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins

    International Nuclear Information System (INIS)

    Hoffman, D.W.; Query, C.C.; Golden, B.L.; White, S.W.; Keene, J.D.

    1991-01-01

    An RNA recognition motif (RRM) of ∼80 amino acids constitutes the core of RNA-binding domains found in a large family of proteins involved in RNA processing. The U1 RNA-binding domain of the A protein component of the human U1 small nuclear ribonucleoprotein (RNP), which encompasses the RRM sequence, was analyzed by using NMR spectroscopy. The domain of the A protein is a highly stable monomer in solution consisting of four antiparallel β-strands and two α-helices. The highly conserved RNP1 and RNP2 consensus sequences, containing residues previously suggested to be involved in nucleic acid binding, are juxtaposed in adjacent β-strands. Conserved aromatic side chains that are critical for RNA binding are clustered on the surface to the molecule adjacent to a variable loop that influences recognition of specific RNA sequences. The secondary structure and topology of the RRM are similar to those of ribosomal proteins L12 and L30, suggesting a distant evolutionary relationship between these two types of RNA-associated proteins

  9. Kinetic and Thermodynamic Rationale for SAHA Being a Preferential Human HDAC8 Inhibitor as Compared to the Structurally Similar Ligand, TSA

    Science.gov (United States)

    Singh, Raushan K.; Lall, Naveena; Leedahl, Travis S.; McGillivray, Abigail; Mandal, Tanmay; Haldar, Manas; Mallik, Sanku; Cook, Gregory; Srivastava, D.K.

    2013-01-01

    Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, Suberoylanilide hydroxamic acid (SAHA) has been approved by the FDA for treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, Trichostatin A (TSA), which has a higher in vitro inhibitory-potency against HDAC8, reportedly shows a poor efficacy in clinical settings. In order to gain the molecular insight into the above discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA to the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both the inhibitors to the enzyme showed the biphasic profiles, which represented an initial encounter of enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with the above inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step; which is solely contributed by entropic changes. The standard binding-enthalpy (ΔH0) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2–3 kcal/mol higher as compared to TSA. The experimental data presented herein suggests that SAHA serves as a preferential (target-specific/selective) HDAC8 inhibitor as compared to TSA. Arguments are presented that the detailed kinetic and thermodynamic studies may guide in the rational design of HDAC inhibitors as therapeutic agents. PMID:24079912

  10. Rhythm-based segmentation of Popular Chinese Music

    DEFF Research Database (Denmark)

    Jensen, Karl Kristoffer

    2005-01-01

    We present a new method to segment popular music based on rhythm. By computing a shortest path based on the self-similarity matrix calculated from a model of rhythm, segmenting boundaries are found along the di- agonal of the matrix. The cost of a new segment is opti- mized by matching manual...... and automatic segment boundaries. We compile a small song database of 21 randomly selected popular Chinese songs which come from Chinese Mainland, Taiwan and Hong Kong. The segmenting results on the small corpus show that 78% manual segmentation points are detected and 74% auto- matic segmentation points...

  11. Segmentation of hepatic artery in multi-phase liver CT using directional dilation and connectivity analysis

    Science.gov (United States)

    Wang, Lei; Schnurr, Alena-Kathrin; Zidowitz, Stephan; Georgii, Joachim; Zhao, Yue; Razavi, Mohammad; Schwier, Michael; Hahn, Horst K.; Hansen, Christian

    2016-03-01

    Segmentation of hepatic arteries in multi-phase computed tomography (CT) images is indispensable in liver surgery planning. During image acquisition, the hepatic artery is enhanced by the injection of contrast agent. The enhanced signals are often not stably acquired due to non-optimal contrast timing. Other vascular structure, such as hepatic vein or portal vein, can be enhanced as well in the arterial phase, which can adversely affect the segmentation results. Furthermore, the arteries might suffer from partial volume effects due to their small diameter. To overcome these difficulties, we propose a framework for robust hepatic artery segmentation requiring a minimal amount of user interaction. First, an efficient multi-scale Hessian-based vesselness filter is applied on the artery phase CT image, aiming to enhance vessel structures with specified diameter range. Second, the vesselness response is processed using a Bayesian classifier to identify the most probable vessel structures. Considering the vesselness filter normally performs not ideally on the vessel bifurcations or the segments corrupted by noise, two vessel-reconnection techniques are proposed. The first technique uses a directional morphological operator to dilate vessel segments along their centerline directions, attempting to fill the gap between broken vascular segments. The second technique analyzes the connectivity of vessel segments and reconnects disconnected segments and branches. Finally, a 3D vessel tree is reconstructed. The algorithm has been evaluated using 18 CT images of the liver. To quantitatively measure the similarities between segmented and reference vessel trees, the skeleton coverage and mean symmetric distance are calculated to quantify the agreement between reference and segmented vessel skeletons, resulting in an average of 0:55+/-0:27 and 12:7+/-7:9 mm (mean standard deviation), respectively.

  12. Structure and strength at the bonding interface of a titanium-segmented polyurethane composite through 3-(trimethoxysilyl) propyl methacrylate for artificial organs.

    Science.gov (United States)

    Sakamoto, Harumi; Doi, Hisashi; Kobayashi, Equo; Yoneyama, Takayuki; Suzuki, Yoshiaki; Hanawa, Takao

    2007-07-01

    The objective of this study was to investigate the structure and strength at the bonding interface of a titanium (Ti)-segmented polyurethane (SPU) composite through (3-trimethoxysilyl) propyl methacrylate (gamma-MPS) for artificial organs. The effects of the thickness of the gamma-MPS layer on the shear bonding strength between Ti and SPU were investigated. Ti disks were immersed in various concentrations of gamma-MPS solutions for several immersion times. The depth profiles of elements and the thickness of the gamma-MPS layer were determined by glow discharge optical emission spectroscopy and ellipsometry, respectively. The bonding stress at the Ti/gamma-MPS/SPU interface was evaluated with a shear bonding test. Furthermore, the fractured surface of a Ti-SPU composite was observed by optical microscopy and characterized using X-ray photoelectron spectroscopy. Consequently, the thickness of the gamma-MPS layer was controlled by the concentration of the gamma-MPS solution and immersion time. The shear bonding stress at the interface increased with the increase of the thickness of the gamma-MPS layer. Therefore, the control of the thickness of the gamma-MPS layer is significant to increase the shear bonding stress at the Ti/gamma-MPS/SPU interface. These results are significant to create composites for artificial organs consisting of other metals and polymers. Copyright 2007 Wiley Periodicals, Inc.

  13. Emphasis of spatial cues in the temporal fine structure during the rising segments of amplitude-modulated sounds II: single-neuron recordings

    Science.gov (United States)

    Marquardt, Torsten; Stange, Annette; Pecka, Michael; Grothe, Benedikt; McAlpine, David

    2014-01-01

    Recently, with the use of an amplitude-modulated binaural beat (AMBB), in which sound amplitude and interaural-phase difference (IPD) were modulated with a fixed mutual relationship (Dietz et al. 2013b), we demonstrated that the human auditory system uses interaural timing differences in the temporal fine structure of modulated sounds only during the rising portion of each modulation cycle. However, the degree to which peripheral or central mechanisms contribute to the observed strong dominance of the rising slope remains to be determined. Here, by recording responses of single neurons in the medial superior olive (MSO) of anesthetized gerbils and in the inferior colliculus (IC) of anesthetized guinea pigs to AMBBs, we report a correlation between the position within the amplitude-modulation (AM) cycle generating the maximum response rate and the position at which the instantaneous IPD dominates the total neural response. The IPD during the rising segment dominates the total response in 78% of MSO neurons and 69% of IC neurons, with responses of the remaining neurons predominantly coding the IPD around the modulation maximum. The observed diversity of dominance regions within the AM cycle, especially in the IC, and its comparison with the human behavioral data suggest that only the subpopulation of neurons with rising slope dominance codes the sound-source location in complex listening conditions. A comparison of two models to account for the data suggests that emphasis on IPDs during the rising slope of the AM cycle depends on adaptation processes occurring before binaural interaction. PMID:24554782

  14. Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments

    DEFF Research Database (Denmark)

    Engberg, J; Nielsen, Henrik; Lenaers, G

    1990-01-01

    We have determined the nucleotide sequence of the 26S large subunit (LSU) rRNA genes for two Tetrahymena species, T. thermophila and T. pyriformis. The inferred rRNA sequences are presented in their most probable secondary structures based on compensatory mutations, energy, and conservation crite...

  15. Estimating the surface layer refractive index structure constant over snow and sea ice using Monin-Obukhov similarity theory with a mesoscale atmospheric model.

    Science.gov (United States)

    Qing, Chun; Wu, Xiaoqing; Huang, Honghua; Tian, Qiguo; Zhu, Wenyue; Rao, Ruizhong; Li, Xuebin

    2016-09-05

    Since systematic direct measurements of refractive index structure constant ( Cn2) for many climates and seasons are not available, an indirect approach is developed in which Cn2 is estimated from the mesoscale atmospheric model outputs. In previous work, we have presented an approach that a state-of-the-art mesoscale atmospheric model called Weather Research and Forecasting (WRF) model coupled with Monin-Obukhov Similarity (MOS) theory which can be used to estimate surface layer Cn2 over the ocean. Here this paper is focused on surface layer Cn2 over snow and sea ice, which is the extending of estimating surface layer Cn2 utilizing WRF model for ground-based optical application requirements. This powerful approach is validated against the corresponding 9-day Cn2 data from a field campaign of the 30th Chinese National Antarctic Research Expedition (CHINARE). We employ several statistical operators to assess how this approach performs. Besides, we present an independent analysis of this approach performance using the contingency tables. Such a method permits us to provide supplementary key information with respect to statistical operators. These methods make our analysis more robust and permit us to confirm the excellent performances of this approach. The reasonably good agreement in trend and magnitude is found between estimated values and measurements overall, and the estimated Cn2 values are even better than the ones obtained by this approach over the ocean surface layer. The encouraging performance of this approach has a concrete practical implementation of ground-based optical applications over snow and sea ice.

  16. Segmentally structured disk triboelectric nanogenerator

    Science.gov (United States)

    Wang, Zhong Lin; Zhu, Guang; Lin, Long; Wang, Sihong; Chen, Jun

    2016-11-01

    A generator includes a disc shaped first unit, a disc shaped second unit and an axle. The first unit includes a substrate layer, a double complementary electrode layer and an electrification material layer. The electrode layer includes a first electrode member and a second electrode member. The first electrode member includes evenly spaced apart first electrode legs extending inwardly. The second electrode member is complementary in shape to the first electrode member. The legs of the first electrode member and the second electrode member are interleaved with each other and define a continuous gap therebetween. The electrification material includes a first material that is in a first position on the triboelectric series. The second unit defines elongated openings and corresponding elongated leg portions, and includes a second material that is at a second position on a triboelectric series, different than the first position.

  17. Segmentation of corpus callosum using diffusion tensor imaging: validation in patients with glioblastoma

    International Nuclear Information System (INIS)

    Nazem-Zadeh, Mohammad-Reza; Saksena, Sona; Babajani-Fermi, Abbas; Jiang, Quan; Soltanian-Zadeh, Hamid; Rosenblum, Mark; Mikkelsen, Tom; Jain, Rajan

    2012-01-01

    This paper presents a three-dimensional (3D) method for segmenting corpus callosum in normal subjects and brain cancer patients with glioblastoma. Nineteen patients with histologically confirmed treatment naïve glioblastoma and eleven normal control subjects underwent DTI on a 3T scanner. Based on the information inherent in diffusion tensors, a similarity measure was proposed and used in the proposed algorithm. In this algorithm, diffusion pattern of corpus callosum was used as prior information. Subsequently, corpus callosum was automatically divided into Witelson subdivisions. We simulated the potential rotation of corpus callosum under tumor pressure and studied the reproducibility of the proposed segmentation method in such cases. Dice coefficients, estimated to compare automatic and manual segmentation results for Witelson subdivisions, ranged from 94% to 98% for control subjects and from 81% to 95% for tumor patients, illustrating closeness of automatic and manual segmentations. Studying the effect of corpus callosum rotation by different Euler angles showed that although segmentation results were more sensitive to azimuth and elevation than skew, rotations caused by brain tumors do not have major effects on the segmentation results. The proposed method and similarity measure segment corpus callosum by propagating a hyper-surface inside the structure (resulting in high sensitivity), without penetrating into neighboring fiber bundles (resulting in high specificity)

  18. Probabilistic Segmentation of Folk Music Recordings

    Directory of Open Access Journals (Sweden)

    Ciril Bohak

    2016-01-01

    Full Text Available The paper presents a novel method for automatic segmentation of folk music field recordings. The method is based on a distance measure that uses dynamic time warping to cope with tempo variations and a dynamic programming approach to handle pitch drifting for finding similarities and estimating the length of repeating segment. A probabilistic framework based on HMM is used to find segment boundaries, searching for optimal match between the expected segment length, between-segment similarities, and likely locations of segment beginnings. Evaluation of several current state-of-the-art approaches for segmentation of commercial music is presented and their weaknesses when dealing with folk music are exposed, such as intolerance to pitch drift and variable tempo. The proposed method is evaluated and its performance analyzed on a collection of 206 folk songs of different ensemble types: solo, two- and three-voiced, choir, instrumental, and instrumental with singing. It outperforms current commercial music segmentation methods for noninstrumental music and is on a par with the best for instrumental recordings. The method is also comparable to a more specialized method for segmentation of solo singing folk music recordings.

  19. Best practices for preparing vessel internals segmentation projects

    International Nuclear Information System (INIS)

    Boucau, Joseph; Segerud, Per; Sanchez, Moises

    2016-01-01

    Westinghouse has been involved in reactor internals segmentation activities in the U.S. and Europe for 30 years. Westinghouse completed in 2015 the segmentation of the reactor vessel and reactor vessel internals at the Jose Cabrera nuclear power plant in Spain and a similar project is on-going at Chooz A in France. For all reactor dismantling projects, it is essential that all activities are thoroughly planned and discussed up-front together with the customer. Detailed planning is crucial for achieving a successful project. One key activity in the preparation phase is the 'Segmentation and Packaging Plan' that documents the sequential steps required to segment, separate, and package each individual component, based on an activation analysis and component characterization study. Detailed procedures and specialized rigging equipment have to be developed to provide safeguards for preventing certain identified risks. The preparatory work can include some plant civil structure modifications for making the segmentation work easier and safer. Some original plant equipment is sometimes not suitable enough and need to be replaced. Before going to the site, testing and qualification are performed on full scale mock-ups in a specially designed pool for segmentation purposes. The mockup testing is an important step in order to verify the function of the equipment and minimize risk on site. This paper is describing the typical activities needed for preparing the reactor internals segmentation activities using under water mechanical cutting techniques. It provides experiences and lessons learned that Westinghouse has collected from its recent projects and that will be applied for the new awarded projects. (authors)

  20. Structure of the 1906 near-surface rupture zone of the San Andreas Fault, San Francisco Peninsula segment, near Woodside, California

    Science.gov (United States)

    Rosa, C.M.; Catchings, R.D.; Rymer, M.J.; Grove, Karen; Goldman, M.R.

    2016-07-08

    High-resolution seismic-reflection and refraction images of the 1906 surface rupture zone of the San Andreas Fault near Woodside, California reveal evidence for one or more additional near-surface (within about 3 meters [m] depth) fault strands within about 25 m of the 1906 surface rupture. The 1906 surface rupture above the groundwater table (vadose zone) has been observed in paleoseismic trenches that coincide with our seismic profile and is seismically characterized by a discrete zone of low P-wave velocities (Vp), low S-wave velocities (Vs), high Vp/Vs ratios, and high Poisson’s ratios. A second near-surface fault strand, located about 17 m to the southwest of the 1906 surface rupture, is inferred by similar seismic anomalies. Between these two near-surface fault strands and below 5 m depth, we observed a near-vertical fault strand characterized by a zone of high Vp, low Vs, high Vp/Vs ratios, and high Poisson’s ratios on refraction tomography images and near-vertical diffractions on seismic-reflection images. This prominent subsurface zone of seismic anomalies is laterally offset from the 1906 surface rupture by about 8 m and likely represents the active main (long-term) strand of the San Andreas Fault at 5 to 10 m depth. Geometries of the near-surface and subsurface (about 5 to 10 m depth) fault zone suggest that the 1906 surface rupture dips southwestward to join the main strand of the San Andreas Fault at about 5 to 10 m below the surface. The 1906 surface rupture forms a prominent groundwater barrier in the upper 3 to 5 m, but our interpreted secondary near-surface fault strand to the southwest forms a weaker barrier, suggesting that there has been less or less-recent near-surface slip on that strand. At about 6 m depth, the main strand of the San Andreas Fault consists of water-saturated blue clay (collected from a hand-augered borehole), which is similar to deeply weathered serpentinite observed within the main strand of the San Andreas Fault at

  1. Multiple Segmentation of Image Stacks

    DEFF Research Database (Denmark)

    Smets, Jonathan; Jaeger, Manfred

    2014-01-01

    We propose a method for the simultaneous construction of multiple image segmentations by combining a recently proposed “convolution of mixtures of Gaussians” model with a multi-layer hidden Markov random field structure. The resulting method constructs for a single image several, alternative...

  2. Segmented trapped vortex cavity

    Science.gov (United States)

    Grammel, Jr., Leonard Paul (Inventor); Pennekamp, David Lance (Inventor); Winslow, Jr., Ralph Henry (Inventor)

    2010-01-01

    An annular trapped vortex cavity assembly segment comprising includes a cavity forward wall, a cavity aft wall, and a cavity radially outer wall there between defining a cavity segment therein. A cavity opening extends between the forward and aft walls at a radially inner end of the assembly segment. Radially spaced apart pluralities of air injection first and second holes extend through the forward and aft walls respectively. The segment may include first and second expansion joint features at distal first and second ends respectively of the segment. The segment may include a forward subcomponent including the cavity forward wall attached to an aft subcomponent including the cavity aft wall. The forward and aft subcomponents include forward and aft portions of the cavity radially outer wall respectively. A ring of the segments may be circumferentially disposed about an axis to form an annular segmented vortex cavity assembly.

  3. Pavement management segment consolidation

    Science.gov (United States)

    1998-01-01

    Dividing roads into "homogeneous" segments has been a major problem for all areas of highway engineering. SDDOT uses Deighton Associates Limited software, dTIMS, to analyze life-cycle costs for various rehabilitation strategies on each segment of roa...

  4. Aging and the segmentation of narrative film.

    Science.gov (United States)

    Kurby, Christopher A; Asiala, Lillian K E; Mills, Steven R

    2014-01-01

    The perception of event structure in continuous activity is important for everyday comprehension. Although the segmentation of experience into events is a normal concomitant of perceptual processing, previous research has shown age differences in the ability to perceive structure in naturalistic activity, such as a movie of someone washing a car. However, past research has also shown that older adults have a preserved ability to comprehend events in narrative text, which suggests that narrative may improve the event processing of older adults. This study tested whether there are age differences in event segmentation at the intersection of continuous activity and narrative: narrative film. Younger and older adults watched and segmented a narrative film, The Red Balloon, into coarse and fine events. Changes in situational features, such as changes in characters, goals, and objects predicted segmentation. Analyses revealed little age-difference in segmentation behavior. This suggests the possibility that narrative structure supports event understanding for older adults.

  5. Speaker segmentation and clustering

    OpenAIRE

    Kotti, M; Moschou, V; Kotropoulos, C

    2008-01-01

    07.08.13 KB. Ok to add the accepted version to Spiral, Elsevier says ok whlile mandate not enforced. This survey focuses on two challenging speech processing topics, namely: speaker segmentation and speaker clustering. Speaker segmentation aims at finding speaker change points in an audio stream, whereas speaker clustering aims at grouping speech segments based on speaker characteristics. Model-based, metric-based, and hybrid speaker segmentation algorithms are reviewed. Concerning speaker...

  6. Spinal segmental dysgenesis

    Directory of Open Access Journals (Sweden)

    N Mahomed

    2009-06-01

    Full Text Available Spinal segmental dysgenesis is a rare congenital spinal abnormality , seen in neonates and infants in which a segment of the spine and spinal cord fails to develop normally . The condition is segmental with normal vertebrae above and below the malformation. This condition is commonly associated with various abnormalities that affect the heart, genitourinary, gastrointestinal tract and skeletal system. We report two cases of spinal segmental dysgenesis and the associated abnormalities.

  7. Document segmentation via oblique cuts

    Science.gov (United States)

    Svendsen, Jeremy; Branzan-Albu, Alexandra

    2013-01-01

    This paper presents a novel solution for the layout segmentation of graphical elements in Business Intelligence documents. We propose a generalization of the recursive X-Y cut algorithm, which allows for cutting along arbitrary oblique directions. An intermediate processing step consisting of line and solid region removal is also necessary due to presence of decorative elements. The output of the proposed segmentation is a hierarchical structure which allows for the identification of primitives in pie and bar charts. The algorithm was tested on a database composed of charts from business documents. Results are very promising.

  8. A NEW APPROACH TO SEGMENT HANDWRITTEN DIGITS

    NARCIS (Netherlands)

    Oliveira, L.S.; Lethelier, E.; Bortolozzi, F.; Sabourin, R.

    2004-01-01

    This article presents a new segmentation approach applied to unconstrained handwritten digits. The novelty of the proposed algorithm is based on the combination of two types of structural features in order to provide the best segmentation path between connected entities. In this article, we first

  9. Automatic Melody Segmentation

    NARCIS (Netherlands)

    Rodríguez López, Marcelo

    2016-01-01

    The work presented in this dissertation investigates music segmentation. In the field of Musicology, segmentation refers to a score analysis technique, whereby notated pieces or passages of these pieces are divided into “units” referred to as sections, periods, phrases, and so on. Segmentation

  10. Fully-automated approach to hippocampus segmentation using a graph-cuts algorithm combined with atlas-based segmentation and morphological opening.

    Science.gov (United States)

    Kwak, Kichang; Yoon, Uicheul; Lee, Dong-Kyun; Kim, Geon Ha; Seo, Sang Won; Na, Duk L; Shim, Hack-Joon; Lee, Jong-Min

    2013-09-01

    The hippocampus has been known to be an important structure as a biomarker for Alzheimer's disease (AD) and other neurological and psychiatric diseases. However, it requires accurate, robust and reproducible delineation of hippocampal structures. In this study, an automated hippocampal segmentation method based on a graph-cuts algorithm combined with atlas-based segmentation and morphological opening was proposed. First of all, the atlas-based segmentation was applied to define initial hippocampal region for a priori information on graph-cuts. The definition of initial seeds was further elaborated by incorporating estimation of partial volume probabilities at each voxel. Finally, morphological opening was applied to reduce false positive of the result processed by graph-cuts. In the experiments with twenty-seven healthy normal subjects, the proposed method showed more reliable results (similarity index=0.81±0.03) than the conventional atlas-based segmentation method (0.72±0.04). Also as for segmentation accuracy which is measured in terms of the ratios of false positive and false negative, the proposed method (precision=0.76±0.04, recall=0.86±0.05) produced lower ratios than the conventional methods (0.73±0.05, 0.72±0.06) demonstrating its plausibility for accurate, robust and reliable segmentation of hippocampus. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Automatic segmentation of brain MRIs and mapping neuroanatomy across the human lifespan

    Science.gov (United States)

    Keihaninejad, Shiva; Heckemann, Rolf A.; Gousias, Ioannis S.; Rueckert, Daniel; Aljabar, Paul; Hajnal, Joseph V.; Hammers, Alexander

    2009-02-01

    A robust model for the automatic segmentation of human brain images into anatomically defined regions across the human lifespan would be highly desirable, but such structural segmentations of brain MRI are challenging due to age-related changes. We have developed a new method, based on established algorithms for automatic segmentation of young adults' brains. We used prior information from 30 anatomical atlases, which had been manually segmented into 83 anatomical structures. Target MRIs came from 80 subjects (~12 individuals/decade) from 20 to 90 years, with equal numbers of men, women; data from two different scanners (1.5T, 3T), using the IXI database. Each of the adult atlases was registered to each target MR image. By using additional information from segmentation into tissue classes (GM, WM and CSF) to initialise the warping based on label consistency similarity before feeding this into the previous normalised mutual information non-rigid registration, the registration became robust enough to accommodate atrophy and ventricular enlargement with age. The final segmentation was obtained by combination of the 30 propagated atlases using decision fusion. Kernel smoothing was used for modelling the structural volume changes with aging. Example linear correlation coefficients with age were, for lateral ventricular volume, rmale=0.76, rfemale=0.58 and, for hippocampal volume, rmale=-0.6, rfemale=-0.4 (allρ<0.01).

  12. A quality and efficiency analysis of the IMFASTTM segmentation algorithm in head and neck 'step and shoot' IMRT treatments

    International Nuclear Information System (INIS)

    Potter, Larry D.; Chang, Sha X.; Cullip, Timothy J.; Siochi, Alfredo C.

    2002-01-01

    The performance of segmentation algorithms used in IMFAST for 'step and shoot' IMRT treatment delivery is evaluated for three head and neck clinical treatments of different optimization objectives. The segmentation uses the intensity maps generated by the in-house TPS PLANUNC using the index-dose minimization algorithm. The dose optimization objectives include PTV dose uniformity and dose volume histogram-specified critical structure sparing. The optimized continuous intensity maps were truncated into five and ten intensity levels and exported to IMFAST for MLC segments optimization. The MLC segments were imported back to PLUNC for dose optimization quality calculation. The five basic segmentation algorithms included in IMFAST were evaluated alone and in combination with either tongue and groove/match line correction or fluence correction or both. Two criteria were used in the evaluation: treatment efficiency represented by the total number of MLC segments and optimization quality represented by a clinically relevant optimization quality factor. We found that the treatment efficiency depends first on the number of intensity levels used in the intensity map and second the segmentation technique used. The standard optimal segmentation with fluence correction is a consistent good performer for all treatment plans studied. All segmentation techniques evaluated produced treatments with similar dose optimization quality values, especially when ten-level intensity maps are used

  13. Improving Brain Magnetic Resonance Image (MRI Segmentation via a Novel Algorithm based on Genetic and Regional Growth

    Directory of Open Access Journals (Sweden)

    Javadpour A.

    2016-06-01

    Full Text Available Background: Regarding the importance of right diagnosis in medical applications, various methods have been exploited for processing medical images solar. The method of segmentation is used to analyze anal to miscall structures in medical imaging. Objective: This study describes a new method for brain Magnetic Resonance Image (MRI segmentation via a novel algorithm based on genetic and regional growth. Methods: Among medical imaging methods, brains MRI segmentation is important due to high contrast of non-intrusive soft tissue and high spatial resolution. Size variations of brain tissues are often accompanied by various diseases such as Alzheimer’s disease. As our knowledge about the relation between various brain diseases and deviation of brain anatomy increases, MRI segmentation is exploited as the first step in early diagnosis. In this paper, regional growth method and auto-mate selection of initial points by genetic algorithm is used to introduce a new method for MRI segmentation. Primary pixels and similarity criterion are automatically by genetic algorithms to maximize the accuracy and validity in image segmentation. Results: By using genetic algorithms and defining the fixed function of image segmentation, the initial points for the algorithm were found. The proposed algorithms are applied to the images and results are manually selected by regional growth in which the initial points were compared. The results showed that the proposed algorithm could reduce segmentation error effectively. Conclusion: The study concluded that the proposed algorithm could reduce segmentation error effectively and help us to diagnose brain diseases.

  14. Track segment synthesis method for NTA film

    International Nuclear Information System (INIS)

    Kumazawa, Shigeru

    1980-03-01

    A method is presented for synthesizing track segments extracted from a gray-level digital picture of NTA film in automatic counting system. In order to detect each track in an arbitrary direction, even if it has some gaps, as a set of the track segments, the method links extracted segments along the track, in succession, to the linked track segments, according to whether each extracted segment bears a similarity of direction to the track or not and whether it is connected with the linked track segments or not. In the case of a large digital picture, the method is applied to each subpicture, which is a strip of the picture, and then concatenates subsets of track segments linked at each subpicture as a set of track segments belonging to a track. The method was applied to detecting tracks in various directions over the eight 364 x 40-pixel subpictures with the gray scale of 127/pixel (picture element) of the microphotograph of NTA film. It was proved to be able to synthesize track segments correctly for every track in the picture. (author)

  15. Influence of Second Language Proficiency and Syntactic Structure Similarities on the Sensitivity and Processing of English Passive Sentence in Late Chinese-English Bilinguists: An ERP Study

    Science.gov (United States)

    Chang, Xin; Wang, Pei

    2016-01-01

    To investigate the influence of L2 proficiency and syntactic similarity on English passive sentence processing, the present ERP study asked 40 late Chinese-English bilinguals (27 females and 13 males, mean age = 23.88) with high or intermediate L2 proficiency to read the sentences carefully and to indicate for each sentence whether or not it was…

  16. Supervised machine learning-based classification scheme to segment the brainstem on MRI in multicenter brain tumor treatment context.

    Science.gov (United States)

    Dolz, Jose; Laprie, Anne; Ken, Soléakhéna; Leroy, Henri-Arthur; Reyns, Nicolas; Massoptier, Laurent; Vermandel, Maximilien

    2016-01-01

    To constrain the risk of severe toxicity in radiotherapy and radiosurgery, precise volume delineation of organs at risk is required. This task is still manually performed, which is time-consuming and prone to observer variability. To address these issues, and as alternative to atlas-based segmentation methods, machine learning techniques, such as support vector machines (SVM), have been recently presented to segment subcortical structures on magnetic resonance images (MRI). SVM is proposed to segment the brainstem on MRI in multicenter brain cancer context. A dataset composed by 14 adult brain MRI scans is used to evaluate its performance. In addition to spatial and probabilistic information, five different image intensity values (IIVs) configurations are evaluated as features to train the SVM classifier. Segmentation accuracy is evaluated by computing the Dice similarity coefficient (DSC), absolute volumes difference (AVD) and percentage volume difference between automatic and manual contours. Mean DSC for all proposed IIVs configurations ranged from 0.89 to 0.90. Mean AVD values were below 1.5 cm(3), where the value for best performing IIVs configuration was 0.85 cm(3), representing an absolute mean difference of 3.99% with respect to the manual segmented volumes. Results suggest consistent volume estimation and high spatial similarity with respect to expert delineations. The proposed approach outperformed presented methods to segment the brainstem, not only in volume similarity metrics, but also in segmentation time. Preliminary results showed that the approach might be promising for adoption in clinical use.

  17. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  18. Green fluorescent protein (GFP color reporter gene visualizes parvovirus B19 non-structural segment 1 (NS1 transfected endothelial modification.

    Directory of Open Access Journals (Sweden)

    Thomas Wurster

    Full Text Available BACKGROUND: Human Parvovirus B19 (PVB19 has been associated with myocarditis putative due to endothelial infection. Whether PVB19 infects endothelial cells and causes a modification of endothelial function and inflammation and, thus, disturbance of microcirculation has not been elucidated and could not be visualized so far. METHODS AND FINDINGS: To examine the PVB19-induced endothelial modification, we used green fluorescent protein (GFP color reporter gene in the non-structural segment 1 (NS1 of PVB19. NS1-GFP-PVB19 or GFP plasmid as control were transfected in an endothelial-like cell line (ECV304. The endothelial surface expression of intercellular-adhesion molecule-1 (CD54/ICAM-1 and extracellular matrix metalloproteinase inducer (EMMPRIN/CD147 were evaluated by flow cytometry after NS-1-GFP or control-GFP transfection. To evaluate platelet adhesion on NS-1 transfected ECs, we performed a dynamic adhesion assay (flow chamber. NS-1 transfection causes endothelial activation and enhanced expression of ICAM-1 (CD54: mean ± standard deviation: NS1-GFP vs. control-GFP: 85.3 ± 11.2 vs. 61.6 ± 8.1; P<0.05 and induces endothelial expression of EMMPRIN/CD147 (CD147: mean ± SEM: NS1-GFP vs. control-GFP: 114 ± 15.3 vs. 80 ± 0.91; P<0.05 compared to control-GFP transfected cells. Dynamic adhesion assays showed that adhesion of platelets is significantly enhanced on NS1 transfected ECs when compared to control-GFP (P<0.05. The transfection of ECs was verified simultaneously through flow cytometry, immunofluorescence microscopy and polymerase chain reaction (PCR analysis. CONCLUSIONS: GFP color reporter gene shows transfection of ECs and may help to visualize NS1-PVB19 induced endothelial activation and platelet adhesion as well as an enhanced monocyte adhesion directly, providing in vitro evidence of possible microcirculatory dysfunction in PVB19-induced myocarditis and, thus, myocardial tissue damage.

  19. Multiple Scale Music Segmentation Using Rhythm, Timbre, and Harmony

    Directory of Open Access Journals (Sweden)

    Kristoffer Jensen

    2007-01-01

    Full Text Available The segmentation of music into intro-chorus-verse-outro, and similar segments, is a difficult topic. A method for performing automatic segmentation based on features related to rhythm, timbre, and harmony is presented, and compared, between the features and between the features and manual segmentation of a database of 48 songs. Standard information retrieval performance measures are used in the comparison, and it is shown that the timbre-related feature performs best.

  20. Moving Up from the Segment: A Comment on Aichert and Ziegler's Syllable Frequency and Syllable Structure in Apraxia of Speech, "Brain and Language," 88, 148-159, 2004

    Science.gov (United States)

    Varley, Rosemary; Whiteside, Sandra; Windsor, Fay; Fisher, Helen

    2006-01-01

    In a recent article, Aichert and Ziegler (2004) explore whether apraxia of speech (AOS) can be explained by disruption of the phonetic plans for high frequency syllables. This approach is a hybrid one, combining the notion of a mental syllabary with an explanation that the impairment in AOS results from reduced access to supra-segmental phonetic…

  1. Deformable M-Reps for 3D Medical Image Segmentation

    Science.gov (United States)

    Pizer, Stephen M.; Fletcher, P. Thomas; Joshi, Sarang; Thall, Andrew; Chen, James Z.; Fridman, Yonatan; Fritsch, Daniel S.; Gash, Graham; Glotzer, John M.; Jiroutek, Michael R.; Lu, Conglin; Muller, Keith E.; Tracton, Gregg; Yushkevich, Paul; Chaney, Edward L.

    2013-01-01

    M-reps (formerly called DSLs) are a multiscale medial means for modeling and rendering 3D solid geometry. They are particularly well suited to model anatomic objects and in particular to capture prior geometric information effectively in deformable models segmentation approaches. The representation is based on figural models, which define objects at coarse scale by a hierarchy of figures – each figure generally a slab representing a solid region and its boundary simultaneously. This paper focuses on the use of single figure models to segment objects of relatively simple structure. A single figure is a sheet of medial atoms, which is interpolated from the model formed by a net, i.e., a mesh or chain, of medial atoms (hence the name m-reps), each atom modeling a solid region via not only a position and a width but also a local figural frame giving figural directions and an object angle between opposing, corresponding positions on the boundary implied by the m-rep. The special capability of an m-rep is to provide spatial and orientational correspondence between an object in two different states of deformation. This ability is central to effective measurement of both geometric typicality and geometry to image match, the two terms of the objective function optimized in segmentation by deformable models. The other ability of m-reps central to effective segmentation is their ability to support segmentation at multiple levels of scale, with successively finer precision. Objects modeled by single figures are segmented first by a similarity transform augmented by object elongation, then by adjustment of each medial atom, and finally by displacing a dense sampling of the m-rep implied boundary. While these models and approaches also exist in 2D, we focus on 3D objects. The segmentation of the kidney from CT and the hippocampus from MRI serve as the major examples in this paper. The accuracy of segmentation as compared to manual, slice-by-slice segmentation is reported. PMID

  2. Automatic segmentation of male pelvic anatomy on computed tomography images: a comparison with multiple observers in the context of a multicentre clinical trial.

    Science.gov (United States)

    Geraghty, John P; Grogan, Garry; Ebert, Martin A

    2013-04-30

    This study investigates the variation in segmentation of several pelvic anatomical structures on computed tomography (CT) between multiple observers and a commercial automatic segmentation method, in the context of quality assurance and evaluation during a multicentre clinical trial. CT scans of two prostate cancer patients ('benchmarking cases'), one high risk (HR) and one intermediate risk (IR), were sent to multiple radiotherapy centres for segmentation of prostate, rectum and bladder structures according to the TROG 03.04 "RADAR" trial protocol definitions. The same structures were automatically segmented using iPlan software for the same two patients, allowing structures defined by automatic segmentation to be quantitatively compared with those defined by multiple observers. A sample of twenty trial patient datasets were also used to automatically generate anatomical structures for quantitative comparison with structures defined by individual observers for the same datasets. There was considerable agreement amongst all observers and automatic segmentation of the benchmarking cases for bladder (mean spatial variations segmenting a prostate with considerably more volume (mean +113.3%) than that automatically segmented. Similar results were seen across the twenty sample datasets, with disagreement between iPlan and observers dominant at the prostatic apex and superior part of the rectum, which is consistent with observations made during quality assurance reviews during the trial. This study has demonstrated quantitative analysis for comparison of multi-observer segmentation studies. For automatic segmentation algorithms based on image-registration as in iPlan, it is apparent that agreement between observer and automatic segmentation will be a function of patient-specific image characteristics, particularly for anatomy with poor contrast definition. For this reason, it is suggested that automatic registration based on transformation of a single reference dataset

  3. A coarse-to-fine approach for pericardial effusion localization and segmentation in chest CT scans

    Science.gov (United States)

    Liu, Jiamin; Chellamuthu, Karthik; Lu, Le; Bagheri, Mohammadhadi; Summers, Ronald M.

    2018-02-01

    Pericardial effusion on CT scans demonstrates very high shape and volume variability and very low contrast to adjacent structures. This inhibits traditional automated segmentation methods from achieving high accuracies. Deep neural networks have been widely used for image segmentation in CT scans. In this work, we present a two-stage method for pericardial effusion localization and segmentation. For the first step, we localize the pericardial area from the entire CT volume, providing a reliable bounding box for the more refined segmentation step. A coarse-scaled holistically-nested convolutional networks (HNN) model is trained on entire CT volume. The resulting HNN per-pixel probability maps are then threshold to produce a bounding box covering the pericardial area. For the second step, a fine-scaled HNN model is trained only on the bounding box region for effusion segmentation to reduce the background distraction. Quantitative evaluation is performed on a dataset of 25 CT scans of patient (1206 images) with pericardial effusion. The segmentation accuracy of our two-stage method, measured by Dice Similarity Coefficient (DSC), is 75.59+/-12.04%, which is significantly better than the segmentation accuracy (62.74+/-15.20%) of only using the coarse-scaled HNN model.

  4. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets....... Our results show that the proposed functions work better than other methods proposed in the literature....

  5. Phoneme Similarity and Confusability

    Science.gov (United States)

    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…

  6. Box-counting dimension revisited: presenting an efficient method of minimising quantisation error and an assessment of the self-similarity of structural root systems

    Directory of Open Access Journals (Sweden)

    Martin eBouda

    2016-02-01

    Full Text Available Fractal dimension (FD, estimated by box-counting, is a metric used to characterise plant anatomical complexity or space-filling characteristic for a variety of purposes. The vast majority of published studies fail to evaluate the assumption of statistical self-similarity, which underpins the validity of the procedure. The box-counting procedure is also subject to error arising from arbitrary grid placement, known as quantisation error (QE, which is strictly positive and varies as a function of scale, making it problematic for the procedure's slope estimation step. Previous studies either ignore QE or employ inefficient brute-force grid translations to reduce it. The goals of this study were to characterise the effect of QE due to translation and rotation on FD estimates, to provide an efficient method of reducing QE, and to evaluate the assumption of statistical self-similarity of coarse root datasets typical of those used in recent trait studies. Coarse root systems of 36 shrubs were digitised in 3D and subjected to box-counts. A pattern search algorithm was used to minimise QE by optimising grid placement and its efficiency was compared to the brute force method. The degree of statistical self-similarity was evaluated using linear regression residuals and local slope estimates.QE due to both grid position and orientation was a significant source of error in FD estimates, but pattern search provided an efficient means of minimising it. Pattern search had higher initial computational cost but converged on lower error values more efficiently than the commonly employed brute force method. Our representations of coarse root system digitisations did not exhibit details over a sufficient range of scales to be considered statistically self-similar and informatively approximated as fractals, suggesting a lack of sufficient ramification of the coarse root systems for reiteration to be thought of as a dominant force in their development. FD estimates did

  7. Investigations of structure parameters and their similarity relationships in the convective boundary layer by means of large-eddy simulations and comparison with measurement data

    NARCIS (Netherlands)

    Maronga, B.; Moene, A.F.; Dinther, van D.; Raasch, S.

    2012-01-01

    Turbulent fluctuations of the refractive index (n) in the atmospheric boundary layer are related to local fluctuations in the air density, which can be expressed by the refractive-index structure parameter (Cn2). Since these fluctuations depend mainly on temperature and humidity, it is possible to

  8. The Fc-receptor III of cultured human monocytes. Structural similarity with FcRIII of natural killer cells and role in the extracellular lysis of sensitized erythrocytes

    NARCIS (Netherlands)

    Klaassen, R. J.; Ouwehand, W. H.; Huizinga, T. W.; Engelfriet, C. P.; von dem Borne, A. E.

    1990-01-01

    FcRIII is not present on peripheral blood monocytes, but becomes expressed upon culturing and can be demonstrated on tissue macrophages. We studied the expression of FcRIII of cultured monocytes in detail and compared its structure with FcRIII of neutrophils and NK cells. The cell density of FcRIII

  9. Probing the structure of CuInS{sub 2}-ZnS core-shell and similar nanocrystals by Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Dzhagan, Volodymyr, E-mail: dzhagan@isp.kiev.ua [Semiconductor Physics, Technische Universität Chemnitz, 09107 Chemnitz (Germany); V. E. Lashkaryov Institute of Semiconductors Physics, National Academy of Sciences of Ukraine, Kyiv 03028 (Ukraine); Kempken, Björn [Energy and Semiconductor Research Laboratory, Department of Physics, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg (Germany); Valakh, Mykhailo [V. E. Lashkaryov Institute of Semiconductors Physics, National Academy of Sciences of Ukraine, Kyiv 03028 (Ukraine); Parisi, Jürgen; Kolny-Olesiak, Joanna [Energy and Semiconductor Research Laboratory, Department of Physics, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg (Germany); Zahn, Dietrich R.T. [Semiconductor Physics, Technische Universität Chemnitz, 09107 Chemnitz (Germany)

    2017-02-15

    CuInS{sub 2}/ZnS core-shell and alloyed nanocrystals (NCs) are promising candidates for applications in biolabeling, photocatalysis, solar energy conversion, and light emitting diodes. The growth mechanism and subsequent internal structure of such heterogeneous NCs are therefore of crucial importance, as it strongly affects their optical and electronic properties. Here, we investigated using resonant Raman spectroscopy the structure of CuInS{sub 2}/ZnS and Cu-Zn-In-S/ZnS core-shell NCs, as well as the evolution of Cu{sub 2−x}S NCs into CuInS{sub 2}via the heterogeneous Cu{sub 2−x}S/CuInS{sub 2} phase. We demonstrate that the particular phases can be distinguished based on their characteristic Raman modes and tuning the exciting laser energy into resonance with the bandgap of the particular phase.

  10. Dictionary Based Segmentation in Volumes

    DEFF Research Database (Denmark)

    Emerson, Monica Jane; Jespersen, Kristine Munk; Jørgensen, Peter Stanley

    2015-01-01

    We present a method for supervised volumetric segmentation based on a dictionary of small cubes composed of pairs of intensity and label cubes. Intensity cubes are small image volumes where each voxel contains an image intensity. Label cubes are volumes with voxelwise probabilities for a given...... label. The segmentation process is done by matching a cube from the volume, of the same size as the dictionary intensity cubes, to the most similar intensity dictionary cube, and from the associated label cube we get voxel-wise label probabilities. Probabilities from overlapping cubes are averaged...... and hereby we obtain a robust label probability encoding. The dictionary is computed from labeled volumetric image data based on weighted clustering. We experimentally demonstrate our method using two data sets from material science – a phantom data set of a solid oxide fuel cell simulation for detecting...

  11. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  12. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  13. Understory Structure and Vascular Plant Diversity in Naturally Regenerated Deciduous Forests and Spruce Plantations on Similar Clear-Cuts: Implications for Forest Regeneration Strategy Selection

    Directory of Open Access Journals (Sweden)

    ZhiQiang Fang

    2014-04-01

    Full Text Available The active effect of natural regeneration on understory vegetation and diversity on clear-cut forestlands, in contrast to conifer reforestation, is still controversial. Here we investigated differences in understory vegetation by comparing naturally regenerated deciduous forests (NR and reforested spruce plantations (SP aged 20–40 years on 12 similar clear-cuts of subalpine old-growth spruce-fir forests from the eastern Tibetan Plateau. We found that 283 of the 334 vascular plant species recorded were present in NR plots, while only 264 species occurred in SP plots. This was consistent with richer species, higher cover, and stem (or shoot density of tree seedlings, shrubs, and ferns in the NR plots than in the SP plots. Moreover, understory plant diversity was limited under dense canopy cover, which occurred more frequently in the SP plots. Our findings implied that natural deciduous tree regeneration could better preserve understory vegetation and biodiversity than spruce reforestation after clear-cutting. This result further informed practices to reduce tree canopy cover for spruce plantations or to integrate natural regeneration and reforestation for clear-cuts in order to promote understory vegetation and species diversity conservation.

  14. Automatic lung segmentation in the presence of alveolar collapse

    Directory of Open Access Journals (Sweden)

    Noshadi Areg

    2017-09-01

    Full Text Available Lung ventilation and perfusion analyses using chest imaging methods require a correct segmentation of the lung to offer anatomical landmarks for the physiological data. An automatic segmentation approach simplifies and accelerates the analysis. However, the segmentation of the lungs has shown to be difficult if collapsed areas are present that tend to share similar gray values with surrounding non-pulmonary tissue. Our goal was to develop an automatic segmentation algorithm that is able to approximate dorsal lung boundaries even if alveolar collapse is present in the dependent lung areas adjacent to the pleura. Computed tomography data acquired in five supine pigs with injured lungs were used for this purpose. First, healthy lung tissue was segmented using a standard 3D region growing algorithm. Further, the bones in the chest wall surrounding the lungs were segmented to find the contact points of ribs and pleura. Artificial boundaries of the dorsal lung were set by spline interpolation through these contact points. Segmentation masks of the entire lung including the collapsed regions were created by combining the splines with the segmentation masks of the healthy lung tissue through multiple morphological operations. The automatically segmented images were then evaluated by comparing them to manual segmentations and determining the Dice similarity coefficients (DSC as a similarity measure. The developed method was able to accurately segment the lungs including the collapsed regions (DSCs over 0.96.

  15. Segmentation, advertising and prices

    NARCIS (Netherlands)

    Galeotti, Andrea; Moraga González, José

    This paper explores the implications of market segmentation on firm competitiveness. In contrast to earlier work, here market segmentation is minimal in the sense that it is based on consumer attributes that are completely unrelated to tastes. We show that when the market is comprised by two

  16. Sipunculans and segmentation

    DEFF Research Database (Denmark)

    Wanninger, Andreas; Kristof, Alen; Brinkmann, Nora

    2009-01-01

    mechanisms may act on the level of gene expression, cell proliferation, tissue differentiation and organ system formation in individual segments. Accordingly, in some polychaete annelids the first three pairs of segmental peripheral neurons arise synchronously, while the metameric commissures of the ventral...

  17. Documented Safety Analysis for the B695 Segment

    Energy Technology Data Exchange (ETDEWEB)

    Laycak, D

    2008-09-11

    This Documented Safety Analysis (DSA) was prepared for the Lawrence Livermore National Laboratory (LLNL) Building 695 (B695) Segment of the Decontamination and Waste Treatment Facility (DWTF). The report provides comprehensive information on design and operations, including safety programs and safety structures, systems and components to address the potential process-related hazards, natural phenomena, and external hazards that can affect the public, facility workers, and the environment. Consideration is given to all modes of operation, including the potential for both equipment failure and human error. The facilities known collectively as the DWTF are used by LLNL's Radioactive and Hazardous Waste Management (RHWM) Division to store and treat regulated wastes generated at LLNL. RHWM generally processes low-level radioactive waste with no, or extremely low, concentrations of transuranics (e.g., much less than 100 nCi/g). Wastes processed often contain only depleted uranium and beta- and gamma-emitting nuclides, e.g., {sup 90}Sr, {sup 137}Cs, or {sup 3}H. The mission of the B695 Segment centers on container storage, lab-packing, repacking, overpacking, bulking, sampling, waste transfer, and waste treatment. The B695 Segment is used for storage of radioactive waste (including transuranic and low-level), hazardous, nonhazardous, mixed, and other waste. Storage of hazardous and mixed waste in B695 Segment facilities is in compliance with the Resource Conservation and Recovery Act (RCRA). LLNL is operated by the Lawrence Livermore National Security, LLC, for the Department of Energy (DOE). The B695 Segment is operated by the RHWM Division of LLNL. Many operations in the B695 Segment are performed under a Resource Conservation and Recovery Act (RCRA) operation plan, similar to commercial treatment operations with best demonstrated available technologies. The buildings of the B695 Segment were designed and built considering such operations, using proven building

  18. Documented Safety Analysis for the B695 Segment

    International Nuclear Information System (INIS)

    Laycak, D.

    2008-01-01

    This Documented Safety Analysis (DSA) was prepared for the Lawrence Livermore National Laboratory (LLNL) Building 695 (B695) Segment of the Decontamination and Waste Treatment Facility (DWTF). The report provides comprehensive information on design and operations, including safety programs and safety structures, systems and components to address the potential process-related hazards, natural phenomena, and external hazards that can affect the public, facility workers, and the environment. Consideration is given to all modes of operation, including the potential for both equipment failure and human error. The facilities known collectively as the DWTF are used by LLNL's Radioactive and Hazardous Waste Management (RHWM) Division to store and treat regulated wastes generated at LLNL. RHWM generally processes low-level radioactive waste with no, or extremely low, concentrations of transuranics (e.g., much less than 100 nCi/g). Wastes processed often contain only depleted uranium and beta- and gamma-emitting nuclides, e.g., 90 Sr, 137 Cs, or 3 H. The mission of the B695 Segment centers on container storage, lab-packing, repacking, overpacking, bulking, sampling, waste transfer, and waste treatment. The B695 Segment is used for storage of radioactive waste (including transuranic and low-level), hazardous, nonhazardous, mixed, and other waste. Storage of hazardous and mixed waste in B695 Segment facilities is in compliance with the Resource Conservation and Recovery Act (RCRA). LLNL is operated by the Lawrence Livermore National Security, LLC, for the Department of Energy (DOE). The B695 Segment is operated by the RHWM Division of LLNL. Many operations in the B695 Segment are performed under a Resource Conservation and Recovery Act (RCRA) operation plan, similar to commercial treatment operations with best demonstrated available technologies. The buildings of the B695 Segment were designed and built considering such operations, using proven building systems, and keeping

  19. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  20. Case studies to test: A framework for using structural, reactivity, metabolic and physicochemical similarity to evaluate the suitability of analogs for SAR-based toxicological assessments.

    Science.gov (United States)

    Blackburn, Karen; Bjerke, Donald; Daston, George; Felter, Susan; Mahony, Catherine; Naciff, Jorge; Robison, Steven; Wu, Shengde

    2011-06-01

    A process for evaluating analogs for use in SAR (Structure-Activity Relationship) assessments was previously published (Wu et al. 2010). Subsequently, this process has been updated to include a decision tree for estrogen binding (from US EPA) and flags for developmental and reproductive toxicity (DART). This paper presents the results of blinded case studies designed to test this updated framework. The results of these case studies support the conclusion that the process outlined by Wu et al. (2010) can be successfully applied to develop surrogate values for risk assessment. The read across results generated by the process were shown to be protective when compared to the actual toxicity data. Successful application of the approach requires significant expertise as well as discipline to not overstep the boundaries of the defined analogs and the rating system. The end result of this rigor can be the inability to read across all endpoints for all chemicals resulting in data gaps that cannot be filled using read across, however, this reflects the current state of the science and is preferable to making non-protective decisions. Future work will be targeted towards expanding read across capabilities. Two examples of a broader category approach are also shown. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Gender similarities and differences.

    Science.gov (United States)

    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.

  2. Bayesian automated cortical segmentation for neonatal MRI

    Science.gov (United States)

    Chou, Zane; Paquette, Natacha; Ganesh, Bhavana; Wang, Yalin; Ceschin, Rafael; Nelson, Marvin D.; Macyszyn, Luke; Gaonkar, Bilwaj; Panigrahy, Ashok; Lepore, Natasha

    2017-11-01

    Several attempts have been made in the past few years to develop and implement an automated segmentation of neonatal brain structural MRI. However, accurate automated MRI segmentation remains challenging in this population because of the low signal-to-noise ratio, large partial volume effects and inter-individual anatomical variability of the neonatal brain. In this paper, we propose a learning method for segmenting the whole brain cortical grey matter on neonatal T2-weighted images. We trained our algorithm using a neonatal dataset composed of 3 fullterm and 4 preterm infants scanned at term equivalent age. Our segmentation pipeline combines the FAST algorithm from the FSL library software and a Bayesian segmentation approach to create a threshold matrix that minimizes the error of mislabeling brain tissue types. Our method shows promising results with our pilot training set. In both preterm and full-term neonates, automated Bayesian segmentation generates a smoother and more consistent parcellation compared to FAST, while successfully removing the subcortical structure and cleaning the edges of the cortical grey matter. This method show promising refinement of the FAST segmentation by considerably reducing manual input and editing required from the user, and further improving reliability and processing time of neonatal MR images. Further improvement will include a larger dataset of training images acquired from different manufacturers.

  3. A contrario line segment detection

    CERN Document Server

    von Gioi, Rafael Grompone

    2014-01-01

    The reliable detection of low-level image structures is an old and still challenging problem in computer vision. This?book leads a detailed tour through the LSD algorithm, a line segment detector designed to be fully automatic. Based on the a contrario framework, the algorithm works efficiently without the need of any parameter tuning. The design criteria are thoroughly explained and the algorithm's good and bad results are illustrated on real and synthetic images. The issues involved, as well as the strategies used, are common to many geometrical structure detection problems and some possible

  4. Equatorial segment of the mid-atlantic ridge

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    The Equatorial Segment of the Mid-Atlantic Ridge is a part of this mid-oceanic ridge limited by a cluster of fracture zones - Cape Verde, Marathon, Mercury, Vema, Doldrums, Vernadsky and Sierra Leone - in the North, and a similar cluster of fracture zones - St Paul, Romanche and Chain - in the South. During recent decades, following the publication of the 5. edition of the General Bathymetric Chart of the Oceans (GEBCO), there has been a great deal of geological-geophysical research and mapping of the World Ocean. The results have led to the development of a number of theories concerning the essential heterogeneity of the structure of the ocean floor and, in particular, the heterogeneity of the structure and segmentation of mid-oceanic ridges. Research on the nature of such segmentation is of great importance for an understanding of the processes of development of such ridges and oceanic basins as a whole. Chapter 20 is dedicated to the study of the atlantic ocean mantle by using (Th.U)Th, (Th/U)pb and K/Ti systematics 380 refs.

  5. Equatorial segment of the mid-atlantic ridge

    International Nuclear Information System (INIS)

    1996-01-01

    The Equatorial Segment of the Mid-Atlantic Ridge is a part of this mid-oceanic ridge limited by a cluster of fracture zones - Cape Verde, Marathon, Mercury, Vema, Doldrums, Vernadsky and Sierra Leone - in the North, and a similar cluster of fracture zones - St Paul, Romanche and Chain - in the South. During recent decades, following the publication of the 5. edition of the General Bathymetric Chart of the Oceans (GEBCO), there has been a great deal of geological-geophysical research and mapping of the World Ocean. The results have led to the development of a number of theories concerning the essential heterogeneity of the structure of the ocean floor and, in particular, the heterogeneity of the structure and segmentation of mid-oceanic ridges. Research on the nature of such segmentation is of great importance for an understanding of the processes of development of such ridges and oceanic basins as a whole. Chapter 20 is dedicated to the study of the atlantic ocean mantle by using (Th.U)Th, (Th/U)pb and K/Ti systematics

  6. Equatorial segment of the mid-atlantic ridge

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    The Equatorial Segment of the Mid-Atlantic Ridge is a part of this mid-oceanic ridge limited by a cluster of fracture zones - Cape Verde, Marathon, Mercury, Vema, Doldrums, Vernadsky and Sierra Leone - in the North, and a similar cluster of fracture zones - St Paul, Romanche and Chain - in the South. During recent decades, following the publication of the 5. edition of the General Bathymetric Chart of the Oceans (GEBCO), there has been a great deal of geological-geophysical research and mapping of the World Ocean. The results have led to the development of a number of theories concerning the essential heterogeneity of the structure of the ocean floor and, in particular, the heterogeneity of the structure and segmentation of mid-oceanic ridges. Research on the nature of such segmentation is of great importance for an understanding of the processes of development of such ridges and oceanic basins as a whole. Chapter 20 is dedicated to the study of the atlantic ocean mantle by using (Th.U)Th, (Th/U)pb and K/Ti systematics 380 refs.

  7. Pancreas and cyst segmentation

    Science.gov (United States)

    Dmitriev, Konstantin; Gutenko, Ievgeniia; Nadeem, Saad; Kaufman, Arie

    2016-03-01

    Accurate segmentation of abdominal organs from medical images is an essential part of surgical planning and computer-aided disease diagnosis. Many existing algorithms are specialized for the segmentation of healthy organs. Cystic pancreas segmentation is especially challenging due to its low contrast boundaries, variability in shape, location and the stage of the pancreatic cancer. We present a semi-automatic segmentation algorithm for pancreata with cysts. In contrast to existing automatic segmentation approaches for healthy pancreas segmentation which are amenable to atlas/statistical shape approaches, a pancreas with cysts can have even higher variability with respect to the shape of the pancreas due to the size and shape of the cyst(s). Hence, fine results are better attained with semi-automatic steerable approaches. We use a novel combination of random walker and region growing approaches to delineate the boundaries of the pancreas and cysts with respective best Dice coefficients of 85.1% and 86.7%, and respective best volumetric overlap errors of 26.0% and 23.5%. Results show that the proposed algorithm for pancreas and pancreatic cyst segmentation is accurate and stable.

  8. Segmentation of consumer's markets and evaluation of market's segments

    OpenAIRE

    ŠVECOVÁ, Iveta

    2013-01-01

    The goal of this bachelor thesis was to explain a possibly segmentation of consumer´s markets for a chosen company, and to present a suitable goods offer, so it would be suitable to the needs of selected segments. The work is divided into theoretical and practical part. First part describes marketing, segmentation, segmentation of consumer's markets, consumer's market, market's segments a other terms. Second part describes an evaluation of questionnaire survey, discovering of market's segment...

  9. Cluster Ensemble-Based Image Segmentation

    Directory of Open Access Journals (Sweden)

    Xiaoru Wang

    2013-07-01

    Full Text Available Image segmentation is the foundation of computer vision applications. In this paper, we propose a new cluster ensemble-based image segmentation algorithm, which overcomes several problems of traditional methods. We make two main contributions in this paper. First, we introduce the cluster ensemble concept to fuse the segmentation results from different types of visual features effectively, which can deliver a better final result and achieve a much more stable performance for broad categories of images. Second, we exploit the PageRank idea from Internet applications and apply it to the image segmentation task. This can improve the final segmentation results by combining the spatial information of the image and the semantic similarity of regions. Our experiments on four public image databases validate the superiority of our algorithm over conventional single type of feature or multiple types of features-based algorithms, since our algorithm can fuse multiple types of features effectively for better segmentation results. Moreover, our method is also proved to be very competitive in comparison with other state-of-the-art segmentation algorithms.

  10. Incorporation of squalene into rod outer segments

    International Nuclear Information System (INIS)

    Keller, R.K.; Fliesler, S.J.

    1990-01-01

    We have reported previously that squalene is the major radiolabeled nonsaponifiable lipid product derived from [ 3 H]acetate in short term incubations of frog retinas. In the present study, we demonstrate that newly synthesized squalene is incorporated into rod outer segments under similar in vitro conditions. We show further that squalene is an endogenous constituent of frog rod outer segment membranes; its concentration is approximately 9.5 nmol/mumol of phospholipid or about 9% of the level of cholesterol. Pulse-chase experiments with radiolabeled precursors revealed no metabolism of outer segment squalene to sterols in up to 20 h of chase. Taken together with our previous absolute rate studies, these results suggest that most, if not all, of the squalene synthesized by the frog retina is transported to rod outer segments. Synthesis of protein is not required for squalene transport since puromycin had no effect on squalene incorporation into outer segments. Conversely, inhibition of isoprenoid synthesis with mevinolin had no effect on the incorporation of opsin into the outer segment. These latter results support the conclusion that the de novo synthesis and subsequent intracellular trafficking of opsin and isoprenoid lipids destined for the outer segment occur via independent mechanisms

  11. A Kalman Filtering Perspective for Multiatlas Segmentation*

    Science.gov (United States)

    Gao, Yi; Zhu, Liangjia; Cates, Joshua; MacLeod, Rob S.; Bouix, Sylvain; Tannenbaum, Allen

    2016-01-01

    In multiatlas segmentation, one typically registers several atlases to the novel image, and their respective segmented label images are transformed and fused to form the final segmentation. In this work, we provide a new dynamical system perspective for multiatlas segmentation, inspired by the following fact: The transformation that aligns the current atlas to the novel image can be not only computed by direct registration but also inferred from the transformation that aligns the previous atlas to the image together with the transformation between the two atlases. This process is similar to the global positioning system on a vehicle, which gets position by inquiring from the satellite and by employing the previous location and velocity—neither answer in isolation being perfect. To solve this problem, a dynamical system scheme is crucial to combine the two pieces of information; for example, a Kalman filtering scheme is used. Accordingly, in this work, a Kalman multiatlas segmentation is proposed to stabilize the global/affine registration step. The contributions of this work are twofold. First, it provides a new dynamical systematic perspective for standard independent multiatlas registrations, and it is solved by Kalman filtering. Second, with very little extra computation, it can be combined with most existing multiatlas segmentation schemes for better registration/segmentation accuracy. PMID:26807162

  12. Osmotic and Heat Stress Effects on Segmentation.

    Directory of Open Access Journals (Sweden)

    Julian Weiss

    Full Text Available During vertebrate embryonic development, early skin, muscle, and bone progenitor populations organize into segments known as somites. Defects in this conserved process of segmentation lead to skeletal and muscular deformities, such as congenital scoliosis, a curvature of the spine caused by vertebral defects. Environmental stresses such as hypoxia or heat shock produce segmentation defects, and significantly increase the penetrance and severity of vertebral defects in genetically susceptible individuals. Here we show that a brief exposure to a high osmolarity solution causes reproducible segmentation defects in developing zebrafish (Danio rerio embryos. Both osmotic shock and heat shock produce border defects in a dose-dependent manner, with an increase in both frequency and severity of defects. We also show that osmotic treatment has a delayed effect on somite development, similar to that observed in heat shocked embryos. Our results establish osmotic shock as an alternate experimental model for stress, affecting segmentation in a manner comparable to other known environmental stressors. The similar effects of these two distinct environmental stressors support a model in which a variety of cellular stresses act through a related response pathway that leads to disturbances in the segmentation process.

  13. Segmenting high-frequency intracardiac ultrasound images of myocardium into infarcted, ischemic, and normal regions.

    Science.gov (United States)

    Hao, X; Bruce, C J; Pislaru, C; Greenleaf, J F

    2001-12-01

    Segmenting abnormal from normal myocardium using high-frequency intracardiac echocardiography (ICE) images presents new challenges for image processing. Gray-level intensity and texture features of ICE images of myocardium with the same structural/perfusion properties differ. This significant limitation conflicts with the fundamental assumption on which existing segmentation techniques are based. This paper describes a new seeded region growing method to overcome the limitations of the existing segmentation techniques. Three criteria are used for region growing control: 1) Each pixel is merged into the globally closest region in the multifeature space. 2) "Geographic similarity" is introduced to overcome the problem that myocardial tissue, despite having the same property (i.e., perfusion status), may be segmented into several different regions using existing segmentation methods. 3) "Equal opportunity competence" criterion is employed making results independent of processing order. This novel segmentation method is applied to in vivo intracardiac ultrasound images using pathology as the reference method for the ground truth. The corresponding results demonstrate that this method is reliable and effective.

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

    Science.gov (United States)

    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.

  15. Colour application on mammography image segmentation

    Science.gov (United States)

    Embong, R.; Aziz, N. M. Nik Ab.; Karim, A. H. Abd; Ibrahim, M. R.

    2017-09-01

    The segmentation process is one of the most important steps in image processing and computer vision since it is vital in the initial stage of image analysis. Segmentation of medical images involves complex structures and it requires precise segmentation result which is necessary for clinical diagnosis such as the detection of tumour, oedema, and necrotic tissues. Since mammography images are grayscale, researchers are looking at the effect of colour in the segmentation process of medical images. Colour is known to play a significant role in the perception of object boundaries in non-medical colour images. Processing colour images require handling more data, hence providing a richer description of objects in the scene. Colour images contain ten percent (10%) additional edge information as compared to their grayscale counterparts. Nevertheless, edge detection in colour image is more challenging than grayscale image as colour space is considered as a vector space. In this study, we implemented red, green, yellow, and blue colour maps to grayscale mammography images with the purpose of testing the effect of colours on the segmentation of abnormality regions in the mammography images. We applied the segmentation process using the Fuzzy C-means algorithm and evaluated the percentage of average relative error of area for each colour type. The results showed that all segmentation with the colour map can be done successfully even for blurred and noisy images. Also the size of the area of the abnormality region is reduced when compare to the segmentation area without the colour map. The green colour map segmentation produced the smallest percentage of average relative error (10.009%) while yellow colour map segmentation gave the largest percentage of relative error (11.367%).

  16. Segmenting patients and physicians using preferences from discrete choice experiments.

    Science.gov (United States)

    Deal, Ken

    2014-01-01

    People often form groups or segments that have similar interests and needs and seek similar benefits from health providers. Health organizations need to understand whether the same health treatments, prevention programs, services, and products should be applied to everyone in the relevant population or whether different treatments need to be provided to each of several segments that are relatively homogeneous internally but heterogeneous among segments. Our objective was to explain the purposes, benefits, and methods of segmentation for health organizations, and to illustrate the process of segmenting health populations based on preference coefficients from a discrete choice conjoint experiment (DCE) using an example study of prevention of cyberbullying among university students. We followed a two-level procedure for investigating segmentation incorporating several methods for forming segments in Level 1 using DCE preference coefficients and testing their quality, reproducibility, and usability by health decision makers. Covariates (demographic, behavioral, lifestyle, and health state variables) were included in Level 2 to further evaluate quality and to support the scoring of large databases and developing typing tools for assigning those in the relevant population, but not in the sample, to the segments. Several segmentation solution candidates were found during the Level 1 analysis, and the relationship of the preference coefficients to the segments was investigated using predictive methods. Those segmentations were tested for their quality and reproducibility and three were found to be very close in quality. While one seemed better than others in the Level 1 analysis, another was very similar in quality and proved ultimately better in predicting segment membership using covariates in Level 2. The two segments in the final solution were profiled for attributes that would support the development and acceptance of cyberbullying prevention programs among university

  17. Techniques on semiautomatic segmentation using the Adobe Photoshop

    Science.gov (United States)

    Park, Jin Seo; Chung, Min Suk; Hwang, Sung Bae

    2005-04-01

    The purpose of this research is to enable anybody to semiautomatically segment the anatomical structures in the MRIs, CTs, and other medical images on the personal computer. The segmented images are used for making three-dimensional images, which are helpful in medical education and research. To achieve this purpose, the following trials were performed. The entire body of a volunteer was MR scanned to make 557 MRIs, which were transferred to a personal computer. On Adobe Photoshop, contours of 19 anatomical structures in the MRIs were semiautomatically drawn using MAGNETIC LASSO TOOL; successively, manually corrected using either LASSO TOOL or DIRECT SELECTION TOOL to make 557 segmented images. In a likewise manner, 11 anatomical structures in the 8,500 anatomcial images were segmented. Also, 12 brain and 10 heart anatomical structures in anatomical images were segmented. Proper segmentation was verified by making and examining the coronal, sagittal, and three-dimensional images from the segmented images. During semiautomatic segmentation on Adobe Photoshop, suitable algorithm could be used, the extent of automatization could be regulated, convenient user interface could be used, and software bugs rarely occurred. The techniques of semiautomatic segmentation using Adobe Photoshop are expected to be widely used for segmentation of the anatomical structures in various medical images.

  18. Segmental tuberculosis verrucosa cutis

    Directory of Open Access Journals (Sweden)

    Hanumanthappa H

    1994-01-01

    Full Text Available A case of segmental Tuberculosis Verrucosa Cutis is reported in 10 year old boy. The condition was resembling the ascending lymphangitic type of sporotrichosis. The lesions cleared on treatment with INH 150 mg daily for 6 months.

  19. Comparing Harmonic Similarity Measures

    NARCIS (Netherlands)

    de Haas, W.B.; Robine, M.; Hanna, P.; Veltkamp, R.C.; Wiering, F.

    2010-01-01

    We present an overview of the most recent developments in polyphonic music retrieval and an experiment in which we compare two harmonic similarity measures. In contrast to earlier work, in this paper we specifically focus on the symbolic chord description as the primary musical representation and

  20. Interaction features for prediction of perceptual segmentation

    DEFF Research Database (Denmark)

    Hartmann, Martin; Lartillot, Olivier; Toiviainen, Petri

    2017-01-01

    As music unfolds in time, structure is recognised and understood by listeners, regardless of their level of musical expertise. A number of studies have found spectral and tonal changes to quite successfully model boundaries between structural sections. However, the effects of musical expertise...... and experimental task on computational modelling of structure are not yet well understood. These issues need to be addressed to better understand how listeners perceive the structure of music and to improve automatic segmentation algorithms. In this study, computational prediction of segmentation by listeners...... was investigated for six musical stimuli via a real-time task and an annotation (non real-time) task. The proposed approach involved computation of novelty curve interaction features and a prediction model of perceptual segmentation boundary density. We found that, compared to non-musicians’, musicians...

  1. THE RECENT STRUCTURE AND THE ASSUMED HISTORY OF FORMATION OF THE CRUST IN THE SOUTH-EASTERN SEGMENT OF THE NORTH ASIAN CRATON ALONG REFERENCE PROFILE 3-DV

    Directory of Open Access Journals (Sweden)

    E. Yu. Goshko

    2014-01-01

    Full Text Available The article presents results of specialized processing of the deep seismic profile along a part of Reference Profile 3-DV which crosses the Aldan-Stanovoi shield in the meridian direction and goes across its buried northern slope. The study is aimed at determining frequency-energy characteristics of the seismic wave field which are related to physical conditions of geological features of the crust. Based on analysis and interpretation of the dynamic profiles, it is possible to reveal and contour the Archean cores of consolidation of the Aldan shield and its buried continuation that is covered by sediments of the Middle Lena monocline and to input new facts in the proposed geodynamic model showing formation of the crust in the south-eastern segment of the North Asian craton.

  2. Fluence map segmentation

    International Nuclear Information System (INIS)

    Rosenwald, J.-C.

    2008-01-01

    The lecture addressed the following topics: 'Interpreting' the fluence map; The sequencer; Reasons for difference between desired and actual fluence map; Principle of 'Step and Shoot' segmentation; Large number of solutions for given fluence map; Optimizing 'step and shoot' segmentation; The interdigitation constraint; Main algorithms; Conclusions on segmentation algorithms (static mode); Optimizing intensity levels and monitor units; Sliding window sequencing; Synchronization to avoid the tongue-and-groove effect; Accounting for physical characteristics of MLC; Importance of corrections for leaf transmission and offset; Accounting for MLC mechanical constraints; The 'complexity' factor; Incorporating the sequencing into optimization algorithm; Data transfer to the treatment machine; Interface between R and V and accelerator; and Conclusions on fluence map segmentation (Segmentation is part of the overall inverse planning procedure; 'Step and Shoot' and 'Dynamic' options are available for most TPS (depending on accelerator model; The segmentation phase tends to come into the optimization loop; The physical characteristics of the MLC have a large influence on final dose distribution; The IMRT plans (MU and relative dose distribution) must be carefully validated). (P.A.)

  3. Gamifying Video Object Segmentation.

    Science.gov (United States)

    Spampinato, Concetto; Palazzo, Simone; Giordano, Daniela

    2017-10-01

    Video object segmentation can be considered as one of the most challenging computer vision problems. Indeed, so far, no existing solution is able to effectively deal with the peculiarities of real-world videos, especially in cases of articulated motion and object occlusions; limitations that appear more evident when we compare the performance of automated methods with the human one. However, manually segmenting objects in videos is largely impractical as it requires a lot of time and concentration. To address this problem, in this paper we propose an interactive video object segmentation method, which exploits, on one hand, the capability of humans to identify correctly objects in visual scenes, and on the other hand, the collective human brainpower to solve challenging and large-scale tasks. In particular, our method relies on a game with a purpose to collect human inputs on object locations, followed by an accurate segmentation phase achieved by optimizing an energy function encoding spatial and temporal constraints between object regions as well as human-provided location priors. Performance analysis carried out on complex video benchmarks, and exploiting data provided by over 60 users, demonstrated that our method shows a better trade-off between annotation times and segmentation accuracy than interactive video annotation and automated video object segmentation approaches.

  4. Strategic market segmentation

    Directory of Open Access Journals (Sweden)

    Maričić Branko R.

    2015-01-01

    Full Text Available Strategic planning of marketing activities is the basis of business success in modern business environment. Customers are not homogenous in their preferences and expectations. Formulating an adequate marketing strategy, focused on realization of company's strategic objectives, requires segmented approach to the market that appreciates differences in expectations and preferences of customers. One of significant activities in strategic planning of marketing activities is market segmentation. Strategic planning imposes a need to plan marketing activities according to strategically important segments on the long term basis. At the same time, there is a need to revise and adapt marketing activities on the short term basis. There are number of criteria based on which market segmentation is performed. The paper will consider effectiveness and efficiency of different market segmentation criteria based on empirical research of customer expectations and preferences. The analysis will include traditional criteria and criteria based on behavioral model. The research implications will be analyzed from the perspective of selection of the most adequate market segmentation criteria in strategic planning of marketing activities.

  5. Clinical Validation of Atlas-Based Auto-Segmentation of Multiple Target Volumes and Normal Tissue (Swallowing/Mastication) Structures in the Head and Neck

    International Nuclear Information System (INIS)

    Teguh, David N.; Levendag, Peter C.; Voet, Peter W.J.; Al-Mamgani, Abrahim; Han Xiao; Wolf, Theresa K.; Hibbard, Lyndon S.; Nowak, Peter; Akhiat, Hafid; Dirkx, Maarten L.P.; Heijmen, Ben J.M.; Hoogeman, Mischa S.

    2011-01-01

    Purpose: To validate and clinically evaluate autocontouring using atlas-based autosegmentation (ABAS) of computed tomography images. Methods and Materials: The data from 10 head-and-neck patients were selected as input for ABAS, and neck levels I-V and 20 organs at risk were manually contoured according to published guidelines. The total contouring times were recorded. Two different ABAS strategies, multiple and single subject, were evaluated, and the similarity of the autocontours with the atlas contours was assessed using Dice coefficients and the mean distances, using the leave-one-out method. For 12 clinically treated patients, 5 experienced observers edited the autosegmented contours. The editing times were recorded. The Dice coefficients and mean distances were calculated among the clinically used contours, autocontours, and edited autocontours. Finally, an expert panel scored all autocontours and the edited autocontours regarding their adequacy relative to the published atlas. Results: The time to autosegment all the structures using ABAS was 7 min/patient. No significant differences were observed in the autosegmentation accuracy for stage N0 and N+ patients. The multisubject atlas performed best, with a Dice coefficient and mean distance of 0.74 and 2 mm, 0.67 and 3 mm, 0.71 and 2 mm, 0.50 and 2 mm, and 0.78 and 2 mm for the salivary glands, neck levels, chewing muscles, swallowing muscles, and spinal cord-brainstem, respectively. The mean Dice coefficient and mean distance of the autocontours vs. the clinical contours was 0.8 and 2.4 mm for the neck levels and salivary glands, respectively. For the autocontours vs. the edited autocontours, the mean Dice coefficient and mean distance was 0.9 and 1.6 mm, respectively. The expert panel scored 100% of the autocontours as a “minor deviation, editable” or better. The expert panel scored 88% of the edited contours as good compared with 83% of the clinical contours. The total editing time was 66 min

  6. Clinical Validation of Atlas-Based Auto-Segmentation of Multiple Target Volumes and Normal Tissue (Swallowing/Mastication) Structures in the Head and Neck

    Energy Technology Data Exchange (ETDEWEB)

    Teguh, David N. [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands); Levendag, Peter C., E-mail: p.levendag@erasmusmc.nl [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands); Voet, Peter W.J.; Al-Mamgani, Abrahim [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands); Han Xiao; Wolf, Theresa K.; Hibbard, Lyndon S. [Elekta-CMS Software, Maryland Heights, MO 63043 (United States); Nowak, Peter; Akhiat, Hafid; Dirkx, Maarten L.P.; Heijmen, Ben J.M.; Hoogeman, Mischa S. [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands)

    2011-11-15

    Purpose: To validate and clinically evaluate autocontouring using atlas-based autosegmentation (ABAS) of computed tomography images. Methods and Materials: The data from 10 head-and-neck patients were selected as input for ABAS, and neck levels I-V and 20 organs at risk were manually contoured according to published guidelines. The total contouring times were recorded. Two different ABAS strategies, multiple and single subject, were evaluated, and the similarity of the autocontours with the atlas contours was assessed using Dice coefficients and the mean distances, using the leave-one-out method. For 12 clinically treated patients, 5 experienced observers edited the autosegmented contours. The editing times were recorded. The Dice coefficients and mean distances were calculated among the clinically used contours, autocontours, and edited autocontours. Finally, an expert panel scored all autocontours and the edited autocontours regarding their adequacy relative to the published atlas. Results: The time to autosegment all the structures using ABAS was 7 min/patient. No significant differences were observed in the autosegmentation accuracy for stage N0 and N+ patients. The multisubject atlas performed best, with a Dice coefficient and mean distance of 0.74 and 2 mm, 0.67 and 3 mm, 0.71 and 2 mm, 0.50 and 2 mm, and 0.78 and 2 mm for the salivary glands, neck levels, chewing muscles, swallowing muscles, and spinal cord-brainstem, respectively. The mean Dice coefficient and mean distance of the autocontours vs. the clinical contours was 0.8 and 2.4 mm for the neck levels and salivary glands, respectively. For the autocontours vs. the edited autocontours, the mean Dice coefficient and mean distance was 0.9 and 1.6 mm, respectively. The expert panel scored 100% of the autocontours as a 'minor deviation, editable' or better. The expert panel scored 88% of the edited contours as good compared with 83% of the clinical contours. The total editing time was 66 min

  7. Joint statistics and conditional mean strain rates of streamline segments

    International Nuclear Information System (INIS)

    Schaefer, P; Gampert, M; Peters, N

    2013-01-01

    Based on four different direct numerical simulations of turbulent flows with Taylor-based Reynolds numbers ranging from Re λ = 50 to 300 among which are two homogeneous isotropic decaying, one forced and one homogeneous shear flow, streamlines are identified and the obtained space curves are parameterized with the pseudo-time as well as the arclength. Based on local extrema of the absolute value of the velocity along the streamlines, the latter are partitioned into segments following Wang (2010 J. Fluid Mech. 648 183–203). Streamline segments are then statistically analyzed based on both parameterizations using the joint probability density function of the pseudo-time lag τ (arclength l, respectively) between and the velocity difference Δu at the extrema: P(τ,Δu), (P(l,Δu)). We distinguish positive and negative streamline segments depending on the sign of the velocity difference Δu. Differences as well as similarities in the statistical description for both parameterizations are discussed. In particular, it turns out that the normalized probability distribution functions (pdfs) (of both parameterizations) of the length of positive, negative and all segments assume a universal shape for all Reynolds numbers and flow types and are well described by a model derived in Schaefer P et al (2012 Phys. Fluids 24 045104). Particular attention is given to the conditional mean velocity difference at the ending points of the segments, which can be understood as a first-order structure function in the context of streamline segment analysis. It determines to a large extent the stretching (compression) of positive (negative) streamline segments and corresponds to the convective velocity in phase space in the transport model equation for the pdf. While based on the random sweeping hypothesis a scaling ∝ (u rms ετ) 1/3 is found for the parameterization based on the pseudo-time, the parameterization with the arclength l yields a much larger than expected l 1/3 scaling. A

  8. Multimodal MEMPRAGE, FLAIR, and R2* Segmentation to Resolve Dura and Vessels from Cortical Gray Matter

    Directory of Open Access Journals (Sweden)

    Roberto Viviani

    2017-05-01

    Full Text Available While widely in use in automated segmentation approaches for the detection of group differences or of changes associated with continuous predictors in gray matter volume, T1-weighted images are known to represent dura and cortical vessels with signal intensities similar to those of gray matter. By considering multiple signal sources at once, multimodal segmentation approaches may be able to resolve these different tissue classes and address this potential confound. We explored here the simultaneous use of FLAIR and apparent transverse relaxation rates (a signal related to T2* relaxation maps and having similar contrast with T1-weighted images. Relative to T1-weighted images alone, multimodal segmentation had marked positive effects on 1. the separation of gray matter from dura, 2. the exclusion of vessels from the gray matter compartment, and 3. the contrast with extracerebral connective tissue. While obtainable together with the T1-weighted images without increasing scanning times, apparent transverse relaxation rates were less effective than added FLAIR images in providing the above mentioned advantages. FLAIR images also improved the detection of cortical matter in areas prone to susceptibility artifacts in standard MPRAGE T1-weighted images, while the addition of transverse relaxation maps exacerbated the effect of these artifacts on segmentation. Our results confirm that standard MPRAGE segmentation may overestimate gray matter volume by wrongly assigning vessels and dura to this compartment and show that multimodal approaches may greatly improve the specificity of cortical segmentation. Since multimodal segmentation is easily implemented, these benefits are immediately available to studies focusing on translational applications of structural imaging.

  9. A NDVI assisted remote sensing image adaptive scale segmentation method

    Science.gov (United States)

    Zhang, Hong; Shen, Jinxiang; Ma, Yanmei

    2018-03-01

    Multiscale segmentation of images can effectively form boundaries of different objects with different scales. However, for the remote sensing image which widely coverage with complicated ground objects, the number of suitable segmentation scales, and each of the scale size is still difficult to be accurately determined, which severely restricts the rapid information extraction of the remote sensing image. A great deal of experiments showed that the normalized difference vegetation index (NDVI) can effectively express the spectral characteristics of a variety of ground objects in remote sensing images. This paper presents a method using NDVI assisted adaptive segmentation of remote sensing images, which segment the local area by using NDVI similarity threshold to iteratively select segmentation scales. According to the different regions which consist of different targets, different segmentation scale boundaries could be created. The experimental results showed that the adaptive segmentation method based on NDVI can effectively create the objects boundaries for different ground objects of remote sensing images.

  10. On self-similarity of crack layer

    Science.gov (United States)

    Botsis, J.; Kunin, B.

    1987-01-01

    The crack layer (CL) theory of Chudnovsky (1986), based on principles of thermodynamics of irreversible processes, employs a crucial hypothesis of self-similarity. The self-similarity hypothesis states that the value of the damage density at a point x of the active zone at a time t coincides with that at the corresponding point in the initial (t = 0) configuration of the active zone, the correspondence being given by a time-dependent affine transformation of the space variables. In this paper, the implications of the self-similarity hypothesis for qusi-static CL propagation is investigated using polystyrene as a model material and examining the evolution of damage distribution along the trailing edge which is approximated by a straight segment perpendicular to the crack path. The results support the self-similarity hypothesis adopted by the CL theory.

  11. Segmentation of dermatoscopic images by frequency domain filtering and k-means clustering algorithms.

    Science.gov (United States)

    Rajab, Maher I

    2011-11-01

    Since the introduction of epiluminescence microscopy (ELM), image analysis tools have been extended to the field of dermatology, in an attempt to algorithmically reproduce clinical evaluation. Accurate image segmentation of skin lesions is one of the key steps for useful, early and non-invasive diagnosis of coetaneous melanomas. This paper proposes two image segmentation algorithms based on frequency domain processing and k-means clustering/fuzzy k-means clustering. The two methods are capable of segmenting and extracting the true border that reveals the global structure irregularity (indentations and protrusions), which may suggest excessive cell growth or regression of a melanoma. As a pre-processing step, Fourier low-pass filtering is applied to reduce the surrounding noise in a skin lesion image. A quantitative comparison of the techniques is enabled by the use of synthetic skin lesion images that model lesions covered with hair to which Gaussian noise is added. The proposed techniques are also compared with an established optimal-based thresholding skin-segmentation method. It is demonstrated that for lesions with a range of different border irregularity properties, the k-means clustering and fuzzy k-means clustering segmentation methods provide the best performance over a range of signal to noise ratios. The proposed segmentation techniques are also demonstrated to have similar performance when tested on real skin lesions representing high-resolution ELM images. This study suggests that the segmentation results obtained using a combination of low-pass frequency filtering and k-means or fuzzy k-means clustering are superior to the result that would be obtained by using k-means or fuzzy k-means clustering segmentation methods alone. © 2011 John Wiley & Sons A/S.

  12. Geological interpretation of volcanism and segmentation of the Mariana back-arc spreading center between 12.7°N and 18.3°N

    Science.gov (United States)

    Anderson, Melissa O.; Chadwick, William W.; Hannington, Mark D.; Merle, Susan G.; Resing, Joseph A.; Baker, Edward T.; Butterfield, David A.; Walker, Sharon L.; Augustin, Nico

    2017-06-01

    The relationships between tectonic processes, magmatism, and hydrothermal venting along ˜600 km of the slow-spreading Mariana back-arc between 12.7°N and 18.3°N reveal a number of similarities and differences compared to slow-spreading mid-ocean ridges. Analysis of the volcanic geomorphology and structure highlights the complexity of the back-arc spreading center. Here, ridge segmentation is controlled by large-scale basement structures that appear to predate back-arc rifting. These structures also control the orientation of the chains of cross-arc volcanoes that characterize this region. Segment-scale faulting is oriented perpendicular to the spreading direction, allowing precise spreading directions to be determined. Four morphologically distinct segment types are identified: dominantly magmatic segments (Type I); magmatic segments currently undergoing tectonic extension (Type II); dominantly tectonic segments (Type III); and tectonic segments currently undergoing magmatic extension (Type IV). Variations in axial morphology (including eruption styles, neovolcanic eruption volumes, and faulting) reflect magma supply, which is locally enhanced by cross-arc volcanism associated with N-S compression along the 16.5°N and 17.0°N segments. In contrast, cross-arc seismicity is associated with N-S extension and increased faulting along the 14.5°N segment, with structures that are interpreted to be oceanic core complexes—the first with high-resolution bathymetry described in an active back-arc basin. Hydrothermal venting associated with recent magmatism has been discovered along all segment types.

  13. Rediscovering market segmentation.

    Science.gov (United States)

    Yankelovich, Daniel; Meer, David

    2006-02-01

    In 1964, Daniel Yankelovich introduced in the pages of HBR the concept of nondemographic segmentation, by which he meant the classification of consumers according to criteria other than age, residence, income, and such. The predictive power of marketing studies based on demographics was no longer strong enough to serve as a basis for marketing strategy, he argued. Buying patterns had become far better guides to consumers' future purchases. In addition, properly constructed nondemographic segmentations could help companies determine which products to develop, which distribution channels to sell them in, how much to charge for them, and how to advertise them. But more than 40 years later, nondemographic segmentation has become just as unenlightening as demographic segmentation had been. Today, the technique is used almost exclusively to fulfill the needs of advertising, which it serves mainly by populating commercials with characters that viewers can identify with. It is true that psychographic types like "High-Tech Harry" and "Joe Six-Pack" may capture some truth about real people's lifestyles, attitudes, self-image, and aspirations. But they are no better than demographics at predicting purchase behavior. Thus they give corporate decision makers very little idea of how to keep customers or capture new ones. Now, Daniel Yankelovich returns to these pages, with consultant David Meer, to argue the case for a broad view of nondemographic segmentation. They describe the elements of a smart segmentation strategy, explaining how segmentations meant to strengthen brand identity differ from those capable of telling a company which markets it should enter and what goods to make. And they introduce their "gravity of decision spectrum", a tool that focuses on the form of consumer behavior that should be of the greatest interest to marketers--the importance that consumers place on a product or product category.

  14. Generalized pixel profiling and comparative segmentation with application to arteriovenous malformation segmentation.

    Science.gov (United States)

    Babin, D; Pižurica, A; Bellens, R; De Bock, J; Shang, Y; Goossens, B; Vansteenkiste, E; Philips, W

    2012-07-01

    Extraction of structural and geometric information from 3-D images of blood vessels is a well known and widely addressed segmentation problem. The segmentation of cerebral blood vessels is of great importance in diagnostic and clinical applications, with a special application in diagnostics and surgery on arteriovenous malformations (AVM). However, the techniques addressing the problem of the AVM inner structure segmentation are rare. In this work we present a novel method of pixel profiling with the application to segmentation of the 3-D angiography AVM images. Our algorithm stands out in situations with low resolution images and high variability of pixel intensity. Another advantage of our method is that the parameters are set automatically, which yields little manual user intervention. The results on phantoms and real data demonstrate its effectiveness and potentials for fine delineation of AVM structure. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. A hybrid method for airway segmentation and automated measurement of bronchial wall thickness on CT.

    Science.gov (United States)

    Xu, Ziyue; Bagci, Ulas; Foster, Brent; Mansoor, Awais; Udupa, Jayaram K; Mollura, Daniel J

    2015-08-01

    Inflammatory and infectious lung diseases commonly involve bronchial airway structures and morphology, and these abnormalities are often analyzed non-invasively through high resolution computed tomography (CT) scans. Assessing airway wall surfaces and the lumen are of great importance for diagnosing pulmonary diseases. However, obtaining high accuracy from a complete 3-D airway tree structure can be quite challenging. The airway tree structure has spiculated shapes with multiple branches and bifurcation points as opposed to solid single organ or tumor segmentation tasks in other applications, hence, it is complex for manual segmentation as compared with other tasks. For computerized methods, a fundamental challenge in airway tree segmentation is the highly variable intensity levels in the lumen area, which often causes a segmentation method to leak into adjacent lung parenchyma through blurred airway walls or soft boundaries. Moreover, outer wall definition can be difficult due to similar intensities of the airway walls and nearby structures such as vessels. In this paper, we propose a computational framework to accurately quantify airways through (i) a novel hybrid approach for precise segmentation of the lumen, and (ii) two novel methods (a spatially constrained Markov random walk method (pseudo 3-D) and a relative fuzzy connectedness method (3-D)) to estimate the airway wall thickness. We evaluate the performance of our proposed methods in comparison with mostly used algorithms using human chest CT images. Our results demonstrate that, on publicly available data sets and using standard evaluation criteria, the proposed airway segmentation method is accurate and efficient as compared with the state-of-the-art methods, and the airway wall estimation algorithms identified the inner and outer airway surfaces more accurately than the most widely applied methods, namely full width at half maximum and phase congruency. Copyright © 2015. Published by Elsevier B.V.

  16. Atlas-based automatic segmentation of head and neck organs at risk and nodal target volumes: a clinical validation

    International Nuclear Information System (INIS)

    Daisne, Jean-François; Blumhofer, Andreas

    2013-01-01

    Intensity modulated radiotherapy for head and neck cancer necessitates accurate definition of organs at risk (OAR) and clinical target volumes (CTV). This crucial step is time consuming and prone to inter- and intra-observer variations. Automatic segmentation by atlas deformable registration may help to reduce time and variations. We aim to test a new commercial atlas algorithm for automatic segmentation of OAR and CTV in both ideal and clinical conditions. The updated Brainlab automatic head and neck atlas segmentation was tested on 20 patients: 10 cN0-stages (ideal population) and 10 unselected N-stages (clinical population). Following manual delineation of OAR and CTV, automatic segmentation of the same set of structures was performed and afterwards manually corrected. Dice Similarity Coefficient (DSC), Average Surface Distance (ASD) and Maximal Surface Distance (MSD) were calculated for “manual to automatic” and “manual to corrected” volumes comparisons. In both groups, automatic segmentation saved about 40% of the corresponding manual segmentation time. This effect was more pronounced for OAR than for CTV. The edition of the automatically obtained contours significantly improved DSC, ASD and MSD. Large distortions of normal anatomy or lack of iodine contrast were the limiting factors. The updated Brainlab atlas-based automatic segmentation tool for head and neck Cancer patients is timesaving but still necessitates review and corrections by an expert

  17. Atlas-based automatic segmentation of head and neck organs at risk and nodal target volumes: a clinical validation.

    Science.gov (United States)

    Daisne, Jean-François; Blumhofer, Andreas

    2013-06-26

    Intensity modulated radiotherapy for head and neck cancer necessitates accurate definition of organs at risk (OAR) and clinical target volumes (CTV). This crucial step is time consuming and prone to inter- and intra-observer variations. Automatic segmentation by atlas deformable registration may help to reduce time and variations. We aim to test a new commercial atlas algorithm for automatic segmentation of OAR and CTV in both ideal and clinical conditions. The updated Brainlab automatic head and neck atlas segmentation was tested on 20 patients: 10 cN0-stages (ideal population) and 10 unselected N-stages (clinical population). Following manual delineation of OAR and CTV, automatic segmentation of the same set of structures was performed and afterwards manually corrected. Dice Similarity Coefficient (DSC), Average Surface Distance (ASD) and Maximal Surface Distance (MSD) were calculated for "manual to automatic" and "manual to corrected" volumes comparisons. In both groups, automatic segmentation saved about 40% of the corresponding manual segmentation time. This effect was more pronounced for OAR than for CTV. The edition of the automatically obtained contours significantly improved DSC, ASD and MSD. Large distortions of normal anatomy or lack of iodine contrast were the limiting factors. The updated Brainlab atlas-based automatic segmentation tool for head and neck Cancer patients is timesaving but still necessitates review and corrections by an expert.

  18. The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions.

    Science.gov (United States)

    Bartho, Joseph D; Bellini, Dom; Wuerges, Jochen; Demitri, Nicola; Toccafondi, Mirco; Schmitt, Armin O; Zhao, Youfu; Walsh, Martin A; Benini, Stefano

    2017-01-01

    AmyR is a stress and virulence associated protein from the plant pathogenic Enterobacteriaceae species Erwinia amylovora, and is a functionally conserved ortholog of YbjN from Escherichia coli. The crystal structure of E. amylovora AmyR reveals a class I type III secretion chaperone-like fold, despite the lack of sequence similarity between these two classes of protein and lacking any evidence of a secretion-associated role. The results indicate that AmyR, and YbjN proteins in general, function through protein-protein interactions without any enzymatic action. The YbjN proteins of Enterobacteriaceae show remarkably low sequence similarity with other members of the YbjN protein family in Eubacteria, yet a high level of structural conservation is observed. Across the YbjN protein family sequence conservation is limited to residues stabilising the protein core and dimerization interface, while interacting regions are only conserved between closely related species. This study presents the first structure of a YbjN protein from Enterobacteriaceae, the most highly divergent and well-studied subgroup of YbjN proteins, and an in-depth sequence and structural analysis of this important but poorly understood protein family.

  19. Why segmentation matters: experience-driven segmentation errors impair “morpheme” learning

    Science.gov (United States)

    Finn, Amy S.; Hudson Kam, Carla L.

    2015-01-01

    We ask whether an adult learner’s knowledge of their native language impedes statistical learning in a new language beyond just word segmentation (as previously shown). In particular, we examine the impact of native-language word-form phonotactics on learners’ ability to segment words into their component morphemes and learn phonologically triggered variation of morphemes. We find that learning is impaired when words and component morphemes are structured to conflict with a learner’s native-language phonotactic system, but not when native-language phonotactics do not conflict with morpheme boundaries in the artificial language. A learner’s native-language knowledge can therefore have a cascading impact affecting word segmentation and the morphological variation that relies upon proper segmentation. These results show that getting word segmentation right early in learning is deeply important for learning other aspects of language, even those (morphology) that are known to pose a great difficulty for adult language learners. PMID:25730305

  20. Why segmentation matters: Experience-driven segmentation errors impair "morpheme" learning.

    Science.gov (United States)

    Finn, Amy S; Hudson Kam, Carla L

    2015-09-01

    We ask whether an adult learner's knowledge of their native language impedes statistical learning in a new language beyond just word segmentation (as previously shown). In particular, we examine the impact of native-language word-form phonotactics on learners' ability to segment words into their component morphemes and learn phonologically triggered variation of morphemes. We find that learning is impaired when words and component morphemes are structured to conflict with a learner's native-language phonotactic system, but not when native-language phonotactics do not conflict with morpheme boundaries in the artificial language. A learner's native-language knowledge can therefore have a cascading impact affecting word segmentation and the morphological variation that relies upon proper segmentation. These results show that getting word segmentation right early in learning is deeply important for learning other aspects of language, even those (morphology) that are known to pose a great difficulty for adult language learners. (c) 2015 APA, all rights reserved).

  1. Remote sensing image segmentation based on Hadoop cloud platform

    Science.gov (United States)

    Li, Jie; Zhu, Lingling; Cao, Fubin

    2018-01-01

    To solve the problem that the remote sensing image segmentation speed is slow and the real-time performance is poor, this paper studies the method of remote sensing image segmentation based on Hadoop platform. On the basis of analyzing the structural characteristics of Hadoop cloud platform and its component MapReduce programming, this paper proposes a method of image segmentation based on the combination of OpenCV and Hadoop cloud platform. Firstly, the MapReduce image processing model of Hadoop cloud platform is designed, the input and output of image are customized and the segmentation method of the data file is rewritten. Then the Mean Shift image segmentation algorithm is implemented. Finally, this paper makes a segmentation experiment on remote sensing image, and uses MATLAB to realize the Mean Shift image segmentation algorithm to compare the same image segmentation experiment. The experimental results show that under the premise of ensuring good effect, the segmentation rate of remote sensing image segmentation based on Hadoop cloud Platform has been greatly improved compared with the single MATLAB image segmentation, and there is a great improvement in the effectiveness of image segmentation.

  2. Scorpion image segmentation system

    Science.gov (United States)

    Joseph, E.; Aibinu, A. M.; Sadiq, B. A.; Bello Salau, H.; Salami, M. J. E.

    2013-12-01

    Death as a result of scorpion sting has been a major public health problem in developing countries. Despite the high rate of death as a result of scorpion sting, little report exists in literature of intelligent device and system for automatic detection of scorpion. This paper proposed a digital image processing approach based on the floresencing characteristics of Scorpion under Ultra-violet (UV) light for automatic detection and identification of scorpion. The acquired UV-based images undergo pre-processing to equalize uneven illumination and colour space channel separation. The extracted channels are then segmented into two non-overlapping classes. It has been observed that simple thresholding of the green channel of the acquired RGB UV-based image is sufficient for segmenting Scorpion from other background components in the acquired image. Two approaches to image segmentation have also been proposed in this work, namely, the simple average segmentation technique and K-means image segmentation. The proposed algorithm has been tested on over 40 UV scorpion images obtained from different part of the world and results obtained show an average accuracy of 97.7% in correctly classifying the pixel into two non-overlapping clusters. The proposed 1system will eliminate the problem associated with some of the existing manual approaches presently in use for scorpion detection.

  3. TH-CD-206-02: BEST IN PHYSICS (IMAGING): 3D Prostate Segmentation in MR Images Using Patch-Based Anatomical Signature

    International Nuclear Information System (INIS)

    Yang, X; Jani, A; Rossi, P; Mao, H; Curran, W; Liu, T

    2016-01-01

    Purpose: MRI has shown promise in identifying prostate tumors with high sensitivity and specificity for the detection of prostate cancer. Accurate segmentation of the prostate plays a key role various tasks: to accurately localize prostate boundaries for biopsy needle placement and radiotherapy, to initialize multi-modal registration algorithms or to obtain the region of interest for computer-aided detection of prostate cancer. However, manual segmentation during biopsy or radiation therapy can be time consuming and subject to inter- and intra-observer variation. This study’s purpose it to develop an automated method to address this technical challenge. Methods: We present an automated multi-atlas segmentation for MR prostate segmentation using patch-based label fusion. After an initial preprocessing for all images, all the atlases are non-rigidly registered to a target image. And then, the resulting transformation is used to propagate the anatomical structure labels of the atlas into the space of the target image. The top L similar atlases are further chosen by measuring intensity and structure difference in the region of interest around prostate. Finally, using voxel weighting based on patch-based anatomical signature, the label that the majority of all warped labels predict for each voxel is used for the final segmentation of the target image. Results: This segmentation technique was validated with a clinical study of 13 patients. The accuracy of our approach was assessed using the manual segmentation (gold standard). The mean volume Dice Overlap Coefficient was 89.5±2.9% between our and manual segmentation, which indicate that the automatic segmentation method works well and could be used for 3D MRI-guided prostate intervention. Conclusion: We have developed a new prostate segmentation approach based on the optimal feature learning label fusion framework, demonstrated its clinical feasibility, and validated its accuracy. This segmentation technique could be

  4. TH-CD-206-02: BEST IN PHYSICS (IMAGING): 3D Prostate Segmentation in MR Images Using Patch-Based Anatomical Signature

    Energy Technology Data Exchange (ETDEWEB)

    Yang, X; Jani, A; Rossi, P; Mao, H; Curran, W; Liu, T [Emory University, Atlanta, GA (United States)

    2016-06-15

    Purpose: MRI has shown promise in identifying prostate tumors with high sensitivity and specificity for the detection of prostate cancer. Accurate segmentation of the prostate plays a key role various tasks: to accurately localize prostate boundaries for biopsy needle placement and radiotherapy, to initialize multi-modal registration algorithms or to obtain the region of interest for computer-aided detection of prostate cancer. However, manual segmentation during biopsy or radiation therapy can be time consuming and subject to inter- and intra-observer variation. This study’s purpose it to develop an automated method to address this technical challenge. Methods: We present an automated multi-atlas segmentation for MR prostate segmentation using patch-based label fusion. After an initial preprocessing for all images, all the atlases are non-rigidly registered to a target image. And then, the resulting transformation is used to propagate the anatomical structure labels of the atlas into the space of the target image. The top L similar atlases are further chosen by measuring intensity and structure difference in the region of interest around prostate. Finally, using voxel weighting based on patch-based anatomical signature, the label that the majority of all warped labels predict for each voxel is used for the final segmentation of the target image. Results: This segmentation technique was validated with a clinical study of 13 patients. The accuracy of our approach was assessed using the manual segmentation (gold standard). The mean volume Dice Overlap Coefficient was 89.5±2.9% between our and manual segmentation, which indicate that the automatic segmentation method works well and could be used for 3D MRI-guided prostate intervention. Conclusion: We have developed a new prostate segmentation approach based on the optimal feature learning label fusion framework, demonstrated its clinical feasibility, and validated its accuracy. This segmentation technique could be

  5. SVM Pixel Classification on Colour Image Segmentation

    Science.gov (United States)

    Barui, Subhrajit; Latha, S.; Samiappan, Dhanalakshmi; Muthu, P.

    2018-04-01

    The aim of image segmentation is to simplify the representation of an image with the help of cluster pixels into something meaningful to analyze. Segmentation is typically used to locate boundaries and curves in an image, precisely to label every pixel in an image to give each pixel an independent identity. SVM pixel classification on colour image segmentation is the topic highlighted in this paper. It holds useful application in the field of concept based image retrieval, machine vision, medical imaging and object detection. The process is accomplished step by step. At first we need to recognize the type of colour and the texture used as an input to the SVM classifier. These inputs are extracted via local spatial similarity measure model and Steerable filter also known as Gabon Filter. It is then trained by using FCM (Fuzzy C-Means). Both the pixel level information of the image and the ability of the SVM Classifier undergoes some sophisticated algorithm to form the final image. The method has a well developed segmented image and efficiency with respect to increased quality and faster processing of the segmented image compared with the other segmentation methods proposed earlier. One of the latest application result is the Light L16 camera.

  6. Modeling of market segmentation for new IT product development

    Science.gov (United States)

    Nasiopoulos, Dimitrios K.; Sakas, Damianos P.; Vlachos, D. S.; Mavrogianni, Amanda

    2015-02-01

    Businesses from all Information Technology sectors use market segmentation[1] in their product development[2] and strategic planning[3]. Many studies have concluded that market segmentation is considered as the norm of modern marketing. With the rapid development of technology, customer needs are becoming increasingly diverse. These needs can no longer be satisfied by a mass marketing approach and follow one rule. IT Businesses can face with this diversity by pooling customers[4] with similar requirements and buying behavior and strength into segments. The result of the best choices about which segments are the most appropriate to serve can then be made, thus making the best of finite resources. Despite the attention which segmentation gathers and the resources that are invested in it, growing evidence suggests that businesses have problems operationalizing segmentation[5]. These problems take various forms. There may have been a rule that the segmentation process necessarily results in homogeneous groups of customers for whom appropriate marketing programs and procedures for dealing with them can be developed. Then the segmentation process, that a company follows, can fail. This increases concerns about what causes segmentation failure and how it might be overcome. To prevent the failure, we created a dynamic simulation model of market segmentation[6] based on the basic factors leading to this segmentation.

  7. Connecting textual segments

    DEFF Research Database (Denmark)

    Brügger, Niels

    2017-01-01

    history than just the years of the emergence of the web, the chapter traces the history of how segments of text have deliberately been connected to each other by the use of specific textual and media features, from clay tablets, manuscripts on parchment, and print, among others, to hyperlinks on stand......In “Connecting textual segments: A brief history of the web hyperlink” Niels Brügger investigates the history of one of the most fundamental features of the web: the hyperlink. Based on the argument that the web hyperlink is best understood if it is seen as another step in a much longer and broader...

  8. Acute Zonal Cone Photoreceptor Outer Segment Loss.

    Science.gov (United States)

    Aleman, Tomas S; Sandhu, Harpal S; Serrano, Leona W; Traband, Anastasia; Lau, Marisa K; Adamus, Grazyna; Avery, Robert A

    2017-05-01

    The diagnostic path presented narrows down the cause of acute vision loss to the cone photoreceptor outer segment and will refocus the search for the cause of similar currently idiopathic conditions. To describe the structural and functional associations found in a patient with acute zonal occult photoreceptor loss. A case report of an adolescent boy with acute visual field loss despite a normal fundus examination performed at a university teaching hospital. Results of a complete ophthalmic examination, full-field flash electroretinography (ERG) and multifocal ERG, light-adapted achromatic and 2-color dark-adapted perimetry, and microperimetry. Imaging was performed with spectral-domain optical coherence tomography (SD-OCT), near-infrared (NIR) and short-wavelength (SW) fundus autofluorescence (FAF), and NIR reflectance (REF). The patient was evaluated within a week of the onset of a scotoma in the nasal field of his left eye. Visual acuity was 20/20 OU, and color vision was normal in both eyes. Results of the fundus examination and of SW-FAF and NIR-FAF imaging were normal in both eyes, whereas NIR-REF imaging showed a region of hyporeflectance temporal to the fovea that corresponded with a dense relative scotoma noted on light-adapted static perimetry in the left eye. Loss in the photoreceptor outer segment detected by SD-OCT co-localized with an area of dense cone dysfunction detected on light-adapted perimetry and multifocal ERG but with near-normal rod-mediated vision according to results of 2-color dark-adapted perimetry. Full-field flash ERG findings were normal in both eyes. The outer nuclear layer and inner retinal thicknesses were normal. Localized, isolated cone dysfunction may represent the earliest photoreceptor abnormality or a distinct entity within the acute zonal occult outer retinopathy complex. Acute zonal occult outer retinopathy should be considered in patients with acute vision loss and abnormalities on NIR-REF imaging, especially if

  9. Comparing Individual Tree Segmentation Based on High Resolution Multispectral Image and Lidar Data

    Science.gov (United States)

    Xiao, P.; Kelly, M.; Guo, Q.

    2014-12-01

    This study compares the use of high-resolution multispectral WorldView images and high density Lidar data for individual tree segmentation. The application focuses on coniferous and deciduous forests in the Sierra Nevada Mountains. The tree objects are obtained in two ways: a hybrid region-merging segmentation method with multispectral images, and a top-down and bottom-up region-growing method with Lidar data. The hybrid region-merging method is used to segment individual tree from multispectral images. It integrates the advantages of global-oriented and local-oriented region-merging strategies into a unified framework. The globally most-similar pair of regions is used to determine the starting point of a growing region. The merging iterations are constrained within the local vicinity, thus the segmentation is accelerated and can reflect the local context. The top-down region-growing method is adopted in coniferous forest to delineate individual tree from Lidar data. It exploits the spacing between the tops of trees to identify and group points into a single tree based on simple rules of proximity and likely tree shape. The bottom-up region-growing method based on the intensity and 3D structure of Lidar data is applied in deciduous forest. It segments tree trunks based on the intensity and topological relationships of the points, and then allocate other points to exact tree crowns according to distance. The accuracies for each method are evaluated with field survey data in several test sites, covering dense and sparse canopy. Three types of segmentation results are produced: true positive represents a correctly segmented individual tree, false negative represents a tree that is not detected and assigned to a nearby tree, and false positive represents that a point or pixel cluster is segmented as a tree that does not in fact exist. They respectively represent correct-, under-, and over-segmentation. Three types of index are compared for segmenting individual tree

  10. Influence of pH on Morphology and Structure during Hydrolytic Degradation of the Segmented GL-b-[GL-co-TMC-co-CL]-b-GL Copolymer

    Directory of Open Access Journals (Sweden)

    Yolanda Márquez

    2015-09-01

    Full Text Available Hydrolytic degradation in media having a continuous variation of pH from 2 to 12 was studied for a copolymer having two polyglycolide hard blocks and a middle soft segment constituted by glycolide, trimethylene carbonate, and ɛ-caprolactone units. The last units were susceptible to cross-linking reactions by γ irradiation that led to an increase of the molecular weight of the sample. Nevertheless, the susceptibility to hydrolytic degradation was enhanced with respect to non-irradiated samples and consequently such samples were selected to analyze the degradation process through weight loss measurements and the evaluation of changes on molecular weight, morphology, and SAXS patterns. Results reflected the different hydrolytic mechanisms that took place in acid and basic media and the different solubilization of the degradation products. Thus, degradation was faster and solubilization higher in the basic media. In this case, fibers showed a high surface erosion and the formation of both longitudinal and deep circumferential cracks that contrasted with the peeling process detected at intermediate pHs (from 6 to 8 and the absence of longitudinal cracks at low pHs. SAXS measurements indicated that degradation was initiated through the hydrolysis of the irregular molecular folds placed on the amorphous interlamellar domains but also affected lamellar crystals at the last stages. Subsequent heating processes performed with degraded samples were fundamental to reveal the changes in microstructure that occurred during degradation and even the initial lamellar arrangement. In particular, the presence of interfibrillar domains and the disposition of lamellar domains at different levels along the fiber axis for a determined cross-section were evidenced.

  11. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni

    2018-01-01

    Previous research has identified researcher community and supervisory support as key determinants of the doctoral journey contributing to students’ persistence and robustness. However, we still know little about cross-cultural variation in the researcher community and supervisory support experien...... counter partners, whereas the Finnish students perceived lower levels of instrumental support than the Danish students. The findings imply that seemingly similar contexts hold valid differences in experienced social support and educational strategies at the PhD level....... experienced by PhD students within the same discipline. This study explores the support experiences of 381 PhD students within the humanities and social sciences from three research-intensive universities in Denmark (n=145) and Finland (n=236). The mixed methods design was utilized. The data were collected...... counter partners. The results also indicated that the only form of support in which the students expressed more matched support than mismatched support was informational support. Further investigation showed that the Danish students reported a high level of mismatch in emotional support than their Finnish...

  12. Pathogenesis of Focal Segmental Glomerulosclerosis

    Directory of Open Access Journals (Sweden)

    Beom Jin Lim

    2016-11-01

    Full Text Available Focal segmental glomerulosclerosis (FSGS is characterized by focal and segmental obliteration of glomerular capillary tufts with increased matrix. FSGS is classified as collapsing, tip, cellular, perihilar and not otherwise specified variants according to the location and character of the sclerotic lesion. Primary or idiopathic FSGS is considered to be related to podocyte injury, and the pathogenesis of podocyte injury has been actively investigated. Several circulating factors affecting podocyte permeability barrier have been proposed, but not proven to cause FSGS. FSGS may also be caused by genetic alterations. These genes are mainly those regulating slit diaphragm structure, actin cytoskeleton of podocytes, and foot process structure. The mode of inheritance and age of onset are different according to the gene involved. Recently, the role of parietal epithelial cells (PECs has been highlighted. Podocytes and PECs have common mesenchymal progenitors, therefore, PECs could be a source of podocyte repopulation after podocyte injury. Activated PECs migrate along adhesion to the glomerular tuft and may also contribute to the progression of sclerosis. Markers of activated PECs, including CD44, could be used to distinguish FSGS from minimal change disease. The pathogenesis of FSGS is very complex; however, understanding basic mechanisms of podocyte injury is important not only for basic research, but also for daily diagnostic pathology practice.

  13. Process Segmentation Typology in Czech Companies

    Directory of Open Access Journals (Sweden)

    Tucek David

    2016-03-01

    Full Text Available This article describes process segmentation typology during business process management implementation in Czech companies. Process typology is important for a manager’s overview of process orientation as well as for a manager’s general understanding of business process management. This article provides insight into a process-oriented organizational structure. The first part analyzes process segmentation typology itself as well as some original results of quantitative research evaluating process segmentation typology in the specific context of Czech company strategies. Widespread data collection was carried out in 2006 and 2013. The analysis of this data showed that managers have more options regarding process segmentation and its selection. In terms of practicality and ease of use, the most frequently used method of process segmentation (managerial, main, and supportive stems directly from the requirements of ISO 9001. Because of ISO 9001:2015, managers must now apply risk planning in relation to the selection of processes that are subjected to process management activities. It is for this fundamental reason that this article focuses on process segmentation typology.

  14. Lung segment geometry study: simulation of largest possible tumours that fit into bronchopulmonary segments.

    Science.gov (United States)

    Welter, S; Stöcker, C; Dicken, V; Kühl, H; Krass, S; Stamatis, G

    2012-03-01

    Segmental resection in stage I non-small cell lung cancer (NSCLC) has been well described and is considered to have similar survival rates as lobectomy but with increased rates of local tumour recurrence due to inadequate parenchymal margins. In consequence, today segmentectomy is only performed when the tumour is smaller than 2 cm. Three-dimensional reconstructions from 11 thin-slice CT scans of bronchopulmonary segments were generated, and virtual spherical tumours were placed over the segments, respecting all segmental borders. As a next step, virtual parenchymal safety margins of 2 cm and 3 cm were subtracted and the size of the remaining tumour calculated. The maximum tumour diameters with a 30-mm parenchymal safety margin ranged from 26.1 mm in right-sided segments 7 + 8 to 59.8 mm in the left apical segments 1-3. Using a three-dimensional reconstruction of lung CT scans, we demonstrated that segmentectomy or resection of segmental groups should be feasible with adequate margins, even for larger tumours in selected cases. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  15. Unsupervised Image Segmentation

    Czech Academy of Sciences Publication Activity Database

    Haindl, Michal; Mikeš, Stanislav

    2014-01-01

    Roč. 36, č. 4 (2014), s. 23-23 R&D Projects: GA ČR(CZ) GA14-10911S Institutional support: RVO:67985556 Keywords : unsupervised image segmentation Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2014/RO/haindl-0434412.pdf

  16. Metrics for image segmentation

    Science.gov (United States)

    Rees, Gareth; Greenway, Phil; Morray, Denise

    1998-07-01

    An important challenge in mapping image-processing techniques onto applications is the lack of quantitative performance measures. From a systems engineering perspective these are essential if system level requirements are to be decomposed into sub-system requirements which can be understood in terms of algorithm selection and performance optimization. Nowhere in computer vision is this more evident than in the area of image segmentation. This is a vigorous and innovative research activity, but even after nearly two decades of progress, it remains almost impossible to answer the question 'what would the performance of this segmentation algorithm be under these new conditions?' To begin to address this shortcoming, we have devised a well-principled metric for assessing the relative performance of two segmentation algorithms. This allows meaningful objective comparisons to be made between their outputs. It also estimates the absolute performance of an algorithm given ground truth. Our approach is an information theoretic one. In this paper, we describe the theory and motivation of our method, and present practical results obtained from a range of state of the art segmentation methods. We demonstrate that it is possible to measure the objective performance of these algorithms, and to use the information so gained to provide clues about how their performance might be improved.

  17. Short segment search method for phylogenetic analysis using nested sliding windows

    Science.gov (United States)

    Iskandar, A. A.; Bustamam, A.; Trimarsanto, H.

    2017-10-01

    To analyze phylogenetics in Bioinformatics, coding DNA sequences (CDS) segment is needed for maximal accuracy. However, analysis by CDS cost a lot of time and money, so a short representative segment by CDS, which is envelope protein segment or non-structural 3 (NS3) segment is necessary. After sliding window is implemented, a better short segment than envelope protein segment and NS3 is found. This paper will discuss a mathematical method to analyze sequences using nested sliding window to find a short segment which is representative for the whole genome. The result shows that our method can find a short segment which more representative about 6.57% in topological view to CDS segment than an Envelope segment or NS3 segment.

  18. Methods for recognition and segmentation of active fault

    International Nuclear Information System (INIS)

    Hyun, Chang Hun; Noh, Myung Hyun; Lee, Kieh Hwa; Chang, Tae Woo; Kyung, Jai Bok; Kim, Ki Young

    2000-03-01

    In order to identify and segment the active faults, the literatures of structural geology, paleoseismology, and geophysical explorations were investigated. The existing structural geological criteria for segmenting active faults were examined. These are mostly based on normal fault systems, thus, the additional criteria are demanded for application to different types of fault systems. Definition of the seismogenic fault, characteristics of fault activity, criteria and study results of fault segmentation, relationship between segmented fault length and maximum displacement, and estimation of seismic risk of segmented faults were examined in paleoseismic study. The history of earthquake such as dynamic pattern of faults, return period, and magnitude of the maximum earthquake originated by fault activity can be revealed by the study. It is confirmed through various case studies that numerous geophysical explorations including electrical resistivity, land seismic, marine seismic, ground-penetrating radar, magnetic, and gravity surveys have been efficiently applied to the recognition and segmentation of active faults

  19. An LG-graph-based early evaluation of segmented images

    International Nuclear Information System (INIS)

    Tsitsoulis, Athanasios; Bourbakis, Nikolaos

    2012-01-01

    Image segmentation is one of the first important parts of image analysis and understanding. Evaluation of image segmentation, however, is a very difficult task, mainly because it requires human intervention and interpretation. In this work, we propose a blind reference evaluation scheme based on regional local–global (RLG) graphs, which aims at measuring the amount and distribution of detail in images produced by segmentation algorithms. The main idea derives from the field of image understanding, where image segmentation is often used as a tool for scene interpretation and object recognition. Evaluation here derives from summarization of the structural information content and not from the assessment of performance after comparisons with a golden standard. Results show measurements for segmented images acquired from three segmentation algorithms, applied on different types of images (human faces/bodies, natural environments and structures (buildings)). (paper)

  20. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos

    2015-08-01

    The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

  1. CT-based manual segmentation and evaluation of paranasal sinuses.

    Science.gov (United States)

    Pirner, S; Tingelhoff, K; Wagner, I; Westphal, R; Rilk, M; Wahl, F M; Bootz, F; Eichhorn, Klaus W G

    2009-04-01

    Manual segmentation of computed tomography (CT) datasets was performed for robot-assisted endoscope movement during functional endoscopic sinus surgery (FESS). Segmented 3D models are needed for the robots' workspace definition. A total of 50 preselected CT datasets were each segmented in 150-200 coronal slices with 24 landmarks being set. Three different colors for segmentation represent diverse risk areas. Extension and volumetric measurements were performed. Three-dimensional reconstruction was generated after segmentation. Manual segmentation took 8-10 h for each CT dataset. The mean volumes were: right maxillary sinus 17.4 cm(3), left side 17.9 cm(3), right frontal sinus 4.2 cm(3), left side 4.0 cm(3), total frontal sinuses 7.9 cm(3), sphenoid sinus right side 5.3 cm(3), left side 5.5 cm(3), total sphenoid sinus volume 11.2 cm(3). Our manually segmented 3D-models present the patient's individual anatomy with a special focus on structures in danger according to the diverse colored risk areas. For safe robot assistance, the high-accuracy models represent an average of the population for anatomical variations, extension and volumetric measurements. They can be used as a database for automatic model-based segmentation. None of the segmentation methods so far described provide risk segmentation. The robot's maximum distance to the segmented border can be adjusted according to the differently colored areas.

  2. Millisecond single-molecule localization microscopy combined with convolution analysis and automated image segmentation to determine protein concentrations in complexly structured, functional cells, one cell at a time.

    Science.gov (United States)

    Wollman, Adam J M; Leake, Mark C

    2015-01-01

    We present a single-molecule tool called the CoPro (concentration of proteins) method that uses millisecond imaging with convolution analysis, automated image segmentation and super-resolution localization microscopy to generate robust estimates for protein concentration in different compartments of single living cells, validated using realistic simulations of complex multiple compartment cell types. We demonstrate its utility experimentally on model Escherichia coli bacteria and Saccharomyces cerevisiae budding yeast cells, and use it to address the biological question of how signals are transduced in cells. Cells in all domains of life dynamically sense their environment through signal transduction mechanisms, many involving gene regulation. The glucose sensing mechanism of S. cerevisiae is a model system for studying gene regulatory signal transduction. It uses the multi-copy expression inhibitor of the GAL gene family, Mig1, to repress unwanted genes in the presence of elevated extracellular glucose concentrations. We fluorescently labelled Mig1 molecules with green fluorescent protein (GFP) via chromosomal integration at physiological expression levels in living S. cerevisiae cells, in addition to the RNA polymerase protein Nrd1 with the fluorescent protein reporter mCherry. Using CoPro we make quantitative estimates of Mig1 and Nrd1 protein concentrations in the cytoplasm and nucleus compartments on a cell-by-cell basis under physiological conditions. These estimates indicate a ∼4-fold shift towards higher values in the concentration of diffusive Mig1 in the nucleus if the external glucose concentration is raised, whereas equivalent levels in the cytoplasm shift to smaller values with a relative change an order of magnitude smaller. This compares with Nrd1 which is not involved directly in glucose sensing, and which is almost exclusively localized in the nucleus under high and low external glucose levels. CoPro facilitates time-resolved quantification of

  3. Microscale soil structure development after glacial retreat - using machine-learning based segmentation of elemental distributions obtained by NanoSIMS

    Science.gov (United States)

    Schweizer, Steffen; Schlueter, Steffen; Hoeschen, Carmen; Koegel-Knabner, Ingrid; Mueller, Carsten W.

    2017-04-01

    Soil organic matter (SOM) is distributed on mineral surfaces depending on physicochemical soil properties that vary at the submicron scale. Nanoscale secondary ion mass spectrometry (NanoSIMS) can be used to visualize the spatial distribution of up to seven elements simultaneously at a lateral resolution of approximately 100 nm from which patterns of SOM coatings can be derived. Existing computational methods are mostly confined to visualization and lack spatial quantification measures of coverage and connectivity of organic matter coatings. This study proposes a methodology for the spatial analysis of SOM coatings based on supervised pixel classification and automatic image analysis of the 12C, 12C14N (indicative for SOM) and 16O (indicative for mineral surfaces) secondary ion distributions. The image segmentation of the secondary ion distributions into mineral particle surface and organic coating was done with a machine learning algorithm, which accounts for multiple features like size, color, intensity, edge and texture in all three ion distributions simultaneously. Our workflow allowed the spatial analysis of differences in the SOM coverage during soil development in the Damma glacier forefield (Switzerland) based on NanoSIMS measurements (n=121; containing ca. 4000 particles). The Damma chronosequence comprises several stages of soil development with increasing ice-free period (from ca. 15 to >700 years). To investigate mineral-associated SOM in the developing soil we obtained clay fractions (2.2 g cm3). We found increased coverage and a simultaneous development from patchy-distributed organic coatings to more connected coatings with increasing time after glacial retreat. The normalized N:C ratio (12C14N: (12C14N + 12C)) on the organic matter coatings was higher in the medium-aged soils than in the young and mature ones in both heavy and light mineral fraction. This reflects the sequential accumulation of proteinaceous SOM in the medium-aged soils and C

  4. Automatic and manual segmentation of healthy retinas using high-definition optical coherence tomography.

    Science.gov (United States)

    Golbaz, Isabelle; Ahlers, Christian; Goesseringer, Nina; Stock, Geraldine; Geitzenauer, Wolfgang; Prünte, Christian; Schmidt-Erfurth, Ursula Margarethe

    2011-03-01

    This study compared automatic- and manual segmentation modalities in the retina of healthy eyes using high-definition optical coherence tomography (HD-OCT). Twenty retinas in 20 healthy individuals were examined using an HD-OCT system (Carl Zeiss Meditec, Inc.). Three-dimensional imaging was performed with an axial resolution of 6 μm at a maximum scanning speed of 25,000 A-scans/second. Volumes of 6 × 6 × 2 mm were scanned. Scans were analysed using a matlab-based algorithm and a manual segmentation software system (3D-Doctor). The volume values calculated by the two methods were compared. Statistical analysis revealed a high correlation between automatic and manual modes of segmentation. The automatic mode of measuring retinal volume and the corresponding three-dimensional images provided similar results to the manual segmentation procedure. Both methods were able to visualize retinal and subretinal features accurately. This study compared two methods of assessing retinal volume using HD-OCT scans in healthy retinas. Both methods were able to provide realistic volumetric data when applied to raster scan sets. Manual segmentation methods represent an adequate tool with which to control automated processes and to identify clinically relevant structures, whereas automatic procedures will be needed to obtain data in larger patient populations. © 2009 The Authors. Journal compilation © 2009 Acta Ophthalmol.

  5. a Super Voxel-Based Riemannian Graph for Multi Scale Segmentation of LIDAR Point Clouds

    Science.gov (United States)

    Li, Minglei

    2018-04-01

    Automatically segmenting LiDAR points into respective independent partitions has become a topic of great importance in photogrammetry, remote sensing and computer vision. In this paper, we cast the problem of point cloud segmentation as a graph optimization problem by constructing a Riemannian graph. The scale space of the observed scene is explored by an octree-based over-segmentation with different depths. The over-segmentation produces many super voxels which restrict the structure of the scene and will be used as nodes of the graph. The Kruskal coordinates are used to compute edge weights that are proportional to the geodesic distance between nodes. Then we compute the edge-weight matrix in which the elements reflect the sectional curvatures associated with the geodesic paths between super voxel nodes on the scene surface. The final segmentation results are generated by clustering similar super voxels and cutting off the weak edges in the graph. The performance of this method was evaluated on LiDAR point clouds for both indoor and outdoor scenes. Additionally, extensive comparisons to state of the art techniques show that our algorithm outperforms on many metrics.

  6. The core of Ure2p prion fibrils is formed by the N-terminal segment in a parallel cross-β structure: evidence from solid-state NMR.

    Science.gov (United States)

    Kryndushkin, Dmitry S; Wickner, Reed B; Tycko, Robert

    2011-06-03

    Intracellular fibril formation by Ure2p produces the non-Mendelian genetic element [URE3] in Saccharomyces cerevisiae, making Ure2p a prion protein. We show that solid-state NMR spectra of full-length Ure2p fibrils, seeded with infectious prions from a specific [URE3] strain and labeled with uniformly (15)N-(13)C-enriched Ile, include strong, sharp signals from Ile residues in the globular C-terminal domain (CTD) with both helical and nonhelical (13)C chemical shifts. Treatment with proteinase K eliminates these CTD signals, leaving only nonhelical signals from the Gln-rich and Asn-rich N-terminal segment, which are also observed in the solid-state NMR spectra of Ile-labeled fibrils formed by residues 1-89 of Ure2p. Thus, the N-terminal segment, or "prion domain" (PD), forms the fibril core, while CTD units are located outside the core. We additionally show that, after proteinase K treatment, Ile-labeled Ure2p fibrils formed without prion seeding exhibit a broader set of solid-state NMR signals than do prion-seeded fibrils, consistent with the idea that structural variations within the PD core account for prion strains. Measurements of (13)C-(13)C magnetic dipole-dipole couplings among (13)C-labeled Ile carbonyl sites in full-length Ure2p fibrils support an in-register parallel β-sheet structure for the PD core of Ure2p fibrils. Finally, we show that a model in which CTD units are attached rigidly to the parallel β-sheet core is consistent with steric constraints. Published by Elsevier Ltd.

  7. Energy functionals for medical image segmentation: choices and consequences

    OpenAIRE

    McIntosh, Christopher

    2011-01-01

    Medical imaging continues to permeate the practice of medicine, but automated yet accurate segmentation and labeling of anatomical structures continues to be a major obstacle to computerized medical image analysis. Though there exists numerous approaches for medical image segmentation, one in particular has gained increasing popularity: energy minimization-based techniques, and the large set of methods encompassed therein. With these techniques an energy function must be chosen, segmentations...

  8. Automatic Semantic Segmentation of Brain Gliomas from MRI Images Using a Deep Cascaded Neural Network.

    Science.gov (United States)

    Cui, Shaoguo; Mao, Lei; Jiang, Jingfeng; Liu, Chang; Xiong, Shuyu

    2018-01-01

    Brain tumors can appear anywhere in the brain and have vastly different sizes and morphology. Additionally, these tumors are often diffused and poorly contrasted. Consequently, the segmentation of brain tumor and intratumor subregions using magnetic resonance imaging (MRI) data with minimal human interventions remains a challenging task. In this paper, we present a novel fully automatic segmentation method from MRI data containing in vivo brain gliomas. This approach can not only localize the entire tumor region but can also accurately segment the intratumor structure. The proposed work was based on a cascaded deep learning convolutional neural network consisting of two subnetworks: (1) a tumor localization network (TLN) and (2) an intratumor classification network (ITCN). The TLN, a fully convolutional network (FCN) in conjunction with the transfer learning technology, was used to first process MRI data. The goal of the first subnetwork was to define the tumor region from an MRI slice. Then, the ITCN was used to label the defined tumor region into multiple subregions. Particularly, ITCN exploited a convolutional neural network (CNN) with deeper architecture and smaller kernel. The proposed approach was validated on multimodal brain tumor segmentation (BRATS 2015) datasets, which contain 220 high-grade glioma (HGG) and 54 low-grade glioma (LGG) cases. Dice similarity coefficient (DSC), positive predictive value (PPV), and sensitivity were used as evaluation metrics. Our experimental results indicated that our method could obtain the promising segmentation results and had a faster segmentation speed. More specifically, the proposed method obtained comparable and overall better DSC values (0.89, 0.77, and 0.80) on the combined (HGG + LGG) testing set, as compared to other methods reported in the literature. Additionally, the proposed approach was able to complete a segmentation task at a rate of 1.54 seconds per slice.

  9. An Improved FCM Medical Image Segmentation Algorithm Based on MMTD

    Directory of Open Access Journals (Sweden)

    Ningning Zhou

    2014-01-01

    Full Text Available Image segmentation plays an important role in medical image processing. Fuzzy c-means (FCM is one of the popular clustering algorithms for medical image segmentation. But FCM is highly vulnerable to noise due to not considering the spatial information in image segmentation. This paper introduces medium mathematics system which is employed to process fuzzy information for image segmentation. It establishes the medium similarity measure based on the measure of medium truth degree (MMTD and uses the correlation of the pixel and its neighbors to define the medium membership function. An improved FCM medical image segmentation algorithm based on MMTD which takes some spatial features into account is proposed in this paper. The experimental results show that the proposed algorithm is more antinoise than the standard FCM, with more certainty and less fuzziness. This will lead to its practicable and effective applications in medical image segmentation.

  10. Algorithms for Cytoplasm Segmentation of Fluorescence Labelled Cells

    Directory of Open Access Journals (Sweden)

    Carolina Wählby

    2002-01-01

    Full Text Available Automatic cell segmentation has various applications in cytometry, and while the nucleus is often very distinct and easy to identify, the cytoplasm provides a lot more challenge. A new combination of image analysis algorithms for segmentation of cells imaged by fluorescence microscopy is presented. The algorithm consists of an image pre‐processing step, a general segmentation and merging step followed by a segmentation quality measurement. The quality measurement consists of a statistical analysis of a number of shape descriptive features. Objects that have features that differ to that of correctly segmented single cells can be further processed by a splitting step. By statistical analysis we therefore get a feedback system for separation of clustered cells. After the segmentation is completed, the quality of the final segmentation is evaluated. By training the algorithm on a representative set of training images, the algorithm is made fully automatic for subsequent images created under similar conditions. Automatic cytoplasm segmentation was tested on CHO‐cells stained with calcein. The fully automatic method showed between 89% and 97% correct segmentation as compared to manual segmentation.

  11. Rhodopsin Forms Nanodomains in Rod Outer Segment Disc Membranes of the Cold-Blooded Xenopus laevis.

    Directory of Open Access Journals (Sweden)

    Tatini Rakshit

    Full Text Available Rhodopsin forms nanoscale domains (i.e., nanodomains in rod outer segment disc membranes from mammalian species. It is unclear whether rhodopsin arranges in a similar manner in amphibian species, which are often used as a model system to investigate the function of rhodopsin and the structure of photoreceptor cells. Moreover, since samples are routinely prepared at low temperatures, it is unclear whether lipid phase separation effects in the membrane promote the observed nanodomain organization of rhodopsin from mammalian species. Rod outer segment disc membranes prepared from the cold-blooded frog Xenopus laevis were investigated by atomic force microscopy to visualize the organization of rhodopsin in the absence of lipid phase separation effects. Atomic force microscopy revealed that rhodopsin nanodomains form similarly as that observed previously in mammalian membranes. Formation of nanodomains in ROS disc membranes is independent of lipid phase separation and conserved among vertebrates.

  12. Status of the segment interconnect, cable segment ancillary logic, and the cable segment hybrid driver projects

    International Nuclear Information System (INIS)

    Swoboda, C.; Barsotti, E.; Chappa, S.; Downing, R.; Goeransson, G.; Lensy, D.; Moore, G.; Rotolo, C.; Urish, J.

    1985-01-01

    The FASTBUS Segment Interconnect (SI) provides a communication path between two otherwise independent, asynchronous bus segments. In particular, the Segment Interconnect links a backplane crate segment to a cable segment. All standard FASTBUS address and data transactions can be passed through the SI or any number of SIs and segments in a path. Thus systems of arbitrary connection complexity can be formed, allowing simultaneous independent processing, yet still permitting devices associated with one segment to be accessed from others. The model S1 Segment Interconnect and the Cable Segment Ancillary Logic covered in this report comply with all the mandatory features stated in the FASTBUS specification document DOE/ER-0189. A block diagram of the SI is shown

  13. Wide-band segmented power distribution networks

    NARCIS (Netherlands)

    Tereshchenko, O.V.; Buesink, Frederik Johannes Karel; Leferink, Frank Bernardus Johannes

    2013-01-01

    This paper discusses a novel design of Power Distribution Network (PDN). By physical structuring of the power plane into repetitive symmetrical and asymmetrical segments of varying size, suppression of the propagation of unwanted noise throughout the PDN over a wide frequency range is achieved.

  14. Hierarchical pre-segmentation without prior knowledge

    NARCIS (Netherlands)

    Kuijper, A.; Florack, L.M.J.

    2001-01-01

    A new method to pre-segment images by means of a hierarchical description is proposed. This description is obtained from an investigation of the deep structure of a scale space image – the input image and the Gaussian filtered ones simultaneously. We concentrate on scale space critical points –

  15. Segmentation of histological images and fibrosis identification with a convolutional neural network.

    Science.gov (United States)

    Fu, Xiaohang; Liu, Tong; Xiong, Zhaohan; Smaill, Bruce H; Stiles, Martin K; Zhao, Jichao

    2018-05-16

    Segmentation of histological images is one of the most crucial tasks for many biomedical analyses involving quantification of certain tissue types, such as fibrosis via Masson's trichrome staining. However, challenges are posed by the high variability and complexity of structural features in such images, in addition to imaging artifacts. Further, the conventional approach of manual thresholding is labor-intensive, and highly sensitive to inter- and intra-image intensity variations. An accurate and robust automated segmentation method is of high interest. We propose and evaluate an elegant convolutional neural network (CNN) designed for segmentation of histological images, particularly those with Masson's trichrome stain. The network comprises 11 successive convolutional - rectified linear unit - batch normalization layers. It outperformed state-of-the-art CNNs on a dataset of cardiac histological images (labeling fibrosis, myocytes, and background) with a Dice similarity coefficient of 0.947. With 100 times fewer (only 300,000) trainable parameters than the state-of-the-art, our CNN is less susceptible to overfitting, and is efficient. Additionally, it retains image resolution from input to output, captures fine-grained details, and can be trained end-to-end smoothly. To the best of our knowledge, this is the first deep CNN tailored to the problem of concern, and may potentially be extended to solve similar segmentation tasks to facilitate investigations into pathology and clinical treatment. Copyright © 2018. Published by Elsevier Ltd.

  16. Low-complexity atlas-based prostate segmentation by combining global, regional, and local metrics

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Qiuliang; Ruan, Dan, E-mail: druan@mednet.ucla.edu [The Department of Radiation Oncology, University of California Los Angeles, California 90095 (United States)

    2014-04-15

    Purpose: To improve the efficiency of atlas-based segmentation without compromising accuracy, and to demonstrate the validity of the proposed method on MRI-based prostate segmentation application. Methods: Accurate and efficient automatic structure segmentation is an important task in medical image processing. Atlas-based methods, as the state-of-the-art, provide good segmentation at the cost of a large number of computationally intensive nonrigid registrations, for anatomical sites/structures that are subject to deformation. In this study, the authors propose to utilize a combination of global, regional, and local metrics to improve the accuracy yet significantly reduce the number of required nonrigid registrations. The authors first perform an affine registration to minimize the global mean squared error (gMSE) to coarsely align each atlas image to the target. Subsequently, atarget-specific regional MSE (rMSE), demonstrated to be a good surrogate for dice similarity coefficient (DSC), is used to select a relevant subset from the training atlas. Only within this subset are nonrigid registrations performed between the training images and the target image, to minimize a weighted combination of gMSE and rMSE. Finally, structure labels are propagated from the selected training samples to the target via the estimated deformation fields, and label fusion is performed based on a weighted combination of rMSE and local MSE (lMSE) discrepancy, with proper total-variation-based spatial regularization. Results: The proposed method was applied to a public database of 30 prostate MR images with expert-segmented structures. The authors’ method, utilizing only eight nonrigid registrations, achieved a performance with a median/mean DSC of over 0.87/0.86, outperforming the state-of-the-art full-fledged atlas-based segmentation approach of which the median/mean DSC was 0.84/0.82 when applying to their data set. Conclusions: The proposed method requires a fixed number of nonrigid

  17. Market segmentation: Venezuelan ADRs

    Directory of Open Access Journals (Sweden)

    Urbi Garay

    2012-12-01

    Full Text Available The control on foreign exchange imposed by Venezuela in 2003 constitute a natural experiment that allows researchers to observe the effects of exchange controls on stock market segmentation. This paper provides empirical evidence that although the Venezuelan capital market as a whole was highly segmented before the controls were imposed, the shares in the firm CANTV were, through their American Depositary Receipts (ADRs, partially integrated with the global market. Following the imposition of the exchange controls this integration was lost. Research also documents the spectacular and apparently contradictory rise experienced by the Caracas Stock Exchange during the serious economic crisis of 2003. It is argued that, as it happened in Argentina in 2002, the rise in share prices occurred because the depreciation of the Bolívar in the parallel currency market increased the local price of the stocks that had associated ADRs, which were negotiated in dollars.

  18. Scintillation counter, segmented shield

    International Nuclear Information System (INIS)

    Olson, R.E.; Thumim, A.D.

    1975-01-01

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into radiation-responsive areas. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (U.S.)

  19. Quantitative Comparison of SPM, FSL, and Brainsuite for Brain MR Image Segmentation

    Directory of Open Access Journals (Sweden)

    Kazemi K

    2014-03-01

    Full Text Available Background: Accurate brain tissue segmentation from magnetic resonance (MR images is an important step in analysis of cerebral images. There are software packages which are used for brain segmentation. These packages usually contain a set of skull stripping, intensity non-uniformity (bias correction and segmentation routines. Thus, assessment of the quality of the segmented gray matter (GM, white matter (WM and cerebrospinal fluid (CSF is needed for the neuroimaging applications. Methods: In this paper, performance evaluation of three widely used brain segmentation software packages SPM8, FSL and Brainsuite is presented. Segmentation with SPM8 has been performed in three frameworks: i default segmentation, ii SPM8 New-segmentation and iii modified version using hidden Markov random field as implemented in SPM8-VBM toolbox. Results: The accuracy of the segmented GM, WM and CSF and the robustness of the tools against changes of image quality has been assessed using Brainweb simulated MR images and IBSR real MR images. The calculated similarity between the segmented tissues using different tools and corresponding ground truth shows variations in segmentation results. Conclusion: A few studies has investigated GM, WM and CSF segmentation. In these studies, the skull stripping and bias correction are performed separately and they just evaluated the segmentation. Thus, in this study, assessment of complete segmentation framework consisting of pre-processing and segmentation of these packages is performed. The obtained results can assist the users in choosing an appropriate segmentation software package for the neuroimaging application of interest.

  20. Video segmentation using keywords

    Science.gov (United States)

    Ton-That, Vinh; Vong, Chi-Tai; Nguyen-Dao, Xuan-Truong; Tran, Minh-Triet

    2018-04-01

    At DAVIS-2016 Challenge, many state-of-art video segmentation methods achieve potential results, but they still much depend on annotated frames to distinguish between background and foreground. It takes a lot of time and efforts to create these frames exactly. In this paper, we introduce a method to segment objects from video based on keywords given by user. First, we use a real-time object detection system - YOLOv2 to identify regions containing objects that have labels match with the given keywords in the first frame. Then, for each region identified from the previous step, we use Pyramid Scene Parsing Network to assign each pixel as foreground or background. These frames can be used as input frames for Object Flow algorithm to perform segmentation on entire video. We conduct experiments on a subset of DAVIS-2016 dataset in half the size of its original size, which shows that our method can handle many popular classes in PASCAL VOC 2012 dataset with acceptable accuracy, about 75.03%. We suggest widely testing by combining other methods to improve this result in the future.