How Category Structure Influences the Perception of Object Similarity: The Atypicality Bias

PubMed Central

Tanaka, James William; Kantner, Justin; Bartlett, Marni

2011-01-01

Why do some faces appear more similar than others? Beyond structural factors, we speculate that similarity is governed by the organization of faces located in a multi-dimensional face space. To test this hypothesis, we morphed a typical face with an atypical face. If similarity judgments are guided purely by their physical properties, the morph should be perceived to be equally similar to its typical parent as its atypical parent. However, contrary to the structural prediction, our results showed that the morph face was perceived to be more similar to the atypical face than the typical face. Our empirical studies show that the atypicality bias is not limited to faces, but extends to other object categories (birds) whose members share common shape properties. We also demonstrate atypicality bias is malleable and can change subject to category learning and experience. Collectively, the empirical evidence indicates that perceptions of face and object similarity are affected by the distribution of stimuli in a face or object space. In this framework, atypical stimuli are located in a sparser region of the space where there is less competition for recognition and therefore, these representations capture a broader range of inputs. In contrast, typical stimuli are located in a denser region of category space where there is increased competition for recognition and hence, these representation draw a more restricted range of face inputs. These results suggest that the perceived likeness of an object is influenced by the organization of surrounding exemplars in the category space. PMID:22685441

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

PubMed

Yee, Yohan; Fernandes, Darren J; French, Leon; Ellegood, Jacob; Cahill, Lindsay S; Vousden, Dulcie A; Spencer Noakes, Leigh; Scholz, Jan; van Eede, Matthijs C; Nieman, Brian J; Sled, John G; Lerch, Jason P

2018-05-18

An organizational pattern seen in the brain, termed structural covariance, is the statistical association of pairs of brain regions in their anatomical properties. These associations, measured across a population as covariances or correlations usually in cortical thickness or volume, are thought to reflect genetic and environmental underpinnings. Here, we examine the biological basis of structural volume covariance in the mouse brain. We first examined large scale associations between brain region volumes using an atlas-based approach that parcellated the entire mouse brain into 318 regions over which correlations in volume were assessed, for volumes obtained from 153 mouse brain images via high-resolution MRI. We then used a seed-based approach and determined, for 108 different seed regions across the brain and using mouse gene expression and connectivity data from the Allen Institute for Brain Science, the variation in structural covariance data that could be explained by distance to seed, transcriptomic similarity to seed, and connectivity to seed. We found that overall, correlations in structure volumes hierarchically clustered into distinct anatomical systems, similar to findings from other studies and similar to other types of networks in the brain, including structural connectivity and transcriptomic similarity networks. Across seeds, this structural covariance was significantly explained by distance (17% of the variation, up to a maximum of 49% for structural covariance to the visceral area of the cortex), transcriptomic similarity (13% of the variation, up to maximum of 28% for structural covariance to the primary visual area) and connectivity (15% of the variation, up to a maximum of 36% for structural covariance to the intermediate reticular nucleus in the medulla) of covarying structures. Together, distance, connectivity, and transcriptomic similarity explained 37% of structural covariance, up to a maximum of 63% for structural covariance to the

Understand protein functions by comparing the similarity of local structural environments.

PubMed

Chen, Jiawen; Xie, Zhong-Ru; Wu, Yinghao

2017-02-01

The three-dimensional structures of proteins play an essential role in regulating binding between proteins and their partners, offering a direct relationship between structures and functions of proteins. It is widely accepted that the function of a protein can be determined if its structure is similar to other proteins whose functions are known. However, it is also observed that proteins with similar global structures do not necessarily correspond to the same function, while proteins with very different folds can share similar functions. This indicates that function similarity is originated from the local structural information of proteins instead of their global shapes. We assume that proteins with similar local environments prefer binding to similar types of molecular targets. In order to testify this assumption, we designed a new structural indicator to define the similarity of local environment between residues in different proteins. This indicator was further used to calculate the probability that a given residue binds to a specific type of structural neighbors, including DNA, RNA, small molecules and proteins. After applying the method to a large-scale non-redundant database of proteins, we show that the positive signal of binding probability calculated from the local structural indicator is statistically meaningful. In summary, our studies suggested that the local environment of residues in a protein is a good indicator to recognize specific binding partners of the protein. The new method could be a potential addition to a suite of existing template-based approaches for protein function prediction. Copyright © 2016 Elsevier B.V. All rights reserved.

Different Measures of Structural Similarity Tap Different Aspects of Visual Object Processing

PubMed Central

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, this has been based more on implication than on direct empirical demonstrations. Here, the direct influence of two different measures of structural similarity, contour overlap and within-item structural diversity, on object individuation (object decision) and superordinate categorization performance is examined. Both measures can account for performance differences across objects, but in different conditions. It is argued that this reflects differences between the measures in whether they tap: (i) global or local shape characteristics, and (ii) between- or within-category structural similarity. PMID:28861027

LCS-TA to identify similar fragments in RNA 3D structures.

PubMed

Wiedemann, Jakub; Zok, Tomasz; Milostan, Maciej; Szachniuk, Marta

2017-10-23

In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ . The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3

Musical structure analysis using similarity matrix and dynamic programming

NASA Astrophysics Data System (ADS)

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

2005-10-01

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

A community detection algorithm based on structural similarity

NASA Astrophysics Data System (ADS)

Guo, Xuchao; Hao, Xia; Liu, Yaqiong; Zhang, Li; Wang, Lu

2017-09-01

In order to further improve the efficiency and accuracy of community detection algorithm, a new algorithm named SSTCA (the community detection algorithm based on structural similarity with threshold) is proposed. In this algorithm, the structural similarities are taken as the weights of edges, and the threshold k is considered to remove multiple edges whose weights are less than the threshold, and improve the computational efficiency. Tests were done on the Zachary’s network, Dolphins’ social network and Football dataset by the proposed algorithm, and compared with GN and SSNCA algorithm. The results show that the new algorithm is superior to other algorithms in accuracy for the dense networks and the operating efficiency is improved obviously.

Joint reconstruction of PET-MRI by exploiting structural similarity

NASA Astrophysics Data System (ADS)

Ehrhardt, Matthias J.; Thielemans, Kris; Pizarro, Luis; Atkinson, David; Ourselin, Sébastien; Hutton, Brian F.; Arridge, Simon R.

2015-01-01

Recent advances in technology have enabled the combination of positron emission tomography (PET) with magnetic resonance imaging (MRI). These PET-MRI scanners simultaneously acquire functional PET and anatomical or functional MRI data. As function and anatomy are not independent of one another the images to be reconstructed are likely to have shared structures. We aim to exploit this inherent structural similarity by reconstructing from both modalities in a joint reconstruction framework. The structural similarity between two modalities can be modelled in two different ways: edges are more likely to be at similar positions and/or to have similar orientations. We analyse the diffusion process generated by minimizing priors that encapsulate these different models. It turns out that the class of parallel level set priors always corresponds to anisotropic diffusion which is sometimes forward and sometimes backward diffusion. We perform numerical experiments where we jointly reconstruct from blurred Radon data with Poisson noise (PET) and under-sampled Fourier data with Gaussian noise (MRI). Our results show that both modalities benefit from each other in areas of shared edge information. The joint reconstructions have less artefacts and sharper edges compared to separate reconstructions and the ℓ2-error can be reduced in all of the considered cases of under-sampling.

Arthroprotective Effects of Cf-02 Sharing Structural Similarity with Quercetin.

PubMed

Liu, Feng-Cheng; Lu, Jeng-Wei; Chien, Chiao-Yun; Huang, Hsu-Shan; Lee, Chia-Chung; Lien, Shiu-Bii; Lin, Leou-Chyr; Chen, Liv Weichien; Ho, Yi-Jung; Shen, Min-Chung; Ho, Ling-Jun; Lai, Jenn-Haung

2018-05-14

In this study, we synthesized hundreds of analogues based on the structure of small-molecule inhibitors (SMIs) that were previously identified in our laboratory with the aim of identifying potent yet safe compounds for arthritis therapeutics. One of the analogues was shown to share structural similarity with quercetin, a potent anti-inflammatory flavonoid present in many different fruits and vegetables. We investigated the immunomodulatory effects of this compound, namely 6-(2,4-difluorophenyl)-3-(3-(trifluoromethyl)phenyl)-2 H -benzo[ e ][1,3]oxazine-2,4(3 H )-dione (Cf-02), in a side-by-side comparison with quercetin. Chondrocytes were isolated from pig joints or the joints of patients with osteoarthritis that had undergone total knee replacement surgery. Several measures were used to assess the immunomodulatory potency of these compounds in tumor necrosis factor (TNF-α)-stimulated chondrocytes. Characterization included the protein and mRNA levels of molecules associated with arthritis pathogenesis as well as the inducible nitric oxide synthase (iNOS)⁻nitric oxide (NO) system and matrix metalloproteinases (MMPs) in cultured chondrocytes and proteoglycan, and aggrecan degradation in cartilage explants. We also examined the activation of several important transcription factors, including nuclear factor-kappaB (NF-κB), interferon regulatory factor-1 (IRF-1), signal transducer and activator of transcription-3 (STAT-3), and activator protein-1 (AP-1). Our overall results indicate that the immunomodulatory potency of Cf-02 is fifty-fold more efficient than that of quercetin without any indication of cytotoxicity. When tested in vivo using the induced edema method, Cf-02 was shown to suppress inflammation and cartilage damage. The proposed method shows considerable promise for the identification of candidate disease-modifying immunomodulatory drugs and leads compounds for arthritis therapeutics.

Investigation of structural factors of safety for the space shuttle

NASA Technical Reports Server (NTRS)

1972-01-01

A study was made of the factors governing the structural design of the fully reusable space shuttle booster to establish a rational approach to select optimum structural factors of safety. The study included trade studies of structural factors of safety versus booster service life, weight, cost, and reliability. Similar trade studies can be made on other vehicles using the procedures developed. The major structural components of a selected baseline booster were studied in depth, each being examined to determine the fatigue life, safe-life, and fail-safe capabilities of the baseline design. Each component was further examined to determine its reliability and safety requirements, and the change of structural weight with factors of safety. The apparent factors of safety resulting from fatigue, safe-life, proof test, and fail-safe requirements were identified. The feasibility of reduced factors of safety for design loads such as engine thrust, which are well defined, was examined.

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

NASA Astrophysics Data System (ADS)

Wang, Hongbin; Feng, Yinhan; Cheng, Liang

2018-03-01

Sentence similarity computation plays an increasingly important role in text mining, Web page retrieval, machine translation, speech recognition and question answering systems. Thai language as a kind of resources scarce language, it is not like Chinese language with HowNet and CiLin resources. So the Thai sentence similarity research faces some challenges. In order to solve this problem of the Thai language sentence similarity computation. This paper proposes a novel method to compute the similarity of Thai language sentence based on syntactic structure and semantic vector. This method firstly uses the Part-of-Speech (POS) dependency to calculate two sentences syntactic structure similarity, and then through the word vector to calculate two sentences semantic similarity. Finally, we combine the two methods to calculate two Thai language sentences similarity. The proposed method not only considers semantic, but also considers the sentence syntactic structure. The experiment result shows that this method in Thai language sentence similarity computation is feasible.

Similarity and diversity of translational GTPase factors EF-G, EF4, and BipA: From structure to function.

PubMed

Ero, Rya; Kumar, Veerendra; Chen, Yun; Gao, Yong-Gui

2016-12-01

EF-G, EF4, and BipA are members of the translation factor family of GTPases with a common ribosome binding mode and GTPase activation mechanism. However, topological variations of shared as well as unique domains ensure different roles played by these proteins during translation. Recent X-ray crystallography and cryo-electron microscopy studies have revealed the structural basis for the involvement of EF-G domain IV in securing the movement of tRNAs and mRNA during translocation as well as revealing how the unique C-terminal domains of EF4 and BipA interact with the ribosome and tRNAs contributing to the regulation of translation under certain conditions. EF-G, EF-4, and BipA are intriguing examples of structural variations on a common theme that results in diverse behavior and function. Structural studies of translational GTPase factors have been greatly facilitated by the use of antibiotics, which have revealed their mechanism of action.

Structural texture similarity metrics for image analysis and retrieval.

PubMed

Zujovic, Jana; Pappas, Thrasyvoulos N; Neuhoff, David L

2013-07-01

We develop new metrics for texture similarity that accounts for human visual perception and the stochastic nature of textures. The metrics rely entirely on local image statistics and allow substantial point-by-point deviations between textures that according to human judgment are essentially identical. The proposed metrics extend the ideas of structural similarity and are guided by research in texture analysis-synthesis. They are implemented using a steerable filter decomposition and incorporate a concise set of subband statistics, computed globally or in sliding windows. We conduct systematic tests to investigate metric performance in the context of "known-item search," the retrieval of textures that are "identical" to the query texture. This eliminates the need for cumbersome subjective tests, thus enabling comparisons with human performance on a large database. Our experimental results indicate that the proposed metrics outperform peak signal-to-noise ratio (PSNR), structural similarity metric (SSIM) and its variations, as well as state-of-the-art texture classification metrics, using standard statistical measures.

Hematopoietic cytokines: similarities and differences in the structures, with implications for receptor binding.

PubMed Central

Wlodawer, A.; Pavlovsky, A.; Gustchina, A.

1993-01-01

Crystal and NMR structures of helical cytokines--interleukin-4 (IL-4), granulocyte-macrophage colony-stimulating factor (GM-CSF), and interleukin-2 (IL-2)--have been compared. Root mean square deviations in the C alpha coordinates for the conserved regions of the helices were 1-2 A between different cytokines, about twice the differences observed for independently determined crystal and solution structures of IL-4. Considerable similarity in amino acid sequence in the areas expected to interact with the receptors was detected, and the available mutagenesis data for these cytokines were correlated with structure conservation. Models of cytokine-receptor interactions were postulated for IL-4 based on its structure as well as on the published structure of human growth hormone interacting with its receptors (de Vos, A.M., Ultsch, M., & Kossiakoff, A.A., 1992, Science 255, 306-312). Patches of positively charged residues on the surfaces of helices C and D of IL-4 may be responsible for the interactions with the negatively charged residues found in the complementary parts of the IL-4 receptors. PMID:8401223

Froissart bound and self-similarity based models of proton structure functions

NASA Astrophysics Data System (ADS)

Choudhury, D. K.; Saikia, Baishali

2018-03-01

Froissart bound implies that the total proton-proton cross-section (or equivalently proton structure function) cannot rise faster than log2s ˜log2 1 x. Compatibility of such behavior with the notion of self-similarity in proton structure function was suggested by us sometime back. In the present work, we generalize and improve it further by considering more recent self-similarity based models of proton structure functions and compare with recent data as well as with the model of Block, Durand, Ha and McKay.

Protein domain assignment from the recurrence of locally similar structures

PubMed Central

Tai, Chin-Hsien; Sam, Vichetra; Gibrat, Jean-Francois; Garnier, Jean; Munson, Peter J.

2010-01-01

Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6,373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies. PMID:21287617

Factor structure of the Brief Negative Symptom Scale.

PubMed

Strauss, Gregory P; Hong, L Elliot; Gold, James M; Buchanan, Robert W; McMahon, Robert P; Keller, William R; Fischer, Bernard A; Catalano, Lauren T; Culbreth, Adam J; Carpenter, William T; Kirkpatrick, Brian

2012-12-01

The current study examined the factor structure of the Brief Negative Symptom Scale (BNSS), a next-generation negative symptom rating instrument developed in response to the NIMH-sponsored Consensus Development Conference on Negative Symptoms. Participants included 146 individuals with a DSM-IV diagnosis of schizophrenia or schizoaffective disorder. Principal axis factoring indicated two distinct factors explaining 68.7% of the variance. Similar to previous findings, the factors reflected motivation and pleasure and emotional expressivity. These findings provide further support for the construct validity of the BNSS, and for the existence of these two negative symptom factors. Copyright © 2012 Elsevier B.V. All rights reserved.

The structure factor of primes

NASA Astrophysics Data System (ADS)

Zhang, G.; Martelli, F.; Torquato, S.

2018-03-01

Although the prime numbers are deterministic, they can be viewed, by some measures, as pseudo-random numbers. In this article, we numerically study the pair statistics of the primes using statistical-mechanical methods, particularly the structure factor S(k) in an interval M ≤slant p ≤slant M + L with M large, and L/M smaller than unity. We show that the structure factor of the prime-number configurations in such intervals exhibits well-defined Bragg-like peaks along with a small ‘diffuse’ contribution. This indicates that primes are appreciably more correlated and ordered than previously thought. Our numerical results definitively suggest an explicit formula for the locations and heights of the peaks. This formula predicts infinitely many peaks in any non-zero interval, similar to the behavior of quasicrystals. However, primes differ from quasicrystals in that the ratio between the location of any two predicted peaks is rational. We also show numerically that the diffuse part decays slowly as M and L increases. This suggests that the diffuse part vanishes in an appropriate infinite-system-size limit.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.

PubMed

Tyzack, Jonathan D; Fernando, Laurent; Ribeiro, Antonio J M; Borkakoti, Neera; Thornton, Janet M

2018-04-03

There are numerous applications that use the structures of protein-ligand complexes from the PDB, such as 3D pharmacophore identification, virtual screening, and fragment-based drug design. The structures underlying these applications are potentially much more informative if they contain biologically relevant bound ligands, with high similarity to the cognate ligands. We present a study of ligand-enzyme complexes that compares the similarity of bound and cognate ligands, enabling the best matches to be identified. We calculate the molecular similarity scores using a method called PARITY (proportion of atoms residing in identical topology), which can conveniently be combined to give a similarity score for all cognate reactants or products in the reaction. Thus, we generate a rank-ordered list of related PDB structures, according to the biological similarity of the ligands bound in the structures. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural and functional properties of the N transcriptional activation domain of thyroid transcription factor-1: similarities with the acidic activation domains.

PubMed Central

Tell, G; Perrone, L; Fabbro, D; Pellizzari, L; Pucillo, C; De Felice, M; Acquaviva, R; Formisano, S; Damante, G

1998-01-01

The thyroid transcription factor 1 (TTF-1) is a tissue-specific transcription factor involved in the development of thyroid and lung. TTF-1 contains two transcriptional activation domains (N and C domain). The primary amino acid sequence of the N domain does not show any typical characteristic of known transcriptional activation domains. In aqueous solution the N domain exists in a random-coil conformation. The increase of the milieu hydrophobicity, by the addition of trifluoroethanol, induces a considerable gain of alpha-helical structure. Acidic transcriptional activation domains are largely unstructured in solution, but, under hydrophobic conditions, folding into alpha-helices or beta-strands can be induced. Therefore our data indicate that the inducibility of alpha-helix by hydrophobic conditions is a property not restricted to acidic domains. Co-transfections experiments indicate that the acidic domain of herpes simplex virus protein VP16 (VP16) and the TTF-1 N domain are interchangeable and that a chimaeric protein, which combines VP16 linked to the DNA-binding domain of TTF-1, undergoes the same regulatory constraints that operate for the wild-type TTF-1. In addition, we demonstrate that the TTF-1 N domain possesses two typical properties of acidic activation domains: TBP (TATA-binding protein) binding and ability to activate transcription in yeast. Accordingly, the TTF-1 N domain is able to squelch the activity of the p65 acidic domain. Altogether, these structural and functional data suggest that a non-acidic transcriptional activation domain (TTF-1 N domain) activates transcription by using molecular mechanisms similar to those used by acidic domains. TTF-1 N domain and acidic domains define a family of proteins whose common property is to activate transcription through the use of mechanisms largely conserved during evolutionary development. PMID:9425125

Fast structure similarity searches among protein models: efficient clustering of protein fragments

PubMed Central

2012-01-01

Background For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD) comparison is performed. Most of the time is typically spent on comparison of non-similar structures. For sets with more than, say, 10,000 models this procedure is very time-consuming and alternative faster algorithms, restricting comparisons only to most similar structures would be useful. Results We exploit the inverse triangle inequality on the RMSD between two structures given the RMSDs with a third structure. The lower bound on RMSD may be used, when restricting the search of similarity to a reasonably low RMSD threshold value, to speed up similarity searches significantly. Tests are performed on large sets of decoys which are widely used as test cases for predictive methods, with a speed-up of up to 100 times with respect to all-vs-all comparison depending on the set and parameters used. Sample applications are shown. Conclusions The algorithm presented here allows fast comparison of large data sets of structures with limited memory requirements. As an example of application we present clustering of more than 100000 fragments of length 5 from the top500H dataset into few hundred representative fragments. A more realistic scenario is provided by the search of similarity within the very large decoy sets used for the tests. Other applications regard filtering nearly-indentical conformation in selected CASP9 datasets and clustering molecular dynamics snapshots. Availability A linux executable and a Perl script with examples are given in the supplementary material (Additional file 1). The source code is available upon request from the authors. PMID:22642815

Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

PubMed

Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

2016-07-01

Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.

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

PubMed

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.

Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

PubMed Central

Bertazzoni, Umberto; Turci, Marco; Avesani, Francesca; Di Gennaro, Gianfranco; Bidoia, Carlo; Romanelli, Maria Grazia

2011-01-01

Human T-lymphotropic viruses type 1 (HTLV-1) and type 2 (HTLV-2) present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity. PMID:21994745

Protein docking by the interface structure similarity: how much structure is needed?

PubMed

Sinha, Rohita; Kundrotas, Petras J; Vakser, Ilya A

2012-01-01

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.

Befriending Risky Peers: Factors Driving Adolescents’ Selection of Friends with Similar Marijuana Use

PubMed Central

de la Haye, Kayla; Green, Harold D.; Pollard, Michael S.; Kennedy, David P.; Tucker, Joan S.

2014-01-01

Adolescents often befriend peers who are similar to themselves on a range of demographic, behavioral, and social characteristics, including substance use. Similarities in lifetime history of marijuana use have even been found to predict adolescent friendships, and we examine whether this finding is explained by youth’s selection of friends who are similar on a range of more proximate, observable characteristics that are risk factors for marijuana use. Using two waves of individual and social network data from two high schools that participated in Add Health (N = 1,612; 52.7% male), we apply longitudinal models for social networks to test whether or not several observable risky attributes (psychological, behavioral, and social) predict adolescent friendship choices, and if these preferences explain friend’s similarities on lifetime marijuana use. Findings show that similarities on several risk factors predict friendship choices, however controlling for this, the preference to befriend peers with a similar history of marijuana use largely persists. The results highlight the range of social selection processes that lead to similarities in marijuana use among friends and larger peer groups, and that also give rise to friendship groups whose members share similar risk factors for substance use. Friends with high “collective risk” are likely to be important targets for preventing the onset and social diffusion of substance use in adolescents. PMID:25365913

Parallel seed-based approach to multiple protein structure similarities detection

DOE PAGES

Chapuis, Guillaume; Le Boudic-Jamin, Mathilde; Andonov, Rumen; ...

2015-01-01

Finding similarities between protein structures is a crucial task in molecular biology. Most of the existing tools require proteins to be aligned in order-preserving way and only find single alignments even when multiple similar regions exist. We propose a new seed-based approach that discovers multiple pairs of similar regions. Its computational complexity is polynomial and it comes with a quality guarantee—the returned alignments have both root mean squared deviations (coordinate-based as well as internal-distances based) lower than a given threshold, if such exist. We do not require the alignments to be order preserving (i.e., we consider nonsequential alignments), which makesmore » our algorithm suitable for detecting similar domains when comparing multidomain proteins as well as to detect structural repetitions within a single protein. Because the search space for nonsequential alignments is much larger than for sequential ones, the computational burden is addressed by extensive use of parallel computing techniques: a coarse-grain level parallelism making use of available CPU cores for computation and a fine-grain level parallelism exploiting bit-level concurrency as well as vector instructions.« less

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

PubMed

Dallaston, Michael C; Fontelos, Marco A; Tseluiko, Dmitri; Kalliadasis, Serafim

2018-01-19

The formation of iterated structures, such as satellite and subsatellite drops, filaments, and bubbles, is a common feature in interfacial hydrodynamics. Here we undertake a computational and theoretical study of their origin in the case of thin films of viscous fluids that are destabilized by long-range molecular or other forces. We demonstrate that iterated structures appear as a consequence of discrete self-similarity, where certain patterns repeat themselves, subject to rescaling, periodically in a logarithmic time scale. The result is an infinite sequence of ridges and filaments with similarity properties. The character of these discretely self-similar solutions as the result of a Hopf bifurcation from ordinarily self-similar solutions is also described.

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

DOEpatents

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.

Clay Mineral Structure Similar to Clays Observed in Mudstone on Mars

NASA Image and Video Library

2013-12-09

This schematic shows the atomic structure of the smallest units that make up the layers and interlayer region of clay minerals. This structure is similar to the clay mineral in drilled rock powder collected by NASA Curiosity Mars rover.

How similar is the electronic structures of β-lactam and alanine?

NASA Astrophysics Data System (ADS)

Chatterjee, Subhojyoti; Ahmed, Marawan; Wang, Feng

2016-02-01

The C1s spectra of β-lactam i.e. 2-azetidinone (C3H5NO), a drug and L-alanine (C3H7NO2), an amino acid, exhibit striking similarities, which may be responsible for the competition between 2-azetidinone and the alanyl-alanine moiety in biochemistry. The present study is to reveal the degree of similarities and differences between their electronic structures of the two model molecular pairs. It is found that the similarities in C1s and inner valence binding energy spectra are due to their bonding connections but other properties such as ring structure (in 2-azetidinone) and chiral carbon (alanine) can be very different. Further, the inner valence region of ionization potential greater than 18 eV for 2-azetidinone and alanine is also significantly similar. Finally the strained lactam ring exhibits more chemical reactivity measured at all non-hydrogen atoms by Fukui functions with respect to alanine.

A new similarity measure for link prediction based on local structures in social networks

NASA Astrophysics Data System (ADS)

Aghabozorgi, Farshad; Khayyambashi, Mohammad Reza

2018-07-01

Link prediction is a fundamental problem in social network analysis. There exist a variety of techniques for link prediction which applies the similarity measures to estimate proximity of vertices in the network. Complex networks like social networks contain structural units named network motifs. In this study, a newly developed similarity measure is proposed where these structural units are applied as the source of similarity estimation. This similarity measure is tested through a supervised learning experiment framework, where other similarity measures are compared with this similarity measure. The classification model trained with this similarity measure outperforms others of its kind.

Exploring the Factor Structure of Neurocognitive Measures in Older Individuals

PubMed Central

Santos, Nadine Correia; Costa, Patrício Soares; Amorim, Liliana; Moreira, Pedro Silva; Cunha, Pedro; Cotter, Jorge; Sousa, Nuno

2015-01-01

Here we focus on factor analysis from a best practices point of view, by investigating the factor structure of neuropsychological tests and using the results obtained to illustrate on choosing a reasonable solution. The sample (n=1051 individuals) was randomly divided into two groups: one for exploratory factor analysis (EFA) and principal component analysis (PCA), to investigate the number of factors underlying the neurocognitive variables; the second to test the “best fit” model via confirmatory factor analysis (CFA). For the exploratory step, three extraction (maximum likelihood, principal axis factoring and principal components) and two rotation (orthogonal and oblique) methods were used. The analysis methodology allowed exploring how different cognitive/psychological tests correlated/discriminated between dimensions, indicating that to capture latent structures in similar sample sizes and measures, with approximately normal data distribution, reflective models with oblimin rotation might prove the most adequate. PMID:25880732

Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive molecules.

PubMed

Wassermann, Anne Mai; Lounkine, Eugen; Glick, Meir

2013-03-25

Virtual screening using bioactivity profiles has become an integral part of currently applied hit finding methods in pharmaceutical industry. However, a significant drawback of this approach is that it is only applicable to compounds that have been biologically tested in the past and have sufficient activity annotations for meaningful profile comparisons. Although bioactivity data generated in pharmaceutical institutions are growing on an unprecedented scale, the number of biologically annotated compounds still covers only a minuscule fraction of chemical space. For a newly synthesized compound or an isolated natural product to be biologically characterized across multiple assays, it may take a considerable amount of time. Consequently, this chemical matter will not be included in virtual screening campaigns based on bioactivity profiles. To overcome this problem, we herein introduce bioturbo similarity searching that uses chemical similarity to map molecules without biological annotations into bioactivity space and then searches for biologically similar compounds in this reference system. In benchmark calculations on primary screening data, we demonstrate that our approach generally achieves higher hit rates and identifies structurally more diverse compounds than approaches using chemical information only. Furthermore, our method is able to discover hits with novel modes of inhibition that traditional 2D and 3D similarity approaches are unlikely to discover. Test calculations on a set of natural products reveal the practical utility of the approach for identifying novel and synthetically more accessible chemical matter.

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

PubMed

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.

Cloud4Psi: cloud computing for 3D protein structure similarity searching

PubMed Central

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

2014-01-01

Summary: 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. Availability and implementation: 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. Contact: dariusz.mrozek@polsl.pl PMID:24930141

Measuring the dynamic structure factor of a quantum gas undergoing a structural phase transition

PubMed Central

Landig, Renate; Brennecke, Ferdinand; Mottl, Rafael; Donner, Tobias; Esslinger, Tilman

2015-01-01

The dynamic structure factor is a central quantity describing the physics of quantum many-body systems, capturing structure and collective excitations of a material. In condensed matter, it can be measured via inelastic neutron scattering, which is an energy-resolving probe for the density fluctuations. In ultracold atoms, a similar approach could so far not be applied because of the diluteness of the system. Here we report on a direct, real-time and nondestructive measurement of the dynamic structure factor of a quantum gas exhibiting cavity-mediated long-range interactions. The technique relies on inelastic scattering of photons, stimulated by the enhanced vacuum field inside a high finesse optical cavity. We extract the density fluctuations, their energy and lifetime while the system undergoes a structural phase transition. We observe an occupation of the relevant quasi-particle mode on the level of a few excitations, and provide a theoretical description of this dissipative quantum many-body system. PMID:25944151

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

PubMed

Saberi Fathi, S M

2016-10-01

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

Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes.

PubMed Central

Dougherty, W G; Semler, B L

1993-01-01

Many viruses express their genome, or part of their genome, initially as a polyprotein precursor that undergoes proteolytic processing. Molecular genetic analyses of viral gene expression have revealed that many of these processing events are mediated by virus-encoded proteinases. Biochemical activity studies and structural analyses of these viral enzymes reveal that they have remarkable similarities to cellular proteinases. However, the viral proteinases have evolved unique features that permit them to function in a cellular environment. In this article, the current status of plant and animal virus proteinases is described along with their role in the viral replication cycle. The reactions catalyzed by viral proteinases are not simple enzyme-substrate interactions; rather, the processing steps are highly regulated, are coordinated with other viral processes, and frequently involve the participation of other factors. Images PMID:8302216

Factor structure of PTSD, and relation with gender in trauma survivors from India.

PubMed

Charak, Ruby; Armour, Cherie; Elklit, Ask; Angmo, Disket; Elhai, Jon D; Koot, Hans M

2014-01-01

The factor structure of posttraumatic stress disorder (PTSD) has been extensively studied in Western countries. Some studies have assessed its factor structure in Asia (China, Sri Lanka, and Malaysia), but few have directly assessed the factor structure of PTSD in an Indian adult sample. Furthermore, in a largely patriarchal society in India with strong gender roles, it becomes imperative to assess the association between the factors of PTSD and gender. The purpose of the present study was to assess the factor structure of PTSD in an Indian sample of trauma survivors based on prevailing models of PTSD defined in the DSM-IV-TR (APA, 2000), and to assess the relation between PTSD factors and gender. The sample comprised of 313 participants (55.9% female) from Jammu and Kashmir, India, who had experienced a natural disaster (N=200) or displacement due to cross-border firing (N=113). Three existing PTSD models-two four-factor models (Emotional Numbing and Dysphoria), and a five-factor model (Dysphoric Arousal)-were tested using Confirmatory Factor Analysis with addition of gender as a covariate. The three competing models had similar fit indices although the Dysphoric Arousal model fit significantly better than Emotional Numbing and Dysphoria models. Gender differences were found across the factors of Re-experiencing and Anxious arousal. Findings indicate that the Dysphoric Arousal model of PTSD was the best model; albeit the fit indices of all models were fairly similar. Compared to males, females scored higher on factors of Re-experiencing and Anxious arousal. Gender differences found across two factors of PTSD are discussed in light of the social milieu in India.

Factor structure of PTSD, and relation with gender in trauma survivors from India

PubMed Central

Charak, Ruby; Armour, Cherie; Elklit, Ask; Angmo, Disket; Elhai, Jon D.; Koot, Hans M.

2014-01-01

Background The factor structure of posttraumatic stress disorder (PTSD) has been extensively studied in Western countries. Some studies have assessed its factor structure in Asia (China, Sri Lanka, and Malaysia), but few have directly assessed the factor structure of PTSD in an Indian adult sample. Furthermore, in a largely patriarchal society in India with strong gender roles, it becomes imperative to assess the association between the factors of PTSD and gender. Objective The purpose of the present study was to assess the factor structure of PTSD in an Indian sample of trauma survivors based on prevailing models of PTSD defined in the DSM-IV-TR (APA, 2000), and to assess the relation between PTSD factors and gender. Method The sample comprised of 313 participants (55.9% female) from Jammu and Kashmir, India, who had experienced a natural disaster (N=200) or displacement due to cross-border firing (N=113). Results Three existing PTSD models—two four-factor models (Emotional Numbing and Dysphoria), and a five-factor model (Dysphoric Arousal)—were tested using Confirmatory Factor Analysis with addition of gender as a covariate. The three competing models had similar fit indices although the Dysphoric Arousal model fit significantly better than Emotional Numbing and Dysphoria models. Gender differences were found across the factors of Re-experiencing and Anxious arousal. Conclusions Findings indicate that the Dysphoric Arousal model of PTSD was the best model; albeit the fit indices of all models were fairly similar. Compared to males, females scored higher on factors of Re-experiencing and Anxious arousal. Gender differences found across two factors of PTSD are discussed in light of the social milieu in India. PMID:25413575

Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia.

PubMed

Ertl, Peter; Patiny, Luc; Sander, Thomas; Rufener, Christian; Zasso, Michaël

2015-01-01

Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation. The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

Score reliability and factor similarity of the Sociocultural Attitudes Towards Appearance Questionnaire-3 (SATAQ-3) among four ethnic groups

PubMed Central

2013-01-01

Background This study evaluated the score reliability and equivalence of factor structure of the Sociocultural Attitudes towards Appearance Questionnaire-3 (SATAQ-3) [1] in a sample of female college students from the four largest ethnic groups in the USA. Methods Participants were 1245 women who self-identified as European American/White (n = 543), African American/Black (n = 137), Asian American (n = 317), or Latina/Hispanic (n = 248). All completed the SATAQ-3 and a demographic questionnaire. To test the factor similarity and score reliability across groups, we used exploratory factor analysis and calculated Cronbach’s alphas (respectively). Results Score reliability was high for all groups. Tests of factor equivalence suggested that the four pre-established factors of the SATAQ-3 (i.e., knowledge, perceived pressure, thin-ideal internalization, athletic-ideal internalization) were similar for women of all ethnic groups. Only two items (20 and 27) did not consistently load on the previously identified scale across all four groups. When scored, African Americans reported significantly less perceived pressure and internalization than all other groups. Conclusions Results support the use of the SATAQ-3 in female college students of these four ethnicities. PMID:24999395

Similarities in Acquired Factors Related to Postmenopausal Osteoporosis and Sarcopenia

PubMed Central

Sirola, Joonas; Kröger, Heikki

2011-01-01

Postmenopausal population is at increased risk of musculoskeletal impairments. Sarcopenia and osteoporosis are associated with significant morbidity and social and health-care costs. These two conditions are uniquely linked with similarities in pathophysiology and diagnostic methods. Uniform diagnostic criteria for sarcopenia are still evolving. Postmenopausal sarcopenia and osteoporosis share many environmental risk- and preventive factors. Moreover, geriatric frailty syndrome may result from interaction of osteoporosis and sarcopenia and may lead to increased mortality. The present paper reviews the factors in evolution of postmenopausal sarcopenia and osteoporosis. PMID:21904688

Roof structural system, similar in design to peaked roofs of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Roof structural system, similar in design to peaked roofs of rolling mill, yet note abandonment of phoenix columns for compression members. - Phoenix Iron Company, Girder Shop No. 6, North of French Creek, west of Gay Street, Phoenixville, Chester County, PA

Factor Structure of the WPPSI in Mental Health Clinic Settings.

ERIC Educational Resources Information Center

Haynes, Jack P.; Atkinson, David

1984-01-01

Factor-analyzed the Wechsler Preschool and Primary Scale of Intelligence (WPPSI) scores of emotionally disturbed children (N=181). The results suggested that the structure of intelligence for emotionally disturbed children is similar to that for normal children. WPPSI profile analysis that uses subtest scores may be invalid in clinical settings.…

Lewis Structure Representation of Free Radicals Similar to ClO

ERIC Educational Resources Information Center

Hirsch, Warren; Kobrak, Mark

2007-01-01

The study describes the Lewis structure representation of various free radicals, which are quite similar to the ClO radical and its isoelectronic analogues. The analysis of the periodic trends of these radicals shows that oxygen is the most electronegative atom among them.

Structure Modulates Similarity-Based Interference in Sluicing: An Eye Tracking study

PubMed Central

Harris, Jesse A.

2015-01-01

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 or diagnosticity of retrieval cues. PMID:26733893

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Sex similarities and differences in risk factors for recurrence of major depression.

PubMed

van Loo, Hanna M; Aggen, Steven H; Gardner, Charles O; Kendler, Kenneth S

2017-11-27

Major depression (MD) occurs about twice as often in women as in men, but it is unclear whether sex differences subsist after disease onset. This study aims to elucidate potential sex differences in rates and risk factors for MD recurrence, in order to improve prediction of course of illness and understanding of its underlying mechanisms. We used prospective data from a general population sample (n = 653) that experienced a recent episode of MD. A diverse set of potential risk factors for recurrence of MD was analyzed using Cox models subject to elastic net regularization for males and females separately. Accuracy of the prediction models was tested in same-sex and opposite-sex test data. Additionally, interactions between sex and each of the risk factors were investigated to identify potential sex differences. Recurrence rates and the impact of most risk factors were similar for men and women. For both sexes, prediction models were highly multifactorial including risk factors such as comorbid anxiety, early traumas, and family history. Some subtle sex differences were detected: for men, prediction models included more risk factors concerning characteristics of the depressive episode and family history of MD and generalized anxiety, whereas for women, models included more risk factors concerning early and recent adverse life events and socioeconomic problems. No prominent sex differences in risk factors for recurrence of MD were found, potentially indicating similar disease maintaining mechanisms for both sexes. Course of MD is a multifactorial phenomenon for both males and females.

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

PubMed

Teixeira, Ana L; Falcao, Andre O

2014-07-28

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

Empirical comparison of local structural similarity indices for collaborative-filtering-based recommender systems

NASA Astrophysics Data System (ADS)

Zhang, Qian-Ming; Shang, Ming-Sheng; Zeng, Wei; Chen, Yong; Lü, Linyuan

2010-08-01

Collaborative filtering is one of the most successful recommendation techniques, which can effectively predict the possible future likes of users based on their past preferences. The key problem of this method is how to define the similarity between users. A standard approach is using the correlation between the ratings that two users give to a set of objects, such as Cosine index and Pearson correlation coefficient. However, the costs of computing this kind of indices are relatively high, and thus it is impossible to be applied in the huge-size systems. To solve this problem, in this paper, we introduce six local-structure-based similarity indices and compare their performances with the above two benchmark indices. Experimental results on two data sets demonstrate that the structure-based similarity indices overall outperform the Pearson correlation coefficient. When the data is dense, the structure-based indices can perform competitively good as Cosine index, while with lower computational complexity. Furthermore, when the data is sparse, the structure-based indices give even better results than Cosine index.

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Structural fabrication quality as a factor of industrial facilities safety

NASA Astrophysics Data System (ADS)

Tishkov, E. V.; Kardaev, E. M.; Stolbova, S. Yu; Shishova, O. S.

2018-04-01

In the conditions of industrial facilities high wear degree, it is very important to ensure the possibility of their safe operation in order to avoid various kinds of accidents and catastrophes. As practice shows, industrial plant collapses can occur suddenly under normal operating conditions. Usually, such accidents can take place at different stages of structures life cycle. One of the reasons for this is the initially low quality of reinforced concrete structures fabrication. The article considers the factors contributing to the collapse of reinforced concrete structures of water purification tanks located on the territory of the Omsk Region. The main surveys results on tank structures after collapse with the use of ultrasonic and physical methods of investigation are presented. On the basis of the obtained data analysis, it was found that the main cause of the accidents was the insufficient load-bearing capacity of typical reinforced concrete structures, caused by defects in their fabrication in the factory conditions because of exceeding the standard displacement from the design position of the working reinforcement. Recommendations are given on the identification of defective structures and the prevention of similar accidents when operating similar tanks at manufacturing plants constructed from standard designs.

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Temperament Factor Structure in Fragile X Syndrome: The Children's Behavior Questionnaire

PubMed Central

Roberts, Jane E.; Tonnsen, Bridgette L.; Robinson, Marissa; McQuillin, Samuel D.; Hatton, Deborah D.

2014-01-01

Early patterns of temperament lay the foundation for a variety of developmental constructs such as self-regulation, psychopathology, and resilience. Children with fragile X syndrome (FXS) display unique patterns of temperament compared to age-matched clinical and non-clinical samples, and early patterns of temperament have been associated with later anxiety in this population. Despite these unique patterns in FXS and recent reports of atypical factor structure of temperament questionnaires in Williams Syndrome (Leyfer, John, Woodruff-Borden, & Mervis, 2012), no studies have examined the latent factor structure of temperament scales in FXS to ensure measurement validity in this sample. The present study used confirmatory factor analysis to examine the factor structure of a well-validated parent-reported temperament questionnaire, the Children's Behavior Questionnaire (Rothbart, Ahadi, Hershey, & Fisher, 2001), in a sample of 90 males with FXS ages 3-9 years. Our data produced a similar, but not identical, three-factor model that retained the original CBQ factors of negative affectivity, effortful control, and extraversion/surgency. In particular, our FXS sample demonstrated stronger factor loadings for fear and shyness than previously reported loadings in non-clinical samples, consistent with reports of poor social approach and elevated anxiety in this population. Although the original factor structure of the Children's Behavior Questionnaire is largely retained in children with FXS, differences in factor loading magnitudes may reflect phenotypic characteristics of the syndrome. These findings may inform future developmental and translational research efforts. PMID:24380785

An integral-factorized implementation of the driven similarity renormalization group second-order multireference perturbation theory

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

Hannon, Kevin P.; Li, Chenyang; Evangelista, Francesco A., E-mail: francesco.evangelista@emory.edu

2016-05-28

We report an efficient implementation of a second-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT2) [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)]. Our implementation employs factorized two-electron integrals to avoid storage of large four-index intermediates. It also exploits the block structure of the reference density matrices to reduce the computational cost to that of second-order Møller–Plesset perturbation theory. Our new DSRG-MRPT2 implementation is benchmarked on ten naphthyne isomers using basis sets up to quintuple-ζ quality. We find that the singlet-triplet splittings (Δ{sub ST}) of the naphthyne isomers strongly depend onmore » the equilibrium structures. For a consistent set of geometries, the Δ{sub ST} values predicted by the DSRG-MRPT2 are in good agreements with those computed by the reduced multireference coupled cluster theory with singles, doubles, and perturbative triples.« less

Scientific literacy: Factor structure and gender differences

NASA Astrophysics Data System (ADS)

Manhart, James Joseph

The purpose of this study was to investigate the factor structure of scientific literacy and to document any gender differences with respect to each factor. Participants included 1139 students (574 females, 565 males) in grades 9 through 12 who were taking a science class at one of four Midwestern high schools. Based on National Science Education Standards, a 100 item multiple-choice test was constructed to assess scientific literacy. Confirmatory factor analysis of item parcels suggested a three factor model was the best way to explain the data resulting from the administration of this test. The factors were labeled constructs of science, abilities necessary to do scientific inquiry, and social aspects of science. Gender differences with respect to these factors were examined using analysis of variance procedures. Because differential enrollment in science classes could cause gender differences in grades 11 and 12, parallel analyses were conducted on the grades 9 and 10 subsample and the grades 11 and 12 subsample. However, the results of the two analyses were similar. The most consistent gender difference observed was that females performed better than males on the social aspects of science factor. Males tended to perform better than females on the constructs of science factor, although no consistent gender difference was noted for items dealing with life science. With respect to the abilities necessary to do scientific inquiry factor, females tended to perform better than males in grades 9 and 10, while no consistent gender difference was observed in grades 11 and 12. Gender differences were also examined using the Mantel-Haenszel procedure to flag individual items that functioned differently for females and males of the same ability. Twelve items were flagged for grades 9 and 10 (8 in favor of females, 4 in favor of males). Fourteen items were flagged for grades 11 and 12 (7 in favor of females, 7 in favor of males). All of the flagged items exhibited only

The Factor Structure of the Vocational Preference Inventory for Black and White College Students

ERIC Educational Resources Information Center

Yom, B. Lee; And Others

1975-01-01

In the present study, the Vocational Preference Inventory scores for a group of black students and white students were factor analyzed and the black structure was rotated to correspond to the white structure. The correspondence between the variables for black and white students was found to be very similar. (Author)

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

NASA Astrophysics Data System (ADS)

Rosinger, Elemér E.

2010-05-01

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

The Secondary Structure of Human Hageman Factor (Factor XII) and its Alteration by Activating Agents

PubMed Central

McMillin, Carl R.; Saito, Hidehiko; Ratnoff, Oscar D.; Walton, Alan G.

1974-01-01

Hageman factor (factor XII) is activated by exposure to surfaces such as glass or by solutions of certain compounds, notably ellagic acid. Changes in the structure of Hageman factor accompanying activation have been examined in this study by circular dichroism spectroscopy. The spectrum of unactivated Hageman factor in aqueous solutions suggests that its conformation is mainly aperiodic. Various perturbants altered the conformation of Hageman factor in differing ways, demonstrating the sensitivity of Hageman factor to its environment. After activation of Hageman factor with solutions of ellagic acid, a negative trough appeared in the region of the circular dichroism spectrum commonly assigned to tyrosine residues, along with other minor changes in the peptide spectral region. Some of these changes are similar to changes that occurred upon partial neutralization of the basic residues at alkali pH. Activation of Hageman factor by adsorption to quartz surfaces (in an aqueous environment) also produced changes similar to those in the ellagic acid-activated Hageman factor, including the negative ellipticity in the tyrosine region. These observations suggest that the activation process may be related to a change in status of some of the basic amino acid residues, coupled with a specific change in the environment of some tyrosine residues. The importance of these changes during the activation process remains to be determined. The sensitivity of Hageman factor to its environment is consistent with the view that the initiation of clotting by exposure of plasma to appropriate agents is brought about by alterations in the conformation of Hageman factor that occur in the apparent absence of Fletcher factor or other recognized clotting factors. Images PMID:4373492

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

PubMed

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-05-01

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

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

PubMed Central

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-01-01

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

Structural analysis of the human fibroblast growth factor receptor 4 kinase.

PubMed

Lesca, E; Lammens, A; Huber, R; Augustin, M

2014-11-11

The family of fibroblast growth factor receptors (FGFRs) plays an important and well-characterized role in a variety of pathological disorders. FGFR4 is involved in myogenesis and muscle regeneration. Mutations affecting the kinase domain of FGFR4 may cause cancer, for example, breast cancer or rhabdomyosarcoma. Whereas FGFR1-FGFR3 have been structurally characterized, the structure of the FGFR4 kinase domain has not yet been reported. In this study, we present four structures of the kinase domain of FGFR4, in its apo-form and in complex with different types of small-molecule inhibitors. The two apo-FGFR4 kinase domain structures show an activation segment similar in conformation to an autoinhibitory segment observed in the hepatocyte growth factor receptor kinase but different from the known structures of other FGFR kinases. The structures of FGFR4 in complex with the type I inhibitor Dovitinib and the type II inhibitor Ponatinib reveal the molecular interactions with different types of kinase inhibitors and may assist in the design and development of FGFR4 inhibitors. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Graphic Representation of Structure in Similarity/Dissimilarity Matrices: Alternative Methods.

ERIC Educational Resources Information Center

Rudnitsky, Alan N.

Three approaches to the graphic representation of similarity and dissimilarity matrices are compared and contrasted. Specifically, Kruskal's multidimensional scaling, Johnson's hierarchical clustering, and Waern's graphing techniques are employed to depict, in two dimensions, data representing the structure of a set of botanical concepts. Each of…

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

PubMed

Perualila-Tan, Nolen Joy; Shkedy, Ziv; Talloen, Willem; Göhlmann, Hinrich W H; Moerbeke, Marijke Van; Kasim, Adetayo

2016-08-01

The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach.

Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination.

PubMed

Jia, Lei; Li, Lin; Gui, Tao; Liu, Siyang; Li, Hanping; Han, Jingwan; Guo, Wei; Liu, Yongjian; Li, Jingyun

2016-09-21

With increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms. Near full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated. Pearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination. These results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our

Structure of rat acidic fibroblast growth factor at 1.4 Å resolution

PubMed Central

Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Arthur; Kristensen, Ole; Kastrup, Jette Sandholm; Berezin, Vladimir; Bock, Elisabeth; Gajhede, Michael

2007-01-01

Fibroblast growth factors (FGFs) constitute a family of 22 structurally related heparin-binding polypeptides that are involved in the regulation of cell growth, survival, differentiation and migration. Here, a 1.4 Å resolution X-ray structure of rat FGF1 is presented. Two molecules are present in the asymmetric unit of the crystal and they coordinate a total of five sulfate ions. The structures of human, bovine and newt FGF1 have been published previously. Human and rat FGF1 are found to have very similar structures. PMID:17277441

An analysis of the structure of the compound biological effectiveness factor.

PubMed

Ono, Koji

2016-08-01

This report is an analysis of the structure of the compound biological effectiveness (CBE) factor. The value of the CBE factor previously reported was revalued for the central nervous system, skin and lung. To describe the structure, the following terms are introduced: the vascular CBE (v-CBE), intraluminal CBE (il-CBE), extraluminal CBE (el-CBE) and non-vascular CBE (nv-CBE) factors and the geometric biological factor (GBF), i.e. the contributions that are derived from the total dose to the vasculature, each dose to vasculature from the intraluminal side and the extraluminal side, the dose to the non-vascular tissue and the factor to calculate el-CBE from il-CBE, respectively. The el-CBE factor element was also introduced to relate il-CBE to el-CBE factors. A CBE factor of 0.36 for disodium mercaptoundecahydrododecaborate (BSH) for the CNS was independent of the (10)B level in the blood; however, that for p-Boron-L-phenylalanine (BPA) increased with the (10)B level ratio of the normal tissue to the blood (N/B). The CBE factor was expressed as follows: factor = 0.32 + N/B × 1.65. The factor of 0.32 at 0 of N/B was close to the CBE factor for BSH. GBFs had similar values, between BSH and BPA, 1.39 and 1.52, respectively. The structure of the CBE factor for BPA to the lung was also elucidated based on this idea. The factor is described as follows: CBE factor = 0.32 + N/B × 1.80. By this elucidation of the structure of the CBE factor, it is expected that basic and clinical research into boron neutron capture therapy will progress. © The Author 2016. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Factor Structure of a Multidimensional Gender Identity Scale in a Sample of Chinese Elementary School Children

PubMed Central

Yu, Lu; Xie, Dong; Shek, Daniel T. L.

2012-01-01

This study examined the factor structure of a scale based on the four-dimensional gender identity model (Egan and Perry, 2001) in 726 Chinese elementary school students. Exploratory factor analyses suggested a three-factor model, two of which corresponded to “Felt Pressure” and “Intergroup Bias” in the original model. The third factor “Gender Compatibility” appeared to be a combination of “Gender Typicality” and “Gender Contentment” in the original model. Follow-up confirmatory factor analysis (CFA) indicated that, relative to the initial four-factor structure, the three-factor model fits the current Chinese sample better. These results are discussed in light of cross-cultural similarities and differences in development of gender identity. PMID:22701363

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

NASA Astrophysics Data System (ADS)

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

Factor Structure of Cognition and Functional Capacity in Two Studies of Schizophrenia and Bipolar Disorder: Implications for Genomic Studies

PubMed Central

Harvey, Philip D.; Aslan, Mihaela; Du, Mengtian; Zhao, Hongyu; Siever, Larry J.; Pulver, Ann; Gaziano, J. Michael; Concato, John

2015-01-01

Objective Impairments in cognition and everyday functioning are common in schizophrenia and bipolar disorder. Based on two studies of schizophrenia (SCZ) and bipolar I disorder (BPI) with similar methods, this paper presents factor analyses of cognitive and functional capacity (FC) measures. The overall goal of these analyses was to determine whether performance-based assessments should be examined individually, or aggregated on the basis of the correlational structure of the tests and as well as to evaluate the similarity of factor structures in SCZ and BPI. Method Veterans Affairs (VA) Cooperative Studies Program study #572, evaluated cognitive and FC measures among 5,414 BPI and 3,942 SZ patients. A second study evaluated similar neuropsychological (NP) and FC measures among 368 BPI and 436 SZ patients. Principal components analysis, as well as exploratory and confirmatory factor analyses, were used to examine the data. Results Analyses in both datasets suggested that NP and FC measures were explained by of a single underlying factor in BPI and SCZ patients, both when analyzed separately or as in a combined sample. The factor structure in both studies was similar, with or without inclusion of FC measures; homogeneous loadings were observed for that single factor across cognitive and FC domains across the samples. Conclusions The empirically derived factor model suggests that NP performance and FC are best explained as a single latent trait applicable to people with schizophrenia and bipolar illness. This single measure may enhance the robustness of the analyses relating genomic data to performance-based phenotypes. PMID:26710094

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011

Leonardo's branching rule in trees: How self-similar structures resist wind

NASA Astrophysics Data System (ADS)

Eloy, Christophe

2011-11-01

In his notebooks, Leonardo da Vinci observed that ``all the branches of a tree at every stage of its height when put together are equal in thickness to the trunk,'' which means that the total cross-sectional area of branches is conserved across branching nodes. The usual explanation for this rule involves vascular transport of sap, but this argument is questionable because the portion of wood devoted to transport varies across species and can be as low as 5%. It is proposed here that Leonardo's rule is a consequence of the tree skeleton having a self-similar structure and the branch diameters being adjusted to resist wind-induced loads. To address this problem, a continuous model is first considered by neglecting the geometrical details of branching and wind incident angles. The robustness of this analytical model is then assessed with numerical simulations on tree skeletons generated with a simple branching rule producing self-similar structures. This study was supported by the European Union through the fellowship PIOF-GA-2009-252542.

Comparing Factor Structures of Adolescent Psychopathology

ERIC Educational Resources Information Center

Verona, Edelyn; Javdani, Shabnam; Sprague, Jenessa

2011-01-01

Research on the structure of adolescent psychopathology can provide information on broad factors that underlie different forms of maladjustment in youths. Multiple studies from the literature on adult populations suggest that 2 factors, Internalizing and Externalizing, meaningfully comprise the factor structure of adult psychopathology (e.g.,…

Structure and similarity of helminth communities of six species of Australian turtles.

PubMed

Zelmer, Derek A; Platt, Thomas R

2008-08-01

Patterns of infracommunity structure and infra- and component community similarity were examined for helminths of 6 species of turtles, each collected from a single locality in Australia in 1993 and 1994. Elseya latisternum (N = 11) and Emydura kreffti (N = 16) were collected from northern Queensland, Emydura macquarii macquarii (N = 11) from southern Queensland, Emydura macquarii dhara (N = 11) and Chelodina longicollis (N = 11) from northern New South Wales, and Chelodina oblonga (N = 5) from Western Australia. Local parasite species richness was not correlated with host geographical range. Differences in parasite diversity among host species were related primarily to differences in evenness, a pattern attributed to local habitat characteristics, rather than species-specific differences in colonization potential. Ordination and analysis of similarity demonstrated the patterns of infracommunity structure of Chelodina spp. to be distinct from those of the other host species sampled, which showed considerable overlap among patterns of infracommunity structure. Despite overlap with the component communities of Em. kreffti and El. latisternum, the component communities of Em. m. dhara and Em. m. macquarii were more distinct from one another than either was to the component communities of Em. kreffti or El. latisternum.

Factor structure of cognition and functional capacity in two studies of schizophrenia and bipolar disorder: Implications for genomic studies.

PubMed

Harvey, Philip D; Aslan, Mihaela; Du, Mengtian; Zhao, Hongyu; Siever, Larry J; Pulver, Ann; Gaziano, J Michael; Concato, John

2016-01-01

Impairments in cognition and everyday functioning are common in schizophrenia and bipolar disorder (BPD). In this article, we present factor analyses of cognitive and functional capacity (FC) measures based on 2 studies of schizophrenia (SCZ) and bipolar I disorder (BPI) using similar methods. The overall goal of these analyses was to determine whether performance-based assessments should be examined individually, or aggregated on the basis of the correlational structure of the tests, as well as to evaluate the similarity of factor structures of SCZ and BPI. Veterans Affairs Cooperative Studies Program Study #572 (Harvey et al., 2014) evaluated cognitive and FC measures among 5,414 BPI and 3,942 SCZ patients. A 2nd study evaluated similar neuropsychological (NP) and FC measures among 368 BPI and 436 SCZ patients. Principal components analysis, as well as exploratory and CFAs, were used to examine the data. Analyses in both datasets suggested that NP and FC measures were explained by a single underlying factor in BPI and SCZ patients, both when analyzed separately or as in a combined sample. The factor structure in both studies was similar, with or without inclusion of FC measures; homogeneous loadings were observed for that single factor across cognitive and FC domains across the samples. The empirically derived factor model suggests that NP performance and FC are best explained as a single latent trait applicable to people with SCZ and BPD. This single measure may enhance the robustness of the analyses relating genomic data to performance-based phenotypes. (c) 2015 APA, all rights reserved).

The crystal structure of a multifunctional protein: phosphoglucose isomerase/autocrine motility factor/neuroleukin.

PubMed

Sun, Y J; Chou, C C; Chen, W S; Wu, R T; Meng, M; Hsiao, C D

1999-05-11

Phosphoglucose isomerase (PGI) plays a central role in both the glycolysis and the gluconeogenesis pathways. We present here the complete crystal structure of PGI from Bacillus stearothermophilus at 2.3-A resolution. We show that PGI has cell-motility-stimulating activity on mouse colon cancer cells similar to that of endogenous autocrine motility factor (AMF). PGI can also enhance neurite outgrowth on neuronal progenitor cells similar to that observed for neuroleukin. The results confirm that PGI is neuroleukin and AMF. PGI has an open twisted alpha/beta structural motif consisting of two globular domains and two protruding parts. Based on this substrate-free structure, together with the previously published biological, biochemical, and modeling results, we postulate a possible substrate-binding site that is located within the domains' interface for PGI and AMF. In addition, the structure provides evidence suggesting that the top part of the large domain together with one of the protruding loops might participate in inducing the neurotrophic activity.

Molecular basis of quantitative structure-properties relationships (QSPR): a quantum similarity approach.

PubMed

Ponec, R; Amat, L; Carbó-Dorca, R

1999-05-01

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett sigma constants and the logarithm of the octanol-water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

Molecular basis of quantitative structure-properties relationships (QSPR): A quantum similarity approach

NASA Astrophysics Data System (ADS)

Ponec, Robert; Amat, Lluís; Carbó-dorca, Ramon

1999-05-01

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett σ constants and the logarithm of the octanol- water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

[Factor structure validity of the social capital scale used at baseline in the ELSA-Brasil study].

PubMed

Souto, Ester Paiva; Vasconcelos, Ana Glória Godoi; Chor, Dora; Reichenheim, Michael E; Griep, Rosane Härter

2016-07-21

This study aims to analyze the factor structure of the Brazilian version of the Resource Generator (RG) scale, using baseline data from the Brazilian Longitudinal Health Study in Adults (ELSA-Brasil). Cross-validation was performed in three random subsamples. Exploratory factor analysis using exploratory structural equation models was conducted in the first two subsamples to diagnose the factor structure, and confirmatory factor analysis was used in the third to corroborate the model defined by the exploratory analyses. Based on the 31 initial items, the model with the best fit included 25 items distributed across three dimensions. They all presented satisfactory convergent validity (values greater than 0.50 for the extracted variance) and precision (values greater than 0.70 for compound reliability). All factor correlations were below 0.85, indicating full discriminative factor validity. The RG scale presents acceptable psychometric properties and can be used in populations with similar characteristics.

Similar local order in disordered fluorite and aperiodic pyrochlore structures

DOE PAGES

Shamblin, Jacob; Tracy, Cameron; Palomares, Raul; ...

2017-10-01

A major challenge to understanding the response of materials to extreme environments (e.g., nuclear fuels/waste forms and fusion materials) is to unravel the processes by which a material can incorporate atomic-scale disorder, and at the same time, remain crystalline. While it has long been known that all condensed matter, even liquids and glasses, possess short-range order, the relation between fully-ordered, disordered, and aperiodic structures over multiple length scales is not well understood. For example, when defects are introduced (via pressure or irradiation) into materials adopting the pyrochlore structure, these complex oxides either disorder over specific crystallographic sites, remaining crystalline, ormore » become aperiodic. Here we present neutron total scattering results characterizing the irradiation response of two pyrochlores, one that is known to disorder (Er2Sn2O7) and the other to amorphize (Dy2Sn2O7) under ion irradiation. The results demonstrate that in both cases, the local pyrochlore structure is transformed into similar short range configurations that are best fit by the orthorhombic weberite structure, even though the two compositions have distinctly different structures, aperiodic vs. disordered-crystalline, at longer length scales. Thus, a material's resistance to amorphization may not depend primarily on local defect formation energies, but rather on the structure's compatibility with meso-scale modulations of the local order in a way that maintains long-range periodicity.« less

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

PubMed Central

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

Factor structure and correlates of the Mandarin version of the Managing the Emotions of Others (MEOS) scale.

PubMed

Saklofske, Donald H; Austin, Elizabeth J; Yan, Gonggu; Smith, Martin M

2016-02-01

The English-language version of the Managing the Emotions of Others (MEOS) scale has been found to have a six-factor structure. This includes two pairs (Enhance, Divert and Worsen, Inauthentic) that respectively describe prosocial and non-prosocial interpersonal emotion management, together with an emotional concealment factor (Conceal) and a factor assessing poor self-rated emotional skills. A Mandarin translation of the MEOS was completed by 277 Chinese student participants. Factor analysis indicated a four-factor structure comprising a merged Enhance/Divert factor, together with Worsen, Inauthentic and Conceal factors. The emergence of a different factor structure compared to Western samples may be related to culture-dependent attitudes to emotional expression. The associations of the MEOS factors with Five-Factor model personality, the Dark Triad and trait emotional intelligence (EI) were examined; these were similar to but generally weaker than those found for the English-language version. © 2015 International Union of Psychological Science.

Transformation and Alignment in Similarity

ERIC Educational Resources Information Center

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

2009-01-01

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

Ontology-based structured cosine similarity in document summarization: with applications to mobile audio-based knowledge management.

PubMed

Yuan, Soe-Tsyr; Sun, Jerry

2005-10-01

Development of algorithms for automated text categorization in massive text document sets is an important research area of data mining and knowledge discovery. Most of the text-clustering methods were grounded in the term-based measurement of distance or similarity, ignoring the structure of the documents. In this paper, we present a novel method named structured cosine similarity (SCS) that furnishes document clustering with a new way of modeling on document summarization, considering the structure of the documents so as to improve the performance of document clustering in terms of quality, stability, and efficiency. This study was motivated by the problem of clustering speech documents (of no rich document features) attained from the wireless experience oral sharing conducted by mobile workforce of enterprises, fulfilling audio-based knowledge management. In other words, this problem aims to facilitate knowledge acquisition and sharing by speech. The evaluations also show fairly promising results on our method of structured cosine similarity.

Factor structure and individual patterns of DSM-IV conduct disorder criteria in adolescent psychiatric inpatients.

PubMed

Janson, Harald; Kjelsberg, Ellen

2006-01-01

We investigated the factor structure of the DSM-IV conduct disorder (CD) diagnostic criteria and typical individual patterns of CD subscales in an adolescent inpatient population using detailed hospital records of a Norwegian nationwide sample of 1087 adolescent psychiatric inpatients scored for the 15 DSM-IV CD criteria. Varimax rotated principal components and full-information factor analyses of 12 CD criteria were carried out separately for boys and girls employing two methods. Standardized values on three subscales of CD criteria were subjected to Ward's method of hierarchical cluster analyses followed by k-means relocation employing a double cross-replication design. Similar factor structures emerged regardless of factoring method and gender. With the exception of Criteria 8 ("Fire setting") and 14 ("Run away from home") the factor loadings for both genders were in accordance with Loeber's tripartite model, with Aggression, Delinquency, and Rule Breaking factors largely corresponding to Loeber's overt, covert and authority conflict pathways. A five-cluster solution proved highly replicable and interpretable. One cluster gathered adolescents without CD, and the remaining four described groups with different conceptually meaningful constellations of CD criteria, which were not equally prevalent in each gender. Delinquency appeared in all symptomatic clusters. The cluster analytic results highlighted typical forms of expressions of conduct problems, and the fact that these forms may not be equally prevalent in girls and boys even while the underlying structure of conduct problems may be similar across genders. Future research should address the prediction of specific outcomes from CD criteria subscales or constellations.

Synoptic Factors Affecting Structure Predictability of Hurricane Alex (2016)

NASA Astrophysics Data System (ADS)

Gonzalez-Aleman, J. J.; Evans, J. L.; Kowaleski, A. M.

2016-12-01

On January 7, 2016, a disturbance formed over the western North Atlantic basin. After undergoing tropical transition, the system became the first hurricane of 2016 - and the first North Atlantic hurricane to form in January since 1938. Already an extremely rare hurricane event, Alex then underwent extratropical transition [ET] just north of the Azores Islands. We examine the factors affecting Alex's structural evolution through a new technique called path-clustering. In this way, 51 ensembles from the European Centre for Medium-Range Weather Forecasts Ensemble Prediction System (ECMWF-EPS) are grouped based on similarities in the storm's path through the Cyclone Phase Space (CPS). The differing clusters group various possible scenarios of structural development represented in the ensemble forecasts. As a result, it is possible to shed light on the role of the synoptic scale in changing the structure of this hurricane in the midlatitudes through intercomparison of the most "realistic" forecast of the evolution of Alex and the other physically plausible modes of its development.

Are intrinsic motivational factors of work associated with functional incapacity similarly regardless of the country?

PubMed

Väänänen, A; Pahkin, K; Huuhtanen, P; Kivimäki, M; Vahtera, J; Theorell, T; Kalimo, R

2005-10-01

Many psychosocial models of wellbeing at work emphasise the role of intrinsic motivational factors such as job autonomy, job complexity, and innovativeness. However, little is known about whether the employees of multinational enterprises differ from country to country with regard to intrinsic motivational factors, and whether these factors are associated with wellbeing similarly in the different countries. The purpose of this study was to examine the level of intrinsic motivational factors and their impact on functional incapacity in different countries in a multinational corporation. In 2000, data were collected from a globally operating corporation with a questionnaire survey. The participants were 13 795 employees (response rate 59%; 56% under age 45; 80% men; 61% blue collar employees), who worked in similar industrial occupations in five countries (Canada, China, Finland, France, and Sweden). The Chinese employees reported higher autonomy and lower complexity at work than the employees from the other countries. After adjustment for age, sex, socioeconomic status, and physical work environment, job autonomy, and job complexity at work were associated with functional incapacity in most countries, whereas in China the impact was significantly stronger. In Finland and in China employees with low innovativeness at work were more prone to functional incapacity than corresponding employees in other countries. The level of intrinsic motivational factors varied between the Chinese employees and those in other countries. In line with theoretical notions, the relation between intrinsic motivational factors of work and functional incapacity followed a similar pattern in the different countries. However, these country specific results show that a culture specific approach to employee wellbeing should also be applied.

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.

Length-independent structural similarities enrich the antibody CDR canonical class model.

PubMed

Nowak, Jaroslaw; Baker, Terry; Georges, Guy; Kelm, Sebastian; Klostermann, Stefan; Shi, Jiye; Sridharan, Sudharsan; Deane, Charlotte M

2016-01-01

Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach. To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ∼20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.

Song trait similarity in great tits varies with social structure.

PubMed

Snijders, Lysanne; van der Eijk, Jerine; van Rooij, Erica P; de Goede, Piet; van Oers, Kees; Naguib, Marc

2015-01-01

For many animals, long-range signalling is essential to maintain contact with conspecifics. In territorial species, individuals often have to balance signalling towards unfamiliar potential competitors (to solely broadcast territory ownership) with signalling towards familiar immediate neighbours (to also maintain so-called "dear enemy" relations). Hence, to understand how signals evolve due to these multilevel relationships, it is important to understand how general signal traits vary in relation to the overall social environment. For many territorial songbirds dawn is a key signalling period, with several neighbouring individuals singing simultaneously without immediate conflict. In this study we tested whether sharing a territory boundary, rather than spatial proximity, is related to similarity in dawn song traits between territorial great tits (Parus major) in a wild personality-typed population. We collected a large dataset of automatized dawn song recordings from 72 unique male great tits, during the fertile period of their mate, and compared specific song traits between neighbours and non-neighbours. We show here that both song rate and start time of dawn song were repeatable song traits. Moreover, neighbours were significantly more dissimilar in song rate compared to non-neighbours, while there was no effect of proximity on song rate similarity. Additionally, similarity in start time of dawn song was unrelated to sharing a territory boundary, but birds were significantly more similar in start time of dawn song when they were breeding in close proximity of each other. We suggest that the dissimilarity in dawn song rate between neighbours is either the result of neighbouring great tits actively avoiding similar song rates to possibly prevent interference, or a passive consequence of territory settlement preferences relative to the types of neighbours. Neighbourhood structuring is therefore likely to be a relevant selection pressure shaping variation in

Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information.

PubMed

O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-02-25

We present a new algorithm, based on the multidimensional QR factorization, to remove redundancy from a multiple structural alignment by choosing representative protein structures that best preserve the phylogenetic tree topology of the homologous group. The classical QR factorization with pivoting, developed as a fast numerical solution to eigenvalue and linear least-squares problems of the form Ax=b, was designed to re-order the columns of A by increasing linear dependence. Removing the most linear dependent columns from A leads to the formation of a minimal basis set which well spans the phase space of the problem at hand. By recasting the problem of redundancy in multiple structural alignments into this framework, in which the matrix A now describes the multiple alignment, we adapted the QR factorization to produce a minimal basis set of protein structures which best spans the evolutionary (phase) space. The non-redundant and representative profiles obtained from this procedure, termed evolutionary profiles, are shown in initial results to outperform well-tested profiles in homology detection searches over a large sequence database. A measure of structural similarity between homologous proteins, Q(H), is presented. By properly accounting for the effect and presence of gaps, a phylogenetic tree computed using this metric is shown to be congruent with the maximum-likelihood sequence-based phylogeny. The results indicate that evolutionary information is indeed recoverable from the comparative analysis of protein structure alone. Applications of the QR ordering and this structural similarity metric to analyze the evolution of structure among key, universally distributed proteins involved in translation, and to the selection of representatives from an ensemble of NMR structures are also discussed.

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

PubMed

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

2011-04-01

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

Structural Similarities between Brain and Linguistic Data Provide Evidence of Semantic Relations in the Brain

PubMed Central

Crangle, Colleen E.; Perreau-Guimaraes, Marcos; Suppes, Patrick

2013-01-01

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. PMID:23799009

Molecular similarity measures.

PubMed

Maggiora, Gerald M; Shanmugasundaram, Veerabahu

2011-01-01

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

Perturbation of Chromatin Structure Globally Affects Localization and Recruitment of Splicing Factors

PubMed Central

Risso, Guillermo J.; Pawellek, Andrea; Ule, Jernej; Lamond, Angus I.; Kornblihtt, Alberto R.

2012-01-01

Chromatin structure is an important factor in the functional coupling between transcription and mRNA processing, not only by regulating alternative splicing events, but also by contributing to exon recognition during constitutive splicing. We observed that depolarization of neuroblastoma cell membrane potential, which triggers general histone acetylation and regulates alternative splicing, causes a concentration of SR proteins in nuclear speckles. This prompted us to analyze the effect of chromatin structure on splicing factor distribution and dynamics. Here, we show that induction of histone hyper-acetylation results in the accumulation in speckles of multiple splicing factors in different cell types. In addition, a similar effect is observed after depletion of the heterochromatic protein HP1α, associated with repressive chromatin. We used advanced imaging approaches to analyze in detail both the structural organization of the speckle compartment and nuclear distribution of splicing factors, as well as studying direct interactions between splicing factors and their association with chromatin in vivo. The results support a model where perturbation of normal chromatin structure decreases the recruitment efficiency of splicing factors to nascent RNAs, thus causing their accumulation in speckles, which buffer the amount of free molecules in the nucleoplasm. To test this, we analyzed the recruitment of the general splicing factor U2AF65 to nascent RNAs by iCLIP technique, as a way to monitor early spliceosome assembly. We demonstrate that indeed histone hyper-acetylation decreases recruitment of U2AF65 to bulk 3′ splice sites, coincident with the change in its localization. In addition, prior to the maximum accumulation in speckles, ∼20% of genes already show a tendency to decreased binding, while U2AF65 seems to increase its binding to the speckle-located ncRNA MALAT1. All together, the combined imaging and biochemical approaches support a model where chromatin

Spatial embedding of structural similarity in the cerebral cortex

PubMed Central

Song, H. Francis; Kennedy, Henry; Wang, Xiao-Jing

2014-01-01

Recent anatomical tracing studies have yielded substantial amounts of data on the areal connectivity underlying distributed processing in cortex, yet the fundamental principles that govern the large-scale organization of cortex remain unknown. Here we show that functional similarity between areas as defined by the pattern of shared inputs or outputs is a key to understanding the areal network of cortex. In particular, we report a systematic relation in the monkey, human, and mouse cortex between the occurrence of connections from one area to another and their similarity distance. This characteristic relation is rooted in the wiring distance dependence of connections in the brain. We introduce a weighted, spatially embedded random network model that robustly gives rise to this structure, as well as many other spatial and topological properties observed in cortex. These include features that were not accounted for in any previous model, such as the wide range of interareal connection weights. Connections in the model emerge from an underlying distribution of spatially embedded axons, thereby integrating the two scales of cortical connectivity—individual axons and interareal pathways—into a common geometric framework. These results provide insights into the origin of large-scale connectivity in cortex and have important implications for theories of cortical organization. PMID:25368200

Orientale and Caloris. [lunar basins with similar structural features

NASA Technical Reports Server (NTRS)

Mccauley, J. F.

1977-01-01

Based on revised stratigraphy, structural interpretation, explosion-crater data, and a genetic model for Orientale, it is suggested that Orientale and Caloris have much in common. It is noted that: (1) although the basin fill in Caloris is different from that seen in Orientale, the materials between the most prominent scarp and the weakly-developed outer scarp may be degraded equivalents of the massifs and knobs associated with the Montes Rook, (2) the Montes Rook and the main Caloris scarp have similar stratigraphic and structural features, (3) the lineated ejecta derived from shallower horizons are found near and beyond the weakly-developed outer Caloris scarp which is the counterpart of the Orientale scarp, (4) a well developed field of secondary craters is observed beyond 1 basin diameter at Caloris, (5) the observed textural differences between the material around the main Caloris scarp and the lineated material beyond suggest that Mercury is layered and that Caloris crater excavated coherent materials from one or more of these layers at depth, and (6) the difference in spacing between the Caloris rings is not related to internal layering effects.

Limiting similarity and niche theory for structured populations.

PubMed

Szilágyi, András; Meszéna, Géza

2009-05-07

We develop the theory of limiting similarity and niche for structured populations with finite number of individual states (i-state). In line with a previously published theory for unstructured populations, the niche of a species is specified by the impact and sensitivity niche vectors. They describe the population's impact on and sensitivity towards the variables involved in the population regulation. Robust coexistence requires sufficient segregation of the impact, as well as of the sensitivity niche vectors. Connection between the population-level impact and sensitivity and the impact/sensitivity of the specific i-states is developed. Each i-state contributes to the impact of the population proportional to its frequency in the population. Sensitivity of the population is composed of the sensitivity of the rates of demographic transitions, weighted by the frequency and by the reproductive value of the initial and final i-states of the transition, respectively. Coexistence in a multi-patch environment is studied. This analysis is interpreted as spatial niche segregation.

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

PubMed

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 �

Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family

PubMed Central

Ming, Qianqian; Roske, Yvette; Schuetz, Anja; Walentin, Katharina; Ibraimi, Ibraim; Schmidt-Ott, Kai M

2018-01-01

Abstract Grainyhead (Grh)/CP2 transcription factors are highly conserved in multicellular organisms as key regulators of epithelial differentiation, organ development and skin barrier formation. In addition, they have been implicated as being tumor suppressors in a variety of human cancers. Despite their physiological importance, little is known about their structure and DNA binding mode. Here, we report the first structural study of mammalian Grh/CP2 factors. Crystal structures of the DNA-binding domains of grainyhead-like (Grhl) 1 and Grhl2 reveal a closely similar conformation with immunoglobulin-like core. Both share a common fold with the tumor suppressor p53, but differ in important structural features. The Grhl1 DNA-binding domain binds duplex DNA containing the consensus recognition element in a dimeric arrangement, supporting parsimonious target-sequence selection through two conserved arginine residues. We elucidate the molecular basis of a cancer-related mutation in Grhl1 involving one of these arginines, which completely abrogates DNA binding in biochemical assays and transcriptional activation of a reporter gene in a human cell line. Thus, our studies establish the structural basis of DNA target-site recognition by Grh transcription factors and reveal how tumor-associated mutations inactivate Grhl proteins. They may serve as points of departure for the structure-based development of Grh/CP2 inhibitors for therapeutic applications. PMID:29309642

The Crystal Structure of Cobra Venom Factor, a Cofactor for C3- and C5-Convertase CVFBb

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

Krishnan, Vengadesan; Ponnuraj, Karthe; Xu, Yuanyuan

2009-05-26

Cobra venom factor (CVF) is a functional analog of human complement component C3b, the active fragment of C3. Similar to C3b, in human and mammalian serum, CVF binds factor B, which is then cleaved by factor D, giving rise to the CVFBb complex that targets the same scissile bond in C3 as the authentic complement convertases C4bC2a and C3bBb. Unlike the latter, CVFBb is a stable complex and an efficient C5 convertase. We solved the crystal structure of CVF, isolated from Naja naja kouthia venom, at 2.6 {angstrom} resolution. The CVF crystal structure, an intermediate between C3b and C3c, lacksmore » the TED domain and has the CUB domain in an identical position to that seen in C3b. The similarly positioned CUB and slightly displaced C345c domains of CVF could play a vital role in the formation of C3 convertases by providing important primary binding sites for factor B.« less

The crystal structure of cobra venom factor, a cofactor for C3- and C5-convertase CVFBb.

PubMed

Krishnan, Vengadesan; Ponnuraj, Karthe; Xu, Yuanyuan; Macon, Kevin; Volanakis, John E; Narayana, Sthanam V L

2009-04-15

Cobra venom factor (CVF) is a functional analog of human complement component C3b, the active fragment of C3. Similar to C3b, in human and mammalian serum, CVF binds factor B, which is then cleaved by factor D, giving rise to the CVFBb complex that targets the same scissile bond in C3 as the authentic complement convertases C4bC2a and C3bBb. Unlike the latter, CVFBb is a stable complex and an efficient C5 convertase. We solved the crystal structure of CVF, isolated from Naja naja kouthia venom, at 2.6 A resolution. The CVF crystal structure, an intermediate between C3b and C3c, lacks the TED domain and has the CUB domain in an identical position to that seen in C3b. The similarly positioned CUB and slightly displaced C345c domains of CVF could play a vital role in the formation of C3 convertases by providing important primary binding sites for factor B.

Measurement invariance of the Illness Intrusiveness Ratings Scale's three-factor structure in men and women with cancer.

PubMed

Mah, Kenneth; Bezjak, Andrea; Loblaw, D Andrew; Gotowiec, Andrew; Devins, Gerald M

2011-02-01

Illness- and treatment-related disruptions to valued activities and interests (illness intrusiveness) are central to quality of life in chronic disease and are captured by three subscales of the Illness Intrusiveness Ratings Scale (IIRS): the Instrumental, Intimacy, and Relationships and Personal Development subscales. Using individual (CFA) and multisample confirmatory factor analyses (MSCFA), we evaluated measurement invariance of the IIRS's 3-factor structure in men and women with cancer. Men (n = 210) and women (n = 206) with 1 of 4 cancer diagnoses (gastrointestinal, head and neck, lymphoma, lung) recruited from outpatient clinics completed the IIRS. In the MSCFA, we applied an analysis of means and covariance structures approach to test increasingly stringent equality constraints on factor structure parameters to evaluate weak, strong, and strict measurement invariance of the 3-factor structure between men and women. Individual CFAs demonstrated fit of the hypothesized 3-factor structure for men and women, although more consistently for men. The 3-factor structure was superior to an alternative 1-factor structure. MSCFA results indicated that parameters of the 3-factor structure could be considered equivalent between the sexes up to the level of strong invariance. Strict invariance was not supported. Overall, IIRS scores can be interpreted similarly for men and women with cancer. Illness intrusiveness can be considered as important in the psychosocial adaptation of people with cancer as it is for people affected by other chronic conditions. (c) 2011 APA, all rights reserved

Factor structure of the functional movement screen in marine officer candidates.

PubMed

Kazman, Josh B; Galecki, Jeffrey M; Lisman, Peter; Deuster, Patricia A; OʼConnor, Francis G

2014-03-01

Functional movement screening (FMS) is a musculoskeletal assessment that is intended to fill a gap between preparticipation examinations and performance tests. Functional movement screening consists of 7 standardized movements involving multiple muscle groups that are rated 0-3 during performance; scores are combined into a final score, which is intended to predict injury risk. This use of a sum-score in this manner assumes that the items are unidimensional and scores are internally consistent, which are measures of internal reliability. Despite research into the FMS' predictive value and interrater reliability, research has not assessed its psychometric properties. The present study is a standard psychometric analysis of the FMS and is the first to assess the internal consistency and factor structure of the FMS, using Cronbach's alpha and exploratory factor analysis (EFA). Using a cohort of 877 male and 57 female Marine officer candidates who performed the FMS, EFA of polychoric correlations with varimax rotation was conducted to explore the structure of the FMS. Tests were repeated on the original scores, which integrated feelings of pain during movement (0-3), and then on scores discounting the pain instruction and based only on the performance (1-3), to determine whether pain ratings affected the factor structure. The average FMS score was 16.7 ± 1.8. Cronbach's alpha was 0.39. Exploratory factor analysis availed 2 components accounting for 21 and 17% and consisting of separate individual movements (shoulder mobility and deep squat, respectively). Analysis on scores discounting pain showed similar results. The factor structures were not interpretable, and the low Cronbach's alpha suggests a lack of internal consistency in FMS sum scores. Results do not offer support for validity of the FMS sum score as a unidimensional construct. In the absence of additional psychometric research, caution is warranted when using the FMS sum score.

Structural similarities and differences between the human and the mouse pancreas

PubMed Central

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

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

PubMed

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 .

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

PubMed

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.

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

PubMed

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.

Validity Generalization of the WISC-R Factor Structure with 10 1/2-Year-Old Children.

ERIC Educational Resources Information Center

Shiek, David A.; Miller, John E.

1978-01-01

Investigated robustness of the Wechsler Intelligence Scale for Children-Revised (WISC-R) factor structure. Comparisons of the loadings obtained with generalization sample and 10 1/2-year-old national standardization sample suggest high degree of similarity in composition, magnitude, and pattern. Findings highly support robustness of WISC-R's…

When Experience Counts: The Effects of Experiential and Structural Similarity on Patterns of Support and Interpersonal Stress.

ERIC Educational Resources Information Center

Suitor, J. Jill; And Others

1995-01-01

Draws upon theories of homophily and reference groups to argue that experiential similarity (similar status transition) is more important than structural similarity (age, gender, and marital status) in determining sources of emotional support and stress following life events. Arguments are supported by longitudinal data on social networks of…

Evidence for Structural Alignment during Similarity Judgments.

ERIC Educational Resources Information Center

Markman, Arthur B.; Gentner, Dedre

Similarity plays a central role in cognitive theories. Research has demonstrated that the similarity of a pair increases with its commonalities and decreases with its differences. These common and distinctive elements can take the form of parts of objects, relations between parts of properties of whole objects. Previous work has been unable to…

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

PubMed

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.

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

PubMed

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2015-01-01

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.

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

NASA Astrophysics Data System (ADS)

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.

Analytical and functional similarity of Amgen biosimilar ABP 215 to bevacizumab.

PubMed

Seo, Neungseon; Polozova, Alla; Zhang, Mingxuan; Yates, Zachary; Cao, Shawn; Li, Huimin; Kuhns, Scott; Maher, Gwendolyn; McBride, Helen J; Liu, Jennifer

ABP 215 is a biosimilar product to bevacizumab. Bevacizumab acts by binding to vascular endothelial growth factor A, inhibiting endothelial cell proliferation and new blood vessel formation, thereby leading to tumor vasculature normalization. The ABP 215 analytical similarity assessment was designed to assess the structural and functional similarity of ABP 215 and bevacizumab sourced from both the United States (US) and the European Union (EU). Similarity assessment was also made between the US- and EU-sourced bevacizumab to assess the similarity between the two products. The physicochemical properties and structural similarity of ABP 215 and bevacizumab were characterized using sensitive state-of-the-art analytical techniques capable of detecting small differences in product attributes. ABP 215 has the same amino acid sequence and exhibits similar post-translational modification profiles compared to bevacizumab. The functional similarity assessment employed orthogonal assays designed to interrogate all expected biological activities, including those known to affect the mechanisms of action for ABP 215 and bevacizumab. More than 20 batches of bevacizumab (US) and bevacizumab (EU), and 13 batches of ABP 215 representing unique drug substance lots were assessed for similarity. The large dataset allows meaningful comparisons and garners confidence in the overall conclusion for the analytical similarity assessment of ABP 215 to both US- and EU-sourced bevacizumab. The structural and purity attributes, and biological properties of ABP 215 are demonstrated to be highly similar to those of bevacizumab.

Analytical and functional similarity of Amgen biosimilar ABP 215 to bevacizumab

PubMed Central

Seo, Neungseon; Polozova, Alla; Zhang, Mingxuan; Yates, Zachary; Cao, Shawn; Li, Huimin; Kuhns, Scott; Maher, Gwendolyn; McBride, Helen J.; Liu, Jennifer

2018-01-01

ABSTRACT ABP 215 is a biosimilar product to bevacizumab. Bevacizumab acts by binding to vascular endothelial growth factor A, inhibiting endothelial cell proliferation and new blood vessel formation, thereby leading to tumor vasculature normalization. The ABP 215 analytical similarity assessment was designed to assess the structural and functional similarity of ABP 215 and bevacizumab sourced from both the United States (US) and the European Union (EU). Similarity assessment was also made between the US- and EU-sourced bevacizumab to assess the similarity between the two products. The physicochemical properties and structural similarity of ABP 215 and bevacizumab were characterized using sensitive state-of-the-art analytical techniques capable of detecting small differences in product attributes. ABP 215 has the same amino acid sequence and exhibits similar post-translational modification profiles compared to bevacizumab. The functional similarity assessment employed orthogonal assays designed to interrogate all expected biological activities, including those known to affect the mechanisms of action for ABP 215 and bevacizumab. More than 20 batches of bevacizumab (US) and bevacizumab (EU), and 13 batches of ABP 215 representing unique drug substance lots were assessed for similarity. The large dataset allows meaningful comparisons and garners confidence in the overall conclusion for the analytical similarity assessment of ABP 215 to both US- and EU-sourced bevacizumab. The structural and purity attributes, and biological properties of ABP 215 are demonstrated to be highly similar to those of bevacizumab. PMID:29553864

Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

PubMed Central

Paget, Mark S.

2015-01-01

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2–4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor. PMID:26131973

Measuring self-concept among African-Americans: validating the factor structure of the self-perception profile for adolescents.

PubMed

Powell-Young, Yolanda M; Spruill, Ida J

2011-12-01

The purpose of this investigation was to examine the reliability and factor structure of the Harter Self-Perception Profile for Adolescents (SPPA) with African-Americans. While the SPPA has demonstrated strong psychometric properties with European-Americans, limited information exists with African-Americans. Three hundred and ten (N = 310) female adolescents, from 14 through 18 years of age, completed the SPPA. Estimations of internal consistency reliability with Cronbach's alpha (alpha), item suitability with Pearson (gamma) correlations, and evaluation of factor structure fit utilizing principle axis extraction with oblimin (oblique) rotation were conducted. When compared with Harter's normative data, psychometric properties of the SPPA varied significantly with the current sample. Findings suggested cautious interpretation of data generated with demographically similar cohorts. Further study is warranted to ascertain the factor structure that is most relevant for use with African-American adolescents.

Contributions of pitch contour, tonality, rhythm, and meter to melodic similarity.

PubMed

Prince, Jon B

2014-12-01

The identity of a melody resides in its sequence of pitches and durations, both of which exhibit surface details as well as structural properties. In this study, pitch contour (pattern of ups and downs) served as pitch surface information, and tonality (musical key) as pitch structure; in the temporal dimension, surface information was the ordinal duration ratios of adjacent notes (rhythm), and meter (beat, or pulse) comprised the structure. Factorially manipulating the preservation or alteration of all of these forms of information in 17 novel melodies (typifying Western music) enabled measuring their effect on perceived melodic similarity. In Experiment 1, 34 participants (varied musical training) rated the perceived similarity of melody pairs transposed to new starting pitches. Rhythm was the largest contributor to perceived similarity, then contour, meter, and tonality. Experiment 2 used the same melodies but varied the tempo within a pair, and added a prefix of 3 chords, which oriented the listener to the starting pitch and tempo before the melody began. Now contour was the strongest influence on similarity ratings, followed by tonality, and then rhythm; meter was not significant. Overall, surface features influenced perceived similarity more than structural, but both had observable effects. The primary theoretical advances in melodic similarity research are that (a) the relative emphasis on pitch and temporal factors is flexible; (b) pitch and time functioned independently when factorially manipulated, regardless of which dimension is more influential; and (c) interactions between surface and structural information were unreliable and never occurred between dimensions. PsycINFO Database Record (c) 2014 APA, all rights reserved.

What difference reveals about similarity.

PubMed

Sagi, Eyal; Gentner, Dedre; Lovett, Andrew

2012-08-01

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

Learning deep similarity in fundus photography

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

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

PubMed

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

2009-01-01

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

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

PubMed

Tuncbag, Nurcan; Gursoy, Attila; Nussinov, Ruth; Keskin, Ozlem

2011-08-11

Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.

Crystal structure of enterococcus faecalis sly A-like transcriptional factor.

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

Wu, R.; Zhang, R.; Zagnitko, O.

2003-05-30

The crystal structure of a SlyA transcriptional regulator at 1.6 {angstrom} resolution is presented, and structural relationships between members of the MarR/SlyA family are discussed. The SlyA family, which includes SlyA, Rap, Hor, and RovA proteins, is widely distributed in bacterial and archaeal genomes. Current evidence suggests that SlyA-like factors act as repressors, activators, and modulators of gene transcription. These proteins have been shown to up-regulate the expression of molecular chaperones, acid-resistance proteins, and cytolysin, and down-regulate several biosynthetic enzymes. The structure of SlyA from Enterococcus faecalis, determined as a part of an ongoing structural genomics initiative (www.mcsg.anl.gov), revealed themore » same winged helix DNA-binding motif that was recently found in the MarR repressor from Escherichia coli and the MexR repressor from Pseudomonas aeruginosa, a sequence homologue of MarR. Phylogenetic analysis of the MarR/SlyA family suggests that Sly is placed between the SlyA and MarR subfamilies and shows significant sequence similarity to members of both subfamilies.« less

Optimal design of multichannel equalizers for the structural similarity index.

PubMed

Chai, Li; Sheng, Yuxia

2014-12-01

The optimization of multichannel equalizers is studied for the structural similarity (SSIM) criteria. The closed-form formula is provided for the optimal equalizer when the mean of the source is zero. The formula shows that the equalizer with maximal SSIM index is equal to the one with minimal mean square error (MSE) multiplied by a positive real number, which is shown to be equal to the inverse of the achieved SSIM index. The relation of the maximal SSIM index to the minimal MSE is also established for given blurring filters and fixed length equalizers. An algorithm is also presented to compute the suboptimal equalizer for the general sources. Various numerical examples are given to demonstrate the effectiveness of the results.

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

Thermal and Compositional Variation of Glassy Metal Structure Factors.

NASA Astrophysics Data System (ADS)

From, Milton

The x-ray total structure factor of the glassy -metal alloys Mg_{70}Zn_ {30}, Ca_{70}Mg_{30 } and Mg_{85.5}Cu _{14.5} has been measured at three temperatures: 9K, 150K, and 300K. The data have a statistical precision of about.8% and an absolute accuracy of roughly 3%. Percus-Yevick hard sphere structure factors may be fitted quite accurately to the data in the region of the first peak. In addition, the variation of the experimental structure factor with composition is found to be consistent with the Percus-Yevick theory. At low k values, Percus -Yevick and other theoretical model structure factors are in poor agreement with the data. Within experimental error, the temperature dependence of the structure factors is in agreement with the Debye plane wave phonon model of atomic vibrations. The measured structure factors are used to calculate the electrical resistivity from the Faber-Ziman equation. In most cases, the calculations yield both the correct magnitude of resistivity and sign of the temperature coefficient of resistivity.

Computer-assisted image analysis of human cilia and Chlamydomonas flagella reveals both similarities and differences in axoneme structure.

PubMed

O'Toole, Eileen T; Giddings, Thomas H; Porter, Mary E; Ostrowski, Lawrence E

2012-08-01

In the past decade, investigations from several different fields have revealed the critical role of cilia in human health and disease. Because of the highly conserved nature of the basic axonemal structure, many different model systems have proven useful for the study of ciliopathies, especially the unicellular, biflagellate green alga Chlamydomonas reinhardtii. Although the basic axonemal structure of cilia and flagella is highly conserved, these organelles often perform specialized functions unique to the cell or tissue in which they are found. These differences in function are likely reflected in differences in structural organization. In this work, we directly compare the structure of isolated axonemes from human cilia and Chlamydomonas flagella to identify similarities and differences that potentially play key roles in determining their functionality. Using transmission electron microscopy and 2D image averaging techniques, our analysis has confirmed the overall structural similarity between these two species, but also revealed clear differences in the structure of the outer dynein arms, the central pair projections, and the radial spokes. We also show how the application of 2D image averaging can clarify the underlying structural defects associated with primary ciliary dyskinesia (PCD). Overall, our results document the remarkable similarity between these two structures separated evolutionarily by over a billion years, while highlighting several significant differences, and demonstrate the potential of 2D image averaging to improve the diagnosis and understanding of PCD. Copyright © 2012 Wiley Periodicals, Inc.

Identifying similar and different factors effecting long-term cardiac exercise rehabilitation behavior modification between New Zealand and the United Kingdom.

PubMed

Dunn, Stephanie; Lark, Sally; Fallows, Stephen

2014-07-01

Cardiac Rehabilitation (CR) programs are the most cost-effective measure for reducing morbidity associated with Coronary Vascular Disease (CVD). To be more effective there is a need to understand what influences the maintenance of healthy behaviors. This study identifies similar and different influences in CR of the United Kingdom (UK) and New Zealand (NZ). A retrospective study. Participants had previously been discharged from CR for 6 to 12+ months within the UK (n = 22) and NZ (n = 21). Participant's attended a focus group. Discussions were digitally recorded, transcribed then thematically analyzed. The CR programs were observed over 2 months to enable comment on findings relating to 'theory in practice.' Similar positive patient experiences influencing behavior between groups and countries were; support, education, positive attitude, and motivation. Companionship and exercising alongside people with similar health problems was the major determinant for positive exercise behavior. Barriers to maintaining exercise included; physical disabilities, time constraints, and weather conditions. NZ participants were more affected by external factors (eg, opportunity, access, and time). Both CR programs were successful in facilitating the maintenance of healthy lifestyles. Exercising with other cardiac patients for support in a structured environment was the strongest influence in maintaining healthy lifestyles beyond CR programs.

Role of carbohydrate in multimeric structure of factor VIII/von Willebrand factor protein.

PubMed Central

Gralnick, H R; Williams, S B; Rick, M E

1983-01-01

The carbohydrate moiety of the factor VIII/von Willebrand (vW) factor protein is important in the expression of vW factor activity and the intravascular survival of the protein. Studies of normal human factor VIII/vW factor protein indicate that there is a requirement of a full complement of penultimate galactose for the maintenance of a normal multimeric structure. Release of penultimate galactose by beta-galactosidase or modification by galactose oxidase results in loss of the largest molecular weight multimers and increased numbers of intermediate and smaller multimers. In contrast, terminal galactose on the factor VIII/vW factor protein does not appear to play a significant role in the maintenance of the multimer organization. The abnormalities in multimeric structure and molecular size were demonstrated by NaDodSO4/polyacrylamide/agarose gel electrophoresis, NaDodSO4/glyoxyl-agarose electrophoresis, and sucrose density ultracentrifugation. These studies indicate that the penultimate galactose plays a role in the maintenance of the largest multimers of the factor VIII/vW factor protein. This may explain why, in some patients with variant forms of vW disease, a carbohydrate abnormality also may affect the multimeric structure of the plasma factor VIII/vW factor protein. Images PMID:6601805

Magnetic field effects on charge structure factors of gapped graphene structure

NASA Astrophysics Data System (ADS)

Rezania, Hamed; Tawoose, Nasrin

2018-02-01

We present the behaviors of dynamical and static charge susceptibilities of undoped gapped graphene using the Green's function approach in the context of tight binding model Hamiltonian. Specially, the effects of magnetic field on the plasmon modes of gapped graphene structure are investigated via calculating correlation function of charge density operators. Our results show the increase of magnetic field leads to disappear high frequency plasmon mode for gapped case. We also show that low frequency plasmon mode has not affected by increase of magnetic field and chemical potential. Finally the temperature dependence of static charge structure factor of gapp graphene structure is studied. The effects of both magnetic field and gap parameter on the static structure factor are discusses in details.

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

PubMed Central

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

Common neighbour structure and similarity intensity in complex networks

NASA Astrophysics Data System (ADS)

Hou, Lei; Liu, Kecheng

2017-10-01

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

Classification of document page images based on visual similarity of layout structures

NASA Astrophysics Data System (ADS)

Shin, Christian K.; Doermann, David S.

1999-12-01

Searching for documents by their type or genre is a natural way to enhance the effectiveness of document retrieval. The layout of a document contains a significant amount of information that can be used to classify a document's type in the absence of domain specific models. A document type or genre can be defined by the user based primarily on layout structure. Our classification approach is based on 'visual similarity' of the layout structure by building a supervised classifier, given examples of the class. We use image features, such as the percentages of tex and non-text (graphics, image, table, and ruling) content regions, column structures, variations in the point size of fonts, the density of content area, and various statistics on features of connected components which can be derived from class samples without class knowledge. In order to obtain class labels for training samples, we conducted a user relevance test where subjects ranked UW-I document images with respect to the 12 representative images. We implemented our classification scheme using the OC1, a decision tree classifier, and report our findings.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

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

PubMed

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.

Does similarity in call structure or foraging ecology explain interspecific information transfer in wild Myotis bats?

PubMed

Hügel, Theresa; van Meir, Vincent; Muñoz-Meneses, Amanda; Clarin, B-Markus; Siemers, Björn M; Goerlitz, Holger R

2017-01-01

Animals can gain important information by attending to the signals and cues of other animals in their environment, with acoustic information playing a major role in many taxa. Echolocation call sequences of bats contain information about the identity and behaviour of the sender which is perceptible to close-by receivers. Increasing evidence supports the communicative function of echolocation within species, yet data about its role for interspecific information transfer is scarce. Here, we asked which information bats extract from heterospecific echolocation calls during foraging. In three linked playback experiments, we tested in the flight room and field if foraging Myotis bats approached the foraging call sequences of conspecifics and four heterospecifics that were similar in acoustic call structure only (acoustic similarity hypothesis), in foraging ecology only (foraging similarity hypothesis), both, or none. Compared to the natural prey capture rate of 1.3 buzzes per minute of bat activity, our playbacks of foraging sequences with 23-40 buzzes/min simulated foraging patches with significantly higher profitability. In the flight room, M. capaccinii only approached call sequences of conspecifics and of the heterospecific M. daubentonii with similar acoustics and foraging ecology. In the field, M. capaccinii and M. daubentonii only showed a weak positive response to those two species. Our results confirm information transfer across species boundaries and highlight the importance of context on the studied behaviour, but cannot resolve whether information transfer in trawling Myotis is based on acoustic similarity only or on a combination of similarity in acoustics and foraging ecology. Animals transfer information, both voluntarily and inadvertently, and within and across species boundaries. In echolocating bats, acoustic call structure and foraging ecology are linked, making echolocation calls a rich source of information about species identity, ecology and

Development of Scaffold-Free Elastic Cartilaginous Constructs with Structural Similarities to Auricular Cartilage

PubMed Central

Giardini-Rosa, Renata; Joazeiro, Paulo P.; Thomas, Kathryn; Collavino, Kristina; Weber, Joanna

2014-01-01

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 cm2) 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. PMID:24124666

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

PubMed

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.

Assessing Protective Factors for Violence Risk in U.K. General Mental Health Services Using the Structured Assessment of Protective Factors.

PubMed

Haines, Alina; Brown, Andrew; Javaid, Syed Fahad; Khan, Fayyaz; Noblett, Steve; Omodunbi, Oladipupo; Sadiq, Khurram; Zaman, Wahid; Whittington, Richard

2017-12-01

Violence risk assessment and management are key tasks in mental health services and should be guided by validated instruments covering both risk and protective factors. This article is part of an international effort to validate the Structured Assessment of Protective Factors (SAPROF) for violence. The SAPROF, Historical, Clinical, Risk Management-20 (HCR-20) and the Psychopathy Checklist-Screening Version (PCL-SV) were administered in a sample of 261 patients in U.K. forensic, general inpatient, and community mental health settings. There was significant variation between these groups on SAPROF scores with fewer protective factors in the forensic group. The prospective validity of the SAPROF for nonviolence in the general inpatient and community samples was moderate (area under the curve [AUC] = .60). Adoption of the SAPROF or similar instruments as a supplement to risk-focused assessments has the potential to improve awareness of protective factors and enhance therapeutic engagement in a range of mental health services.

Self-similar seismogenic structure of the crust: A review of the problem and a mathematical model

NASA Astrophysics Data System (ADS)

Stakhovsky, I. R.

2007-12-01

The paper presents a brief review of studies of the structural organization of a seismogenic medium showing that the crust of seismically active regions possesses a fractal structure. A new mathematical model of the self-similar seismogenic structure (SSS) of the crust generalizing the reviewed publications is proposed on the basis of the scaling correspondence between the fault, seismic, and seismic energy multifractal fields of the crust. Multifractal fields of other physical origin can also be incorporated in the SSS model.

Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure.

PubMed

Meitinger, T; Meindl, A; Bork, P; Rost, B; Sander, C; Haasemann, M; Murken, J

1993-12-01

The X-lined gene for Norrie disease, which is characterized by blindness, deafness and mental retardation has been cloned recently. This gene has been thought to code for a putative extracellular factor; its predicted amino acid sequence is homologous to the C-terminal domain of diverse extracellular proteins. Sequence pattern searches and three-dimensional modelling now suggest that the Norrie disease protein (NDP) has a tertiary structure similar to that of transforming growth factor beta (TGF beta). Our model identifies NDP as a member of an emerging family of growth factors containing a cystine knot motif, with direct implications for the physiological role of NDP. The model also sheds light on sequence related domains such as the C-terminal domain of mucins and of von Willebrand factor.

Pronounced differences in genetic structure despite overall ecological similarity for two Ambystoma salamanders in the same landscape

Treesearch

Andrew R. Whiteley; Kevin McGarigal; Michael K. Schwartz

2014-01-01

Studies linking genetic structure in amphibian species with ecological characteristics have focused on large differences in dispersal capabilities. Here, we test whether two species with similar dispersal potential but subtle differences in other ecological characteristics also exhibit strong differences in genetic structure in the same landscape. We examined eight...

Further insights on the French WISC-IV factor structure through Bayesian structural equation modeling.

PubMed

Golay, Philippe; Reverte, Isabelle; Rossier, Jérôme; Favez, Nicolas; Lecerf, Thierry

2013-06-01

The interpretation of the Wechsler Intelligence Scale for Children--Fourth Edition (WISC-IV) is based on a 4-factor model, which is only partially compatible with the mainstream Cattell-Horn-Carroll (CHC) model of intelligence measurement. The structure of cognitive batteries is frequently analyzed via exploratory factor analysis and/or confirmatory factor analysis. With classical confirmatory factor analysis, almost all cross-loadings between latent variables and measures are fixed to zero in order to allow the model to be identified. However, inappropriate zero cross-loadings can contribute to poor model fit, distorted factors, and biased factor correlations; most important, they do not necessarily faithfully reflect theory. To deal with these methodological and theoretical limitations, we used a new statistical approach, Bayesian structural equation modeling (BSEM), among a sample of 249 French-speaking Swiss children (8-12 years). With BSEM, zero-fixed cross-loadings between latent variables and measures are replaced by approximate zeros, based on informative, small-variance priors. Results indicated that a direct hierarchical CHC-based model with 5 factors plus a general intelligence factor better represented the structure of the WISC-IV than did the 4-factor structure and the higher order models. Because a direct hierarchical CHC model was more adequate, it was concluded that the general factor should be considered as a breadth rather than a superordinate factor. Because it was possible for us to estimate the influence of each of the latent variables on the 15 subtest scores, BSEM allowed improvement of the understanding of the structure of intelligence tests and the clinical interpretation of the subtest scores. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Transforming growth factor alpha, Shope fibroma growth factor, and vaccinia growth factor can replace myxoma growth factor in the induction of myxomatosis in rabbits.

PubMed

Opgenorth, A; Nation, N; Graham, K; McFadden, G

1993-02-01

The epidermal growth factor (EGF) homologues encoded by vaccinia virus, myxoma virus, and malignant rabbit fibroma virus have been shown to contribute to the pathogenicity of virus infection upon inoculation of susceptible hosts. However, since the primary structures of these growth factors and the disease profiles induced by different poxvirus genera vary substantially, the degree to which the various EGF homologues perform similar roles in viral pathogenesis remains unclear. In order to determine whether different EGF-like growth factors can perform qualitatively similar functions in the induction of myxomatosis in rabbits, we created recombinant myxoma virus variants in which the native growth factor, myxoma growth factor (MGF), was disrupted and replaced with either vaccinia virus growth factor, Shope fibroma growth factor, or rat transforming growth factor alpha. Unlike the control virus containing an inactivated MGF gene, which caused marked attenuation of the disease syndrome and substantially less proliferation of the epithelial cell layers in the conjunctiva and respiratory tract, the recombinant myxoma virus strains expressing heterologous growth factors produced infections which were both clinically and histopathologically indistinguishable from wild-type myxomatosis. We conclude that these poxviral and cellular EGF-like growth factors, which are diverse with respect to primary structure and origin, have similar biological functions in the context of myxoma virus pathogenesis and are mitogenic for the same target cells.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

PubMed

Konc, Janez; Cesnik, Tomo; Konc, Joanna Trykowska; Penca, Matej; Janežič, Dušanka

2012-02-27

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.

Processes of Similarity Judgment

ERIC Educational Resources Information Center

Larkey, Levi B.; Markman, Arthur B.

2005-01-01

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

A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.

PubMed

Hebels, Dennie G A J; Rasche, Axel; Herwig, Ralf; van Westen, Gerard J P; Jennen, Danyel G J; Kleinjans, Jos C S

2016-01-01

When evaluating compound similarity, addressing multiple sources of information to reach conclusions about common pharmaceutical and/or toxicological mechanisms of action is a crucial strategy. In this chapter, we describe a systems biology approach that incorporates analyses of hepatotoxicant data for 33 compounds from three different sources: a chemical structure similarity analysis based on the 3D Tanimoto coefficient, a chemical structure-based protein target prediction analysis, and a cross-study/cross-platform meta-analysis of in vitro and in vivo human and rat transcriptomics data derived from public resources (i.e., the diXa data warehouse). Hierarchical clustering of the outcome scores of the separate analyses did not result in a satisfactory grouping of compounds considering their known toxic mechanism as described in literature. However, a combined analysis of multiple data types may hypothetically compensate for missing or unreliable information in any of the single data types. We therefore performed an integrated clustering analysis of all three data sets using the R-based tool iClusterPlus. This indeed improved the grouping results. The compound clusters that were formed by means of iClusterPlus represent groups that show similar gene expression while simultaneously integrating a similarity in structure and protein targets, which corresponds much better with the known mechanism of action of these toxicants. Using an integrative systems biology approach may thus overcome the limitations of the separate analyses when grouping liver toxicants sharing a similar mechanism of toxicity.

Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments

PubMed Central

Graham, Catherine H.; Brooks, Thomas M.; Rondinini, Carlo; Hedges, S. Blair; Davidson, Ana D.; Costa, Gabriel C.

2016-01-01

The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale. PMID:27559061

Structure-preserving and rank-revealing QR-factorizations

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

Bischof, C.H.; Hansen, P.C.

1991-11-01

The rank-revealing QR-factorization (RRQR-factorization) is a special QR-factorization that is guaranteed to reveal the numerical rank of the matrix under consideration. This makes the RRQR-factorization a useful tool in the numerical treatment of many rank-deficient problems in numerical linear algebra. In this paper, a framework is presented for the efficient implementation of RRQR algorithms, in particular, for sparse matrices. A sparse RRQR-algorithm should seek to preserve the structure and sparsity of the matrix as much as possible while retaining the ability to capture safely the numerical rank. To this end, the paper proposes to compute an initial QR-factorization using amore » restricted pivoting strategy guarded by incremental condition estimation (ICE), and then applies the algorithm suggested by Chan and Foster to this QR-factorization. The column exchange strategy used in the initial QR factorization will exploit the fact that certain column exchanges do not change the sparsity structure, and compute a sparse QR-factorization that is a good approximation of the sought-after RRQR-factorization. Due to quantities produced by ICE, the Chan/Foster RRQR algorithm can be implemented very cheaply, thus verifying that the sought-after RRQR-factorization has indeed been computed. Experimental results on a model problem show that the initial QR-factorization is indeed very likely to produce RRQR-factorization.« less

Factor Structure of the Psychotherapy Supervisor Development Scale

ERIC Educational Resources Information Center

Barnes, Kristin L.; Moon, Simon M.

2006-01-01

The goodness of fit of 3 models of factor structure of the Psychotherapy Supervisor Development Scale (PSDS; C. E. Watkins, L. J. Schneider, J. Haynes, & R. Nieberding, 1995) were examined using a sample of counseling supervisors. The results indicated that the factor structure of the PSDS was largely consistent with the original 4-factor…

Social cognition in schizophrenia: factor structure, clinical and functional correlates.

PubMed

Buck, Benjamin E; Healey, Kristin M; Gagen, Emily C; Roberts, David L; Penn, David L

2016-08-01

Social cognition is consistently impaired in people with schizophrenia, separable from general neurocognition, predictive of real-world functioning and amenable to psychosocial treatment. Few studies have empirically examined its underlying factor structure. This study (1) examines the factor structure of social cognition in both a sample of individuals with schizophrenia-spectrum disorders and non-clinical controls and (2) explores relationships of factors to neurocognition, symptoms and functioning. A factor analysis was conducted on social cognition measures in a sample of 65 individuals with schizophrenia or schizoaffective disorder, and 50 control participants. The resulting factors were examined for their relationships to symptoms and functioning. Results suggested a two-factor structure in the schizophrenia sample (social cognition skill and hostile attributional style) and a three-factor structure in the non-clinical sample (hostile attributional style, higher-level inferential processing and lower-level cue detection). In the schizophrenia sample, the social cognition skill factor was significantly related to negative symptoms and social functioning, whereas hostile attributional style predicted positive and general psychopathology symptoms. The factor structure of social cognition in schizophrenia separates hostile attributional style and social cognition skill, and each show differential relationships to relevant clinical variables in schizophrenia.

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.

PubMed

Suzuki, Hirofumi; Kawabata, Takeshi; Nakamura, Haruki

2016-02-15

Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1 min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers. Omokage search is freely accessible at http://pdbj.org/omokage/. © The Author 2015. Published by Oxford University Press.

Examining the factor structure of the Multiple Sclerosis Impact Scale.

PubMed

Fitzgerald, Shawn M; Li, Jian; Rumrill, Phillip D; Merchant, William; Bishop, Malachy

2014-01-01

The purpose of this study was to investigate the factor structure of the Multiple Sclerosis Impact Scale (MSIS-29) to assess its suitability for modeling the impact of MS on a nation-wide sample of individuals from the United States. Investigators completed a Confirmatory Factor Analysis (CFA) to examine the two-factor structure proposed by Hobart et al. [17]. Although the original MSIS-29 factor structure did not fit the data exactly, the hypothesized two-factor model was partially supported in the current data. Implications for future instrument development and rehabilitation practice are discussed.

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

PubMed

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.

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

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

Zemla, A; Lang, D; Kostova, T

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 facilitatemore » 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

Social cognition in schizophrenia: Factor structure, clinical and functional correlates

PubMed Central

Buck, Benjamin E.; Healey, Kristin M.; Gagen, Emily C.; Roberts, David L.; Penn, David L.

2016-01-01

Background Social cognition is consistently impaired in people with schizophrenia, separable from general neurocognition, predictive of real-world functioning, and amenable to psychosocial treatment. Few studies have empirically examined its underlying factor structure. Aims The present study (1) examines the factor structure of social cognition in both a sample of individuals with schizophrenia-spectrum disorders and non-clinical controls, and (2) explores relationships of factors to neurocognition, symptoms and functioning. Method A factor analysis was conducted on social cognition measures in a sample of sixty-five individuals with schizophrenia or schizoaffective disorder, and fifty control participants. The resulting factors were examined for their relationships to symptoms and functioning. Results Results suggested a two-factor structure in the schizophrenia sample (social cognition skill and hostile attributional style) and a three-factor structure in the non-clinical sample (hostile attributional style, higher-level inferential processing, and lower-level cue detection). In the schizophrenia sample, the social cognition skill factor was significantly related to negative symptoms and social functioning, while hostile attributional style predicted positive and general psychopathology symptoms. Conclusions The factor structure of social cognition in schizophrenia separates hostile attributional style and social cognition skill, and each show differential relationships to relevant clinical variables in schizophrenia. PMID:26747063

Relativistic effects on x-ray structure factors

NASA Astrophysics Data System (ADS)

Batke, Kilian; Eickerling, Georg

2016-04-01

Today, combined experimental and theoretical charge density studies based on quantum chemical calculations and x-ray diffraction experiments allow for the investigation of the topology of the electron density at subatomic resolution. When studying compounds containing transition metal elements, relativistic effects need to be adequately taken into account not only in quantum chemical calculations of the total electron density ρ ({r}), but also for the atomic scattering factors employed to extract ρ ({r}) from experimental x-ray diffraction data. In the present study, we investigate the magnitude of relativistic effects on x-ray structure factors and for this purpose {F}({{r}}*) have been calculated for the model systems M(C2H2) (M = Ni, Pd, Pt) from four-component molecular wave functions. Relativistic effects are then discussed by a comparison to structure factors obtained from a non-relativistic reference and different quasi-relativistic approximations. We show, that the overall effects of relativity on the structure factors on average amount to 0.81%, 1.51% and 2.78% for the three model systems under investigation, but that for individual reflections or reflection series the effects can be orders of magnitude larger. Employing the quasi-relativistic Douglas-Kroll-Hess second order or the zeroth order regular approximation Hamiltonian takes these effects into account to a large extend, reducing the differences between the (quasi-)relativistic and the non-relativistic result by one order of magnitude. In order to further determine the experimental significance of the results, the magnitude of the relativistic effects is compared to the changes of the model structure factor data when charge transfer and chemical bonding is taken into account by a multipolar expansion of {F}({{r}}*).

Factor structure of the Halstead-Reitan Neuropsychological Battery for children: a brief report supplement.

PubMed

Ross, Sylvia An; Allen, Daniel N; Goldstein, Gerald

2014-01-01

The Halstead-Reitan Neuropsychological Battery (HRNB) is the first factor-analyzed neuropsychological battery and consists of three batteries for young children, older children, and adults. Halstead's original factor analysis extracted four factors from the adult version of the battery, which were the basis for his theory of biological intelligence. These factors were called Central Integrative Field, Abstraction, Power, and Directional. Since this original analysis, Reitan's additions to the battery, and the development of the child versions of the test, this factor-analytic research continued. An introduction and the adult literature are reviewed in Ross, Allen, and Goldstein ( in press ). In this supplemental article, factor-analytic studies of the HRNB with children are reviewed. It is concluded that factor analysis of the HRNB or Reitan-Indiana Neuropsychological Battery with children does not replicate the extensiveness of the adult literature, although there is some evidence that when the traditional battery for older children is used, the factor structure is similar to what is found in adult studies. Reitan's changes to the battery appear to have added factors including language and sensory-perceptual factors. When other tests and scoring methods are used in addition to the core battery, differing solutions are produced.

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

Defining distinct negative beliefs about uncertainty: validating the factor structure of the Intolerance of Uncertainty Scale.

PubMed

Sexton, Kathryn A; Dugas, Michel J

2009-06-01

This study examined the factor structure of the English version of the Intolerance of Uncertainty Scale (IUS; French version: M. H. Freeston, J. Rhéaume, H. Letarte, M. J. Dugas, & R. Ladouceur, 1994; English version: K. Buhr & M. J. Dugas, 2002) using a substantially larger sample than has been used in previous studies. Nonclinical undergraduate students and adults from the community (M age = 23.74 years, SD = 6.36; 73.0% female and 27.0% male) who participated in 16 studies in the Anxiety Disorders Laboratory at Concordia University in Montreal, Canada were randomly assigned to 2 datasets. Exploratory factor analysis with the 1st sample (n = 1,230) identified 2 factors: the beliefs that "uncertainty has negative behavioral and self-referent implications" and that "uncertainty is unfair and spoils everything." This 2-factor structure provided a good fit to the data (Bentler-Bonett normed fit index = .96, comparative fit index = .97, standardized root-mean residual = .05, root-mean-square error of approximation = .07) upon confirmatory factor analysis with the 2nd sample (n = 1,221). Both factors showed similarly high correlations with pathological worry, and Factor 1 showed stronger correlations with generalized anxiety disorder analogue status, trait anxiety, somatic anxiety, and depressive symptomatology. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Structure of a PL17 Family Alginate Lyase Demonstrates Functional Similarities among Exotype Depolymerases

PubMed Central

Park, David; Jagtap, Sujit; Nair, Satish K.

2014-01-01

Brown macroalgae represent an ideal source for complex polysaccharides that can be utilized as precursors for cellulosic biofuels. The lack of recalcitrant lignin components in macroalgae polysaccharide reserves provides a facile route for depolymerization of constituent polysaccharides into simple monosaccharides. The most abundant sugars in macroalgae are alginate, mannitol, and glucan, and although several classes of enzymes that can catabolize the latter two have been characterized, studies of alginate-depolymerizing enzymes have lagged. Here, we present several crystal structures of Alg17c from marine bacterium Saccharophagus degradans along with structure-function characterization of active site residues that are suggested to be involved in the exolytic mechanism of alginate depolymerization. This represents the first structural and biochemical characterization of a family 17 polysaccharide lyase enzyme. Despite the lack of appreciable sequence conservation, the structure and β-elimination mechanism for glycolytic bond cleavage by Alg17c are similar to those observed for family 15 polysaccharide lyases and other lyases. This work illuminates the evolutionary relationships among enzymes within this unexplored class of polysaccharide lyases and reinforces the notion of a structure-based hierarchy in the classification of these enzymes. PMID:24478312

Tree-Structured Infinite Sparse Factor Model

PubMed Central

Zhang, XianXing; Dunson, David B.; Carin, Lawrence

2013-01-01

A tree-structured multiplicative gamma process (TMGP) is developed, for inferring the depth of a tree-based factor-analysis model. This new model is coupled with the nested Chinese restaurant process, to nonparametrically infer the depth and width (structure) of the tree. In addition to developing the model, theoretical properties of the TMGP are addressed, and a novel MCMC sampler is developed. The structure of the inferred tree is used to learn relationships between high-dimensional data, and the model is also applied to compressive sensing and interpolation of incomplete images. PMID:25279389

How large B-factors can be in protein crystal structures.

PubMed

Carugo, Oliviero

2018-02-23

Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.

Recovery of Weak Factor Loadings When Adding the Mean Structure in Confirmatory Factor Analysis: A Simulation Study

PubMed Central

Ximénez, Carmen

2016-01-01

This article extends previous research on the recovery of weak factor loadings in confirmatory factor analysis (CFA) by exploring the effects of adding the mean structure. This issue has not been examined in previous research. This study is based on the framework of Yung and Bentler (1999) and aims to examine the conditions that affect the recovery of weak factor loadings when the model includes the mean structure, compared to analyzing the covariance structure alone. A simulation study was conducted in which several constraints were defined for one-, two-, and three-factor models. Results show that adding the mean structure improves the recovery of weak factor loadings and reduces the asymptotic variances for the factor loadings, particularly for the models with a smaller number of factors and a small sample size. Therefore, under certain circumstances, modeling the means should be seriously considered for covariance models containing weak factor loadings. PMID:26779071

Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions.

PubMed

Li, Yang; Yang, Jianyi

2017-04-24

The prediction of protein-ligand binding affinity has recently been improved remarkably by machine-learning-based scoring functions. For example, using a set of simple descriptors representing the atomic distance counts, the RF-Score improves the Pearson correlation coefficient to about 0.8 on the core set of the PDBbind 2007 database, which is significantly higher than the performance of any conventional scoring function on the same benchmark. A few studies have been made to discuss the performance of machine-learning-based methods, but the reason for this improvement remains unclear. In this study, by systemically controlling the structural and sequence similarity between the training and test proteins of the PDBbind benchmark, we demonstrate that protein structural and sequence similarity makes a significant impact on machine-learning-based methods. After removal of training proteins that are highly similar to the test proteins identified by structure alignment and sequence alignment, machine-learning-based methods trained on the new training sets do not outperform the conventional scoring functions any more. On the contrary, the performance of conventional functions like X-Score is relatively stable no matter what training data are used to fit the weights of its energy terms.

31P NMR Characterization of Tricin and Its Structurally Similar Flavonoids

DOE PAGES

Li, Mi; Pu, Yunqiao; Tschaplinski, Timothy J.; ...

2017-04-24

Tricin, a flavonoid metabolite, has been recently identified as a component of lignin in select monocot plants. This finding has initiated consideration on updating the lignin biosynthesis pathway. Here, we report a rapid method of determination of tricin in corn stover lignin, based on 31P nuclear magnetic resonance (NMR) spectroscopy by phosphitylating with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP). Nine other flavonoids, with similar structure to tricin, have also been examined using the current method. The application of 31P NMR enables rapid identification of tricin-like flavonoids in the heterogeneous lignin polymer. The well resolved spectroscopic peaks from these derivatized flavonoids and lignin functional groupsmore » provide important information for the determination of flavonoids individually or their association with lignin.« less

31P NMR Characterization of Tricin and Its Structurally Similar Flavonoids

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

Li, Mi; Pu, Yunqiao; Tschaplinski, Timothy J.

Tricin, a flavonoid metabolite, has been recently identified as a component of lignin in select monocot plants. This finding has initiated consideration on updating the lignin biosynthesis pathway. Here, we report a rapid method of determination of tricin in corn stover lignin, based on 31P nuclear magnetic resonance (NMR) spectroscopy by phosphitylating with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP). Nine other flavonoids, with similar structure to tricin, have also been examined using the current method. The application of 31P NMR enables rapid identification of tricin-like flavonoids in the heterogeneous lignin polymer. The well resolved spectroscopic peaks from these derivatized flavonoids and lignin functional groupsmore » provide important information for the determination of flavonoids individually or their association with lignin.« less

Probabilistic simulation of the human factor in structural reliability

NASA Technical Reports Server (NTRS)

Shah, Ashwin R.; Chamis, Christos C.

1991-01-01

Many structural failures have occasionally been attributed to human factors in engineering design, analyses maintenance, and fabrication processes. Every facet of the engineering process is heavily governed by human factors and the degree of uncertainty associated with them. Factors such as societal, physical, professional, psychological, and many others introduce uncertainties that significantly influence the reliability of human performance. Quantifying human factors and associated uncertainties in structural reliability require: (1) identification of the fundamental factors that influence human performance, and (2) models to describe the interaction of these factors. An approach is being developed to quantify the uncertainties associated with the human performance. This approach consists of a multi factor model in conjunction with direct Monte-Carlo simulation.

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

PubMed

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.

Improving the Factor Structure of Psychological Scales

PubMed Central

Zhang, Xijuan; Savalei, Victoria

2015-01-01

Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format, which replaces each response option in the Likert scale with a full sentence. We hypothesized that this format would result in a cleaner factor structure as compared with the Likert format. We tested this hypothesis on three popular psychological scales: the Rosenberg Self-Esteem scale, the Conscientiousness subscale of the Big Five Inventory, and the Beck Depression Inventory II. Scales in both formats showed comparable reliabilities. However, scales in the Expanded format had better (i.e., lower and more theoretically defensible) dimensionalities than scales in the Likert format, as assessed by both exploratory factor analyses and confirmatory factor analyses. We encourage further study and wider use of the Expanded format, particularly when a scale’s dimensionality is of theoretical interest. PMID:27182074

Factor structure of the Body Appreciation Scale among Malaysian women.

PubMed

Swami, Viren; Chamorro-Premuzic, Tomas

2008-12-01

The present study examined the factor structure of a Malay version of the Body Appreciation Scale (BAS), a recently developed scale for the assessment of positive body image that has been shown to have a unidimensional structure in Western settings. Results of exploratory and confirmatory factor analyses based on data from community sample of 591 women in Kuala Lumpur, Malaysia, failed to support a unidimensional structure for the Malay BAS. Results of a confirmatory factor analysis suggested two stable factors, which were labelled 'General Body Appreciation' and 'Body Image Investment'. Multi-group analysis showed that the two-factor structure was invariant for both Malaysian Malay and Chinese women, and that there were no significant ethnic differences on either factor. Results also showed that General Body Appreciation was significant negatively correlated with participants' body mass index. These results are discussed in relation to possible cross-cultural differences in positive body image.

Perceptual similarity and the neural correlates of geometrical illusions in human brain structure.

PubMed

Axelrod, Vadim; Schwarzkopf, D Samuel; Gilaie-Dotan, Sharon; Rees, Geraint

2017-01-09

Geometrical visual illusions are an intriguing phenomenon, in which subjective perception consistently misjudges the objective, physical properties of the visual stimulus. Prominent theoretical proposals have been advanced attempting to find common mechanisms across illusions. But empirically testing the similarity between illusions has been notoriously difficult because illusions have very different visual appearances. Here we overcome this difficulty by capitalizing on the variability of the illusory magnitude across participants. Fifty-nine healthy volunteers participated in the study that included measurement of individual illusion magnitude and structural MRI scanning. We tested the Muller-Lyer, Ebbinghaus, Ponzo, and vertical-horizontal geometrical illusions as well as a non-geometrical, contrast illusion. We found some degree of similarity in behavioral judgments of all tested geometrical illusions, but not between geometrical illusions and non-geometrical, contrast illusion. The highest similarity was found between Ebbinghaus and Muller-Lyer geometrical illusions. Furthermore, the magnitude of all geometrical illusions, and particularly the Ebbinghaus and Muller-Lyer illusions, correlated with local gray matter density in the parahippocampal cortex, but not in other brain areas. Our findings suggest that visuospatial integration and scene construction processes might partly mediate individual differences in geometric illusory perception. Overall, these findings contribute to a better understanding of the mechanisms behind geometrical illusions.

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

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

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 help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), 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 we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural 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

Factor Scores, Structure Coefficients, and Communality Coefficients

ERIC Educational Resources Information Center

Goodwyn, Fara

2012-01-01

This paper presents heuristic explanations of factor scores, structure coefficients, and communality coefficients. Common misconceptions regarding these topics are clarified. In addition, (a) the regression (b) Bartlett, (c) Anderson-Rubin, and (d) Thompson methods for calculating factor scores are reviewed. Syntax necessary to execute all four…

Host factors that promote retrotransposon integration are similar in distantly related eukaryotes

PubMed Central

Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak

2017-01-01

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. PMID:29232693

Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

PubMed

Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak; Levin, Henry L

2017-12-01

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

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

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

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

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF)more » CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.« less

Factor Structure of the Exercise Self-Efficacy Scale

ERIC Educational Resources Information Center

Cornick, Jessica E.

2015-01-01

The current study utilized exercise self-efficacy ratings from undergraduate students to assess the factor structure of the Self-Efficacy to Regulate Exercise Scale (Bandura, 1997, 2006). An exploratory factor analysis (n = 759) indicated a two-factor model solution and three separate confirmatory factor analyses (n = 1,798) supported this…

Temperature and composition dependence of Mg-based amorphous-alloy structure factors

NASA Astrophysics Data System (ADS)

From, M.; Muir, W. B.

1992-01-01

Measurements of the x-ray total structure factors for amorphous Mg70Zn30, Ca70Mg30, and Mg85.5Cu14.5 at 9, 150, and 300 K have been made. The composition dependence of the room-temperature structure factors of MgxZn1-x have also been measured for values of x=0.65, 0.70, and 0.75. These compositional changes can be accounted for by the increase in average atomic size as the fraction of the larger Mg atoms increases with x. Also the Perkus-Yevick hard-sphere model is sufficient to calculate the change in structure factor with composition if an experimental structure factor is available from which the sphere diameters and packing fraction can be extracted. The temperature dependence of the structure factors is consistent with the observed thermal expansion and a Debye phonon model with Meisel and Cote's approximation for the multiphonon contribution to the structure factor.

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

PubMed

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

2017-11-01

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

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

PubMed

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.

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

PubMed

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

Phenotypic plasticity and similarity among gall morphotypes on a superhost, Baccharis reticularia (Asteraceae).

PubMed

Formiga, A T; Silveira, F A O; Fernandes, G W; Isaias, R M S

2015-03-01

Understanding factors that modulate plant development is still a challenging task in plant biology. Although research has highlighted the role of abiotic and biotic factors in determining final plant structure, we know little of how these factors combine to produce specific developmental patterns. Here, we studied patterns of cell and tissue organisation in galled and non-galled organs of Baccharis reticularia, a Neotropical shrub that hosts over ten species of galling insects. We employed qualitative and quantitative approaches to understand patterns of growth and differentiation in its four most abundant gall morphotypes. We compared two leaf galls induced by sap-sucking Hemiptera and stem galls induced by a Lepidopteran and a Dipteran, Cecidomyiidae. The hypotheses tested were: (i) the more complex the galls, the more distinct they are from their non-galled host; (ii) galls induced on less plastic host organs, e.g. stems, develop under more morphogenetic constraints and, therefore, should be more similar among themselves than galls induced on more plastic organs. We also evaluated the plant sex preference of gall-inducing insects for oviposition. Simple galls were qualitative and quantitatively more similar to non-galled organs than complex galls, thereby supporting the first hypothesis. Unexpectedly, stem galls had more similarities between them than to their host organ, hence only partially supporting the second hypothesis. Similarity among stem galls may be caused by the restrictive pattern of host stems. The opposite trend was observed for host leaves, which generate either similar or distinct gall morphotypes due to their higher phenotypic plasticity. The Relative Distance of Plasticity Index for non-galled stems and stem galls ranged from 0.02 to 0.42. Our results strongly suggest that both tissue plasticity and gall inducer identity interact to determine plant developmental patterns, and therefore, final gall structure. © 2014 German Botanical Society

A two-dimensional Riemann solver with self-similar sub-structure - Alternative formulation based on least squares projection

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Vides, Jeaniffer; Gurski, Katharine; Nkonga, Boniface; Dumbser, Michael; Garain, Sudip; Audit, Edouard

2016-01-01

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 self-similar formulation of Balsara [16] proves especially useful for this purpose. While that work is based on a Galerkin projection, in this paper we present an analogous self-similar formulation that is based on a different interpretation. In the present formulation, we interpret the shock jumps at the boundary of the strongly-interacting state quite literally. The enforcement of the shock jump conditions is done with a least squares projection (Vides, Nkonga and Audit [67]). With that interpretation, we again show that the multidimensional Riemann solver can be endowed with sub-structure. However, we find that the most efficient implementation arises when we use a flux vector splitting and a least squares projection. An alternative formulation that is based on the full characteristic matrices is also presented. The multidimensional Riemann solvers that are demonstrated here use one-dimensional HLLC Riemann solvers as building blocks. Several stringent test problems drawn from hydrodynamics and MHD are presented to show that the method works. Results from structured and unstructured meshes demonstrate the versatility of our method. The reader is also invited to watch a video introduction to multidimensional Riemann solvers on http://www.nd.edu/ dbalsara/Numerical-PDE-Course.

Similar Ring Structures on Mars and Tibetan Plateau confirm recent tectonism on Martian Northern polar region

NASA Astrophysics Data System (ADS)

Anglés, A.; Li, Y. L.

2017-10-01

The polar regions of Mars feature layered deposits, some of which exist as enclosed zoning structures. These deposits raised strong interest since their discovery and still remain one of the most controversial features on Mars. Zoning structures that are enclosed only appear in the Northern polar region, where the disappearance of water bodies may have left behind huge deposits of evaporate salts. The origin of the layered deposits has been widely debated. Here we propose that the enclosed nature of the zoning structures indicates the result of recent tectonism. We compared similar structures at an analogue site located in the western Qaidam Basin of Tibetan Plateau, a unique tectonic setting with abundant saline deposits. The enclosed structures, which we term Ring Structures, in both the analogue site and in the Northern polar region of Mars, were formed by uplift induced pressurization and buoyancy of salts as the result of recent tectonic activity.

Structural Deterministic Safety Factors Selection Criteria and Verification

NASA Technical Reports Server (NTRS)

Verderaime, V.

1992-01-01

Though current deterministic safety factors are arbitrarily and unaccountably specified, its ratio is rooted in resistive and applied stress probability distributions. This study approached the deterministic method from a probabilistic concept leading to a more systematic and coherent philosophy and criterion for designing more uniform and reliable high-performance structures. The deterministic method was noted to consist of three safety factors: a standard deviation multiplier of the applied stress distribution; a K-factor for the A- or B-basis material ultimate stress; and the conventional safety factor to ensure that the applied stress does not operate in the inelastic zone of metallic materials. The conventional safety factor is specifically defined as the ratio of ultimate-to-yield stresses. A deterministic safety index of the combined safety factors was derived from which the corresponding reliability proved the deterministic method is not reliability sensitive. The bases for selecting safety factors are presented and verification requirements are discussed. The suggested deterministic approach is applicable to all NASA, DOD, and commercial high-performance structures under static stresses.

Quantifying similarity of pore-geometry in nanoporous materials

DOE PAGES

Lee, Yongjin; Barthel, Senja D.; Dłotko, Paweł; ...

2017-05-23

In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. But, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify themmore » using topological data analysis. This then allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.« less

Demonstration of Functional Similarity of Proposed Biosimilar ABP 501 to Adalimumab.

PubMed

Velayudhan, Jyoti; Chen, Yuh-Feng; Rohrbach, Amanda; Pastula, Christina; Maher, Gwen; Thomas, Heather; Brown, Ryan; Born, Teresa L

2016-08-01

Due to the complex molecular structure and proprietary manufacturing processes of monoclonal antibodies (mAbs), differences in structure and function may be expected during development of biosimilar mAbs. Important regulatory requirements for approval of biosimilar products involve comprehensive assessments of any potential differences between proposed biosimilars and reference mAbs, including differences in all known mechanisms of action, using sensitive and relevant methods. Any identified structural differences should not result in differences in biofunctional or clinical activity. A comprehensive assessment comparing the Amgen biosimilar candidate ABP 501 with FDA-licensed adalimumab (adalimumab [US]) and EU-authorized adalimumab (adalimumab [EU]) was conducted to demonstrate similarity in biofunctional activity. The functional similarity assessment included testing of binding kinetics to soluble tumor necrosis factor α (TNFα) and relative binding to transmembrane TNFα. The neutralization of TNFα-induced caspase activation, TNFα- and lymphotoxin-α (LTα)-induced chemokine production, and cytotoxicity was also tested. Binding to Fc-gamma receptors FcγRIa, FcγRIIa (131H), FcγRIIIa (158V and 158F), and neonatal Fc receptor (FcRn) was compared with the reference mAbs, as was antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The data demonstrate that ABP 501 is similar to both adalimumab (US) and adalimumab (EU) with respect to evaluated biofunctional activities. Similarity in biofunctional activity is a critical component of the totality of evidence required for demonstration of biosimilarity. The functional similarity demonstrated for ABP 501 comprehensively assesses the known mechanisms of action of adalimumab, supporting the conclusion that ABP 501, adalimumab (US), and adalimumab (EU) are likely to be clinically similar.

Transforming Static Data Structures to Dynamic Structures.

DTIC Science & Technology

1979-09-03

binary transform. and was then studied in detail by Bentley. Oetiq. Guihms and Saxe E 1979). The name is taken Porn its similarity t the binomial qeeue...costs of the two families of structures would have been equal within a constant factor, each being 0(N3 1 2 ). The present disparity suggests that it...cost being split evenly (within a constant factor) between the two families of structures. The preceding results may be generalized to arbitrary

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

PubMed Central

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

Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex

PubMed Central

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake; Okamoto, Tomoyuki; Ishibashi, Matsujiro; Tokunaga, Masao; Kuroki, Ryota

2006-01-01

A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF) and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8 Å resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry by means of a cross-over interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different from that between human GCSF and the cytokine receptor homologous domain of mouse GCSF-R, but similar to that of the IL-6/gp130 signaling complex. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses. PMID:16492764

A factor analysis of landscape pattern and structure metrics

Treesearch

Kurt H. Riitters; R.V. O' Neill; C.T. Hunsaker; James D. Wickham; D.H. Yankee; S.P. Timmins; K.B. Jones; B.L. Jackson

1995-01-01

Fifty-five metrics of landscape pattern and structure were calculated for 85 maps of land use and land cover. A multivariate factor analysis was used to identify the common axes (or dimensions) of pattern and structure which were measured by a reduced set of 26 metrics. The first six factors explained about 87% of the variation in the 26 landscape metrics. These...

Factor structure and criterion validity across the full scale and ten short forms of the CES-D among Chinese adolescents.

PubMed

Yang, Wenhui; Xiong, Ge; Garrido, Luis Eduardo; Zhang, John X; Wang, Meng-Cheng; Wang, Chong

2018-04-16

We systematically examined the factor structure and criterion validity across the full scale and 10 short forms of the Center for Epidemiological Studies Depression Scale (CES-D) with Chinese youth. Participants were 5,434 Chinese adolescents in Grades 7 to 12 who completed the full CES-D; 612 of them further completed a structured diagnostic interview with the major depressive disorder (MDD) module of the Kiddie Schedule for Affective Disorder and Schizophrenia for School-age Children. Using a split-sample approach, a series of 4-, 3-, 2-, and 1-factor models were tested using exploratory structural equation modeling and cross-validated using confirmatory factor analysis; the dimensionality was also evaluated by parallel analysis in conjunction with the scree test and aided by factor mixture analysis. The results indicated that a single-factor model of depression with a wording method factor fitted the data well, and was the optimal structure underlying the scores of the full and shortened CES-D. Additionally, receiver operating characteristic curve analyses for MDD case detection showed that the CES-D full-scale scores accurately detected MDD youth (area under the curve [AUC] = .84). Furthermore, the short-form scores produced comparable AUCs with the full scale (.82 to .85), as well as similar levels of sensitivity and specificity when using optimal cutoffs. These findings suggest that depression among Chinese adolescents can be adequately measured and screened for by a single-factor structure underlying the CES-D scores, and that the short forms provide a viable alternative to the full instrument. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

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

PubMed

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.

3D-quantitative structure-activity relationship studies on benzothiadiazepine hydroxamates as inhibitors of tumor necrosis factor-alpha converting enzyme.

PubMed

Murumkar, Prashant R; Giridhar, Rajani; Yadav, Mange Ram

2008-04-01

A set of 29 benzothiadiazepine hydroxamates having selective tumor necrosis factor-alpha converting enzyme inhibitory activity were used to compare the quality and predictive power of 3D-quantitative structure-activity relationship, comparative molecular field analysis, and comparative molecular similarity indices models for the atom-based, centroid/atom-based, data-based, and docked conformer-based alignment. Removal of two outliers from the initial training set of molecules improved the predictivity of models. Among the 3D-quantitative structure-activity relationship models developed using the above four alignments, the database alignment provided the optimal predictive comparative molecular field analysis model for the training set with cross-validated r(2) (q(2)) = 0.510, non-cross-validated r(2) = 0.972, standard error of estimates (s) = 0.098, and F = 215.44 and the optimal comparative molecular similarity indices model with cross-validated r(2) (q(2)) = 0.556, non-cross-validated r(2) = 0.946, standard error of estimates (s) = 0.163, and F = 99.785. These models also showed the best test set prediction for six compounds with predictive r(2) values of 0.460 and 0.535, respectively. The contour maps obtained from 3D-quantitative structure-activity relationship studies were appraised for activity trends for the molecules analyzed. The comparative molecular similarity indices models exhibited good external predictivity as compared with that of comparative molecular field analysis models. The data generated from the present study helped us to further design and report some novel and potent tumor necrosis factor-alpha converting enzyme inhibitors.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

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

PubMed

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.

Evidence Regarding the Internal Structure: Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Lewis, Todd F.

2017-01-01

American Educational Research Association (AERA) standards stipulate that researchers show evidence of the internal structure of instruments. Confirmatory factor analysis (CFA) is one structural equation modeling procedure designed to assess construct validity of assessments that has broad applicability for counselors interested in instrument…

The factor structure of the Social Interaction Anxiety Scale and the Social Phobia Scale.

PubMed

Heidenreich, Thomas; Schermelleh-Engel, Karin; Schramm, Elisabeth; Hofmann, Stefan G; Stangier, Ulrich

2011-05-01

The Social Interaction Anxiety Scale (SIAS) and the Social Phobia Scale (SPS) are two compendium measures that have become some of the most popular self-report scales of social anxiety. Despite their popularity, it remains unclear whether it is necessary to maintain two separate scales of social anxiety. The primary objective of the present study was to examine the factor analytic structure of both measures to determine the factorial validity of each scale. For this purpose, we administered both scales to 577 patients at the beginning of outpatient treatment. Analyzing both scales simultaneously, a CFA with two correlated factors showed a better fit to the data than a single factor model. An additional EFA with an oblique rotation on all 40 items using the WLSMV estimator further supported the two factor solution. These results suggest that the SIAS and SPS measure similar, but not identical facets of social anxiety. Thus, our findings provide support to retain the SIAS and SPS as two separate scales. Copyright © 2011 Elsevier Ltd. All rights reserved.

Lack of congruence in species diversity indices and community structures of planktonic groups based on local environmental factors.

PubMed

Doi, Hideyuki; Chang, Kwang-Hyeon; Nishibe, Yuichiro; Imai, Hiroyuki; Nakano, Shin-ichi

2013-01-01

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Salivary proline-rich proteins and gluten: Do structural similarities suggest a role in celiac disease?

PubMed

Tian, Na; Messana, Irene; Leffler, Daniel A; Kelly, Ciaran P; Hansen, Joshua; Cabras, Tiziana; D'Alessandro, Alfredo; Schuppan, Detlef; Castagnola, Massimo; Helmerhorst, Eva J

2015-10-01

Gluten proteins, the culprits in celiac disease (CD), show striking similarities in primary structure with human salivary proline-rich proteins (PRPs). Both are enriched in proline and glutamine residues that often occur consecutively in their sequences. We investigated potential differences in the spectrum of salivary PRPs in health and CD. Stimulated salivary secretions were collected from CD patients, patients with refractory CD, patients with gastrointestinal complaints but no CD, and healthy controls. PRP isoforms/peptides were characterized by anionic and SDS-PAGE, PCR, and LC-ESI-MS. The gene frequencies of the acidic PRP isoforms PIF, Db, Pa, PRP1, and PRP2 did not differ between groups. At the protein level, PRPs peptides showed minor group differences, but these could not differentiate the CD and/or refractory CDs groups from the controls. This extensive study established that salivary PRPs, despite similarity to gluten proteins, show no apparent correlation with CD and thus will not serve as diagnostic markers for the disease. The structural basis for the tolerance to the gluten-like PRP proteins in CD is worthy of further exploration and may lead to the development of gluten-like analogs lacking immunogenicity that could be used therapeutically. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequentially distant but structurally similar proteins exhibit fold specific patterns based on their biophysical properties.

PubMed

Rajendran, Senthilnathan; Jothi, Arunachalam

2018-05-16

The Three-dimensional structure of a protein depends on the interaction between their amino acid residues. These interactions are in turn influenced by various biophysical properties of the amino acids. There are several examples of proteins that share the same fold but are very dissimilar at the sequence level. For proteins to share a common fold some crucial interactions should be maintained despite insignificant sequence similarity. Since the interactions are because of the biophysical properties of the amino acids, we should be able to detect descriptive patterns for folds at such a property level. In this line, the main focus of our research is to analyze such proteins and to characterize them in terms of their biophysical properties. Protein structures with sequence similarity lesser than 40% were selected for ten different subfolds from three different mainfolds (according to CATH classification) and were used for this analysis. We used the normalized values of the 49 physio-chemical, energetic and conformational properties of amino acids. We characterize the folds based on the average biophysical property values. We also observed a fold specific correlational behavior of biophysical properties despite a very low sequence similarity in our data. We further trained three different binary classification models (Naive Bayes-NB, Support Vector Machines-SVM and Bayesian Generalized Linear Model-BGLM) which could discriminate mainfold based on the biophysical properties. We also show that among the three generated models, the BGLM classifier model was able to discriminate protein sequences coming under all beta category with 81.43% accuracy and all alpha, alpha-beta proteins with 83.37% accuracy. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed

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

In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

PubMed

Martínez-Montiel, Nancy; Morales-Lara, Laura; Hernández-Pérez, Julio M; Martínez-Contreras, Rebeca D

2016-01-01

The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability

Emotional and Behavioral Problems among Impoverished Kenyan Youth: Factor Structure and Sex-Differences

PubMed Central

Harder, Valerie S.; Mutiso, Victoria N.; Khasakhala, Lincoln I.; Burke, Heather M.; Rettew, David C.; Ivanova, Masha Y.; Ndetei, David M.

2014-01-01

Data on youth emotional and behavioral problems from societies in Sub-Saharan Africa are lacking. This may be due to the fact that few youth mental health assessments have been tested for construct validity of syndrome structure across multicultural societies that include developing countries, and almost none have been tested in Sub-Saharan Africa. The Youth Self-Report (YSR), for example, has shown great consistency of its syndrome structure across many cultures, yet data from only one developing country in Sub-Saharan Africa have been included. In this study, we test the factor structure of YSR syndromes among Kenyan youth ages 11–18 years from an informal settlement in Nairobi, Kenya and examine sex-differences in levels of emotional and behavioral problems. We find the eight syndrome structure of the YSR to fit these data well (Root Mean Square Error of Approximation=.049). While Kenyan girls have significantly higher internalizing (Anxious/Depressed, Withdrawn/Depressed, Somatic) problem scores than boys, these differences are of similar magnitude to published multicultural findings. The results support the generalizability of the YSR syndrome structure to Kenyan youth and are in line with multicultural findings supporting the YSR as an assessment of emotional and behavioral problems in diverse societies. PMID:25419046

The factor structure and construct validity of the inventory of callous-unemotional traits in Chinese undergraduate students.

PubMed

Wang, Meng-Cheng; Gao, Yu; Deng, Jiaxin; Lai, Hongyu; Deng, Qiaowen; Armour, Cherie

2017-01-01

The current study assesses the factor structure and construct validity of the self-reported Inventory of Callous-Unemotional Traits (ICU) in 637 Chinese community adults (mean age = 25.98, SD = 5.79). A series of theoretical models proposed in previous studies were tested through confirmatory factor analyses. Results indicated that a shortened form that consists of 11 items (ICU-11) to assess callousness and uncaring factors has excellent overall fit. Additionally, correlations with a wide range of external variables demonstrated that this shortened form has similar construct validity compared to the original ICU. In conclusion, our findings suggest that the ICU-11 may be a promising self-report tool that could be a good substitute for the original form to assess callous-uncaring traits in adults.

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

PubMed

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.

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

PubMed Central

Konc, Janez; Janežič, Dušanka

2012-01-01

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. PMID:22600737

The Factor Structure of the English Language Development Assessment: A Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Kuriakose, Anju

2011-01-01

This study investigated the internal factor structure of the English language development Assessment (ELDA) using confirmatory factor analysis. ELDA is an English language proficiency test developed by a consortium of multiple states and is used to identify and reclassify English language learners in kindergarten to grade 12. Scores on item…

Counterfactual Plausibility and Comparative Similarity.

PubMed

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

2017-05-01

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

Factor structure of the Minnesota Satisfaction Questionnaire short form for restaurant employees.

PubMed

Hancer, Mura; George, R Thomas

2004-02-01

The factor structure of the Minnesota Satisfaction Questionnaire short form for nonsupervisory restaurant employees was explored in questions among 2000 employees of three full-service restaurant chains operating in midwestern United States. A total of 2000 surveys were distributed to hourly employees of the three chains. From the mailing, 924 surveys were returned and found useable, a 46.2% response rate. Principal factors analysis identified a four-factor structure for the employees, in contrast to the original two-factor structure, but as in other studies the structure was multifactorial.

Psychometric Structure of a Comprehensive Objective Structured Clinical Examination: A Factor Analytic Approach

ERIC Educational Resources Information Center

Volkan, Kevin; Simon, Steven R.; Baker, Harley; Todres, I. David

2004-01-01

Problem Statement and Background: While the psychometric properties of Objective Structured Clinical Examinations (OSCEs) have been studied, their latent structures have not been well characterized. This study examines a factor analytic model of a comprehensive OSCE and addresses implications for measurement of clinical performance. Methods: An…

Selecting the "Best" Factor Structure and Moving Measurement Validation Forward: An Illustration.

PubMed

Schmitt, Thomas A; Sass, Daniel A; Chappelle, Wayne; Thompson, William

2018-04-09

Despite the broad literature base on factor analysis best practices, research seeking to evaluate a measure's psychometric properties frequently fails to consider or follow these recommendations. This leads to incorrect factor structures, numerous and often overly complex competing factor models and, perhaps most harmful, biased model results. Our goal is to demonstrate a practical and actionable process for factor analysis through (a) an overview of six statistical and psychometric issues and approaches to be aware of, investigate, and report when engaging in factor structure validation, along with a flowchart for recommended procedures to understand latent factor structures; (b) demonstrating these issues to provide a summary of the updated Posttraumatic Stress Disorder Checklist (PCL-5) factor models and a rationale for validation; and (c) conducting a comprehensive statistical and psychometric validation of the PCL-5 factor structure to demonstrate all the issues we described earlier. Considering previous research, the PCL-5 was evaluated using a sample of 1,403 U.S. Air Force remotely piloted aircraft operators with high levels of battlefield exposure. Previously proposed PCL-5 factor structures were not supported by the data, but instead a bifactor model is arguably more statistically appropriate.

Teacher Observation of Classroom Adaptation--Checklist: Development and Factor Structure

ERIC Educational Resources Information Center

Koth, Christine W.; Bradshaw, Catherine P.; Leaf, Philip J.

2009-01-01

Two studies examined the validity and factor structure of the Teacher Observation of Classroom Adaptation-Checklist, an instrument used to evaluate school-based programs. The checklist is a cost-effective alternative to the original interview format, and the factor structure is consistent across gender, race, age, and time of administration.…

An empirical examination of the factor structure of compassion.

PubMed

Gu, Jenny; Cavanagh, Kate; Baer, Ruth; Strauss, Clara

2017-01-01

Compassion has long been regarded as a core part of our humanity by contemplative traditions, and in recent years, it has received growing research interest. Following a recent review of existing conceptualisations, compassion has been defined as consisting of the following five elements: 1) recognising suffering, 2) understanding the universality of suffering in human experience, 3) feeling moved by the person suffering and emotionally connecting with their distress, 4) tolerating uncomfortable feelings aroused (e.g., fear, distress) so that we remain open to and accepting of the person suffering, and 5) acting or being motivated to act to alleviate suffering. As a prerequisite to developing a high quality compassion measure and furthering research in this field, the current study empirically investigated the factor structure of the five-element definition using a combination of existing and newly generated self-report items. This study consisted of three stages: a systematic consultation with experts to review items from existing self-report measures of compassion and generate additional items (Stage 1), exploratory factor analysis of items gathered from Stage 1 to identify the underlying structure of compassion (Stage 2), and confirmatory factor analysis to validate the identified factor structure (Stage 3). Findings showed preliminary empirical support for a five-factor structure of compassion consistent with the five-element definition. However, findings indicated that the 'tolerating' factor may be problematic and not a core aspect of compassion. This possibility requires further empirical testing. Limitations with items from included measures lead us to recommend against using these items collectively to assess compassion. Instead, we call for the development of a new self-report measure of compassion, using the five-element definition to guide item generation. We recommend including newly generated 'tolerating' items in the initial item pool, to determine

Factor Structure Evaluation of the French Version of the Digital Natives Assessment Scale.

PubMed

Wagner, Vincent; Acier, Didier

2017-03-01

"Digital natives" concept defines young adults particularly familiar with emerging technologies such as computers, smartphones, or Internet. This notion is still controversial and so far, the primary identifying criterion was to consider their date of birth. However, literature highlighted the need to describe specific characteristics. The purpose of this research was to evaluate the factor structure of a French version of the Digital Natives Assessment Scale (DNAS). The sample of this study includes 590 participants from a 6-week massive open online course and from Web sites, electronic forums, and social networks. The DNAS was translated in French and then back-translated to English. A principal component analysis with orthogonal rotation followed by a confirmatory factorial analysis showed that a 15-item four-correlated component model provided the best fit for the data of our sample. Factor structure of this French-translated version of the DNAS was rather similar than those found in earlier studies. This study provides evidence of the DNAS robustness through cross-cultural and cross-generational validation. The French version of the DNAS appears to be appropriate as a quick and effective questionnaire to assess digital natives. More studies are needed to better define further features of this particular group.

Graph Kernels for Molecular Similarity.

PubMed

Rupp, Matthias; Schneider, Gisbert

2010-04-12

Molecular similarity measures are important for many cheminformatics applications like ligand-based virtual screening and quantitative structure-property relationships. Graph kernels are formal similarity measures defined directly on graphs, such as the (annotated) molecular structure graph. Graph kernels are positive semi-definite functions, i.e., they correspond to inner products. This property makes them suitable for use with kernel-based machine learning algorithms such as support vector machines and Gaussian processes. We review the major types of kernels between graphs (based on random walks, subgraphs, and optimal assignments, respectively), and discuss their advantages, limitations, and successful applications in cheminformatics. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clustering and visualizing similarity networks of membrane proteins.

PubMed

Hu, Geng-Ming; Mai, Te-Lun; Chen, Chi-Ming

2015-08-01

We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. © 2015 Wiley Periodicals, Inc.

Latent factor structure of a behavioral economic marijuana demand curve.

PubMed

Aston, Elizabeth R; Farris, Samantha G; MacKillop, James; Metrik, Jane

2017-08-01

Drug demand, or relative value, can be assessed via analysis of behavioral economic purchase task performance. Five demand indices are typically obtained from drug purchase tasks. The goal of this research was to determine whether metrics of marijuana reinforcement from a marijuana purchase task (MPT) exhibit a latent factor structure that efficiently characterizes marijuana demand. Participants were regular marijuana users (n = 99; 37.4% female, 71.5% marijuana use days [5 days/week], 15.2% cannabis dependent) who completed study assessments, including the MPT, during a baseline session. Principal component analysis was used to examine the latent structure underlying MPT indices. Concurrent validity was assessed via examination of relationships between latent factors and marijuana use, past quit attempts, and marijuana expectancies. A two-factor solution was confirmed as the best fitting structure, accounting for 88.5% of the overall variance. Factor 1 (65.8% variance) reflected "Persistence," indicating sensitivity to escalating marijuana price, which comprised four MPT indices (elasticity, O max , P max , and breakpoint). Factor 2 (22.7% variance) reflected "Amplitude," indicating the amount consumed at unrestricted price (intensity). Persistence factor scores were associated with fewer past marijuana quit attempts and lower expectancies of negative use outcomes. Amplitude factor scores were associated with more frequent use, dependence symptoms, craving severity, and positive marijuana outcome expectancies. Consistent with research on alcohol and cigarette purchase tasks, the MPT can be characterized with a latent two-factor structure. Thus, demand for marijuana appears to encompass distinct dimensions of price sensitivity and volumetric consumption, with differential relations to other aspects of marijuana motivation.

Similarity of urinary risk factors among stone-forming patients in five regions of the United States

NASA Technical Reports Server (NTRS)

Harvey, J. A.; Hill, K. D.; Pak, C. Y.

1990-01-01

Study Objective: To compare urinary biochemical risk factors among stone-forming patients in the Southeast (SE) or "stone belt" versus four other regions of the United States. Design: Prospective biochemical survey for regional comparisons. Setting: Referral-based nephrolithiasis clinics, urologists, nephrologists, and family practitioners. Patients: Consecutive sample of 3473 stone-forming patients who submitted 24-hour urine collections for biochemical analyses of stone-forming risk factors. Interventions: None. Subjects taking medication known to interfere with stone-forming risk factors were deleted from the final data compilation. Measurements and Main Results: Overall, the mean values for each urinary parameter spanned a narrow range without significant difference between the five regions. Among "metabolic" factors, 40% in the SE had hypercalciuria (> 6.25 mmol/d), compared to 35%-43% in other regions, and hyperuricosuria (> 4.2 mmol/d) was found in 16% in the SE versus 17%-19% elsewhere. Among "environmental" factors, low urine volume ( < 2 L/d) was found in 77% patients in the SE compared to 69%-78% elsewhere, and high sodium was encountered in 27% in the SE versus 24%-29% elsewhere. No differences were noted in occurrence of other abnormal risk factors: hyperoxaluria, hypocitraturia, low pH, high sulfate, high phosphorus, or low magnesium. Conclusions: Despite expected regional differences in nutritional and environmental influences, the results of this study showed a striking similarity in urinary biochemical risk factor profiles of stone-formers in all five regions of the United States.

Ion-ion dynamic structure factor of warm dense mixtures

DOE PAGES

Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

2015-06-25

In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

Factor Structure of Autistic Traits in Children with ADHD

ERIC Educational Resources Information Center

Martin, Joanna; Hamshere, Marian L.; O'Donovan, Michael C.; Rutter, Michael; Thapar, Anita

2014-01-01

Attention-deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) often co-occur. Factor analyses of ASD traits in children with and without ASD indicate the presence of social and restrictive-repetitive behaviour (RRB) factors. This study used exploratory factor analyses to determine the structure of ASD traits (assessed using…

Salient object detection: manifold-based similarity adaptation approach

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Reliability, Validity, and Factor Structure of the Imaginative Capability Scale

ERIC Educational Resources Information Center

Liang, Chaoyun; Chia, Tsorng-Lin

2014-01-01

Three studies were combined to test the reliability, validity, and factor structure of the imaginative capability scale (ICS). The ICS was a new self-report measure, which was developed to be empirically valid and easy to administer. Study 1 consisted in an exploratory factor analysis to determine the most appropriate structure of the ICS in a…

Resolving protein structure-function-binding site relationships from a binding site similarity network perspective.

PubMed

Mudgal, Richa; Srinivasan, Narayanaswamy; Chandra, Nagasuma

2017-07-01

Functional annotation is seldom straightforward with complexities arising due to functional divergence in protein families or functional convergence between non-homologous protein families, leading to mis-annotations. An enzyme may contain multiple domains and not all domains may be involved in a given function, adding to the complexity in function annotation. To address this, we use binding site information from bound cognate ligands and catalytic residues, since it can help in resolving fold-function relationships at a finer level and with higher confidence. A comprehensive database of 2,020 fold-function-binding site relationships has been systematically generated. A network-based approach is employed to capture the complexity in these relationships, from which different types of associations are deciphered, that identify versatile protein folds performing diverse functions, same function associated with multiple folds and one-to-one relationships. Binding site similarity networks integrated with fold, function, and ligand similarity information are generated to understand the depth of these relationships. Apart from the observed continuity in the functional site space, network properties of these revealed versatile families with topologically different or dissimilar binding sites and structural families that perform very similar functions. As a case study, subtle changes in the active site of a set of evolutionarily related superfamilies are studied using these networks. Tracing of such similarities in evolutionarily related proteins provide clues into the transition and evolution of protein functions. Insights from this study will be helpful in accurate and reliable functional annotations of uncharacterized proteins, poly-pharmacology, and designing enzymes with new functional capabilities. Proteins 2017; 85:1319-1335. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The factor structure and construct validity of the inventory of callous-unemotional traits in Chinese undergraduate students

PubMed Central

Gao, Yu; Deng, Jiaxin; Lai, Hongyu; Deng, Qiaowen; Armour, Cherie

2017-01-01

The current study assesses the factor structure and construct validity of the self-reported Inventory of Callous–Unemotional Traits (ICU) in 637 Chinese community adults (mean age = 25.98, SD = 5.79). A series of theoretical models proposed in previous studies were tested through confirmatory factor analyses. Results indicated that a shortened form that consists of 11 items (ICU-11) to assess callousness and uncaring factors has excellent overall fit. Additionally, correlations with a wide range of external variables demonstrated that this shortened form has similar construct validity compared to the original ICU. In conclusion, our findings suggest that the ICU-11 may be a promising self-report tool that could be a good substitute for the original form to assess callous-uncaring traits in adults. PMID:29216240

Factor analysis of regional brain activation in bipolar and healthy individuals reveals a consistent modular structure.

PubMed

Fleck, David E; Welge, Jeffrey A; Eliassen, James C; Adler, Caleb M; DelBello, Melissa P; Strakowski, Stephen M

2018-07-01

The neurophysiological substrates of cognition and emotion, as seen with fMRI, are generally explained using modular structures. The present study was designed to probe the modular structure of cognitive-emotional processing in bipolar and healthy individuals using factor analysis and compare the results with current conceptions of the neurophysiology of bipolar disorder. Exploratory factor analysis was used to assess patterns of covariation among brain regions-of-interest activated during the Continuous Performance Task with Emotional and Neutral Distractors in healthy and bipolar individuals without a priori constraints on the number or composition of latent factors. Results indicated a common cognitive-emotional network consisting of prefrontal, medial temporal, limbic, parietal, anterior cingulate and posterior cingulate modules. However, reduced brain activation to emotional stimuli in the frontal, medial temporal and limbic modules was apparent in the bipolar relative to the healthy group, potentially accounting for emotional dysregulation in bipolar disorder. This study is limited by a relatively small sample size recruited at a single site. The results have yet to be validated on a larger independent sample. Although the modular structure of cognitive-emotional processing is similar in bipolar and healthy individuals, activation in response to emotional/neutral cues varies. These findings are not only consistent with recent conceptions of mood regulation in bipolar disorder, but also suggest that regional activation can be considered within tighter modular structures without compromising data interpretation. This demonstration may serve as a template for data reduction in future region-of-interest analyses to increase statistical power. Copyright © 2018 Elsevier B.V. All rights reserved.

Factor Structure of the Student-Teacher Relationship Scale for Norwegian School-Age Children Explored with Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Drugli, May Britt; Hjemdal, Odin

2013-01-01

The validity of the Student-Teacher Relationship Scale (STRS) was examined in a national sample of 863 Norwegian schoolchildren in grades 1-7 (aged 6-13). The original factor structure of the STRS was tested by confirmatory factor analysis (CFA). The CFA results did not support the original three-factor structure of the STRS. Subsequent CFA of the…

Factor Scores, Structure and Communality Coefficients: A Primer

ERIC Educational Resources Information Center

Odum, Mary

2011-01-01

(Purpose) The purpose of this paper is to present an easy-to-understand primer on three important concepts of factor analysis: Factor scores, structure coefficients, and communality coefficients. Given that statistical analyses are a part of a global general linear model (GLM), and utilize weights as an integral part of analyses (Thompson, 2006;…

Development, factor structure and application of the Dog Obesity Risk and Appetite (DORA) questionnaire

PubMed Central

Smith, Stephen P.; O’Rahilly, Stephen; Wardle, Jane

2015-01-01

Background. Dogs are compelling models in which to study obesity since the condition shares many characteristics between humans and dogs. Differences in eating behaviour are recognised to contribute to obesity susceptibility in other species but this has not been systematically studied in dogs. Aim. To develop and validate an owner-reported measure of canine eating behaviour and owner or dog related factors which can alter the development of obesity. Further, to then test variation in food-motivation in dogs and its association with obesity and owner management. Methods. Owner interviews, a literature review and existing human appetite scales were used to identify relevant topics and generate items for the questionnaire. Following a pilot phase, a 75 item online questionnaire was distributed via social media. Responses from 302 dog/owner dyads were analysed and factor structure and descriptive statistics calculated. Results were compared with descriptions of dog behaviour and management from a subset of respondents during semi-structured interviews. The optimum questions were disseminated as a 34 item final questionnaire completed by 213 owners, with a subset of respondents repeating the questionnaire 3 weeks later to assess test–retest reliability. Results. Analysis of responses to the final questionnaire relating to 213 dog/owner dyads showed a coherent factor structure and good test–retest reliability. There were three dog factors (food responsiveness and satiety, lack of selectivity, Interest in food), four owner factors (owner motivation to control dog weight, owner intervention to control dog weight, restriction of human food, exercise taken) and two dog health factors (signs of gastrointestinal disease, current poor health). Eating behaviour differed between individuals and between breed groups. High scores on dog factors (high food-motivation) and low scores on owner factors (less rigorous control of diet/exercise) were associated with obesity. Owners

Development, factor structure and application of the Dog Obesity Risk and Appetite (DORA) questionnaire.

PubMed

Raffan, Eleanor; Smith, Stephen P; O'Rahilly, Stephen; Wardle, Jane

2015-01-01

Background. Dogs are compelling models in which to study obesity since the condition shares many characteristics between humans and dogs. Differences in eating behaviour are recognised to contribute to obesity susceptibility in other species but this has not been systematically studied in dogs. Aim. To develop and validate an owner-reported measure of canine eating behaviour and owner or dog related factors which can alter the development of obesity. Further, to then test variation in food-motivation in dogs and its association with obesity and owner management. Methods. Owner interviews, a literature review and existing human appetite scales were used to identify relevant topics and generate items for the questionnaire. Following a pilot phase, a 75 item online questionnaire was distributed via social media. Responses from 302 dog/owner dyads were analysed and factor structure and descriptive statistics calculated. Results were compared with descriptions of dog behaviour and management from a subset of respondents during semi-structured interviews. The optimum questions were disseminated as a 34 item final questionnaire completed by 213 owners, with a subset of respondents repeating the questionnaire 3 weeks later to assess test-retest reliability. Results. Analysis of responses to the final questionnaire relating to 213 dog/owner dyads showed a coherent factor structure and good test-retest reliability. There were three dog factors (food responsiveness and satiety, lack of selectivity, Interest in food), four owner factors (owner motivation to control dog weight, owner intervention to control dog weight, restriction of human food, exercise taken) and two dog health factors (signs of gastrointestinal disease, current poor health). Eating behaviour differed between individuals and between breed groups. High scores on dog factors (high food-motivation) and low scores on owner factors (less rigorous control of diet/exercise) were associated with obesity. Owners of

Similar Students, Different Choices: Who Uses a School Voucher in an Otherwise Similar Population of Students?

ERIC Educational Resources Information Center

Fleming, David J.; Cowen, Joshua M.; Witte, John F.; Wolf, Patrick J.

2015-01-01

We examine what factors predict why some parents enroll their children in voucher schools while other parents with similar types of children and from similar neighborhoods do not. Furthermore, we investigate how aware parents are of their educational options, where they get their information, and what school characteristics they deem the most…

Additive-induced aggregate changes of two structurally similar dyes in aqueous solutions: A comparative photophysical study

NASA Astrophysics Data System (ADS)

Ghanadzadeh Gilani, A.; Poormohammadi-Ahandani, Z.; Kian, R.

2018-01-01

Absorption and emission spectral characteristics of the two structurally similar phenothiazine dyes, azure B and toluidine blue, in aqueous solutions of the two sets of molecular additives (ureas and monosaccharides) were studied as a function of the dye and additive concentrations. The absorption spectra of the dyes were also studied in pure tetramethylurea with an aprotic nature. The spectral data were analyzed using DECOM Program. The dimer structure of the interacting molecules in these dyes was discussed using the exciton model. The urea class of additives was found to act as water structure-breakers over the range of studied concentration. The carbohydrate additives were found to act as water structure-breakers at low concentrations. However, the water structure breaking process may be disfavored by the additive-additive interactions at higher concentrations. It can be concluded that at low additive concentrations, the main driving force for breaking the dye association is water-additive interaction, which disrupts the water hydrogen bonds induced by the additives. However, at the high additive concentrations, the different phenomena including additive-additive and additive-dye interactions can change the structure, strength, and aggregative properties of the dyes. Finally, the urea in water induces noticeably fluorescence quenching in emission spectra of both the dyes.

Additive-induced aggregate changes of two structurally similar dyes in aqueous solutions: A comparative photophysical study.

PubMed

Ghanadzadeh Gilani, A; Poormohammadi-Ahandani, Z; Kian, R

2018-01-15

Absorption and emission spectral characteristics of the two structurally similar phenothiazine dyes, azure B and toluidine blue, in aqueous solutions of the two sets of molecular additives (ureas and monosaccharides) were studied as a function of the dye and additive concentrations. The absorption spectra of the dyes were also studied in pure tetramethylurea with an aprotic nature. The spectral data were analyzed using DECOM Program. The dimer structure of the interacting molecules in these dyes was discussed using the exciton model. The urea class of additives was found to act as water structure-breakers over the range of studied concentration. The carbohydrate additives were found to act as water structure-breakers at low concentrations. However, the water structure breaking process may be disfavored by the additive-additive interactions at higher concentrations. It can be concluded that at low additive concentrations, the main driving force for breaking the dye association is water-additive interaction, which disrupts the water hydrogen bonds induced by the additives. However, at the high additive concentrations, the different phenomena including additive-additive and additive-dye interactions can change the structure, strength, and aggregative properties of the dyes. Finally, the urea in water induces noticeably fluorescence quenching in emission spectra of both the dyes. Copyright © 2017 Elsevier B.V. All rights reserved.

Factor structure of the geriatric care environment scale.

PubMed

Kim, Hongsoo; Capezuti, Elizabeth; Boltz, Marie; Fairchild, Susan; Fulmer, Terry; Mezey, Mathy

2007-01-01

Older adults comprise approximately 60% of all adult, nonobstetric hospital admissions. Nurses Improving Care for Health System Elders (NICHE) is a national program aimed at system improvement to achieve patient-centered care for older adults. The NICHE hospitals use the Geriatric Institutional Assessment Profile (GIAP) to assess their institutional readiness to provide quality care to older adults and to document improvement in geriatric care delivery. To explore the factorial structure of the 28-item Geriatric Care Environment Scale (GCES) of the GIAP, test its validity with a sample of staff registered nurses (RNs), and evaluate its invariance across 4 groups of RNs who worked at 4 different types of hospitals. Staff RNs (N = 9,400) at 71 acute hospitals, who responded to the GIAP from 1999 to 2004, were split randomly into 2 groups for cross-validation. A 3-step data analysis was completed. The a priori factor structure was developed using exploratory factor analysis. The obtained factor model was validated, and its invariance by types of hospitals was examined by confirmatory factor analyses. The GCES is internally consistent (Cronbach's alpha = .93) and accounts for approximately 55% of the total variance. The 4 factors extracted from the exploratory factor analysis are Aging-Sensitive Care Delivery, Resource Availability, Institutional Values Regarding Older Adults and Staff, and Capacity for Collaboration. The 4-factor structured model is validated in a half-randomly selected sample (normed fit index [NFI] = .931, nonnormed fit index [NNFI] = .933, comparative fit index [CFI] = .939, root-mean-square error of approximation [RMSEA] = .058) and does not vary significantly across the 4 groups of RNs who worked at the 4 different types of hospitals (NFI = .969, NNFI = .975, CFI = .976, RMSEA = .027). The GCES is a reliable measure of RN perception of how care provided to older adults reflects age-sensitive principles and the organizational practice environment

Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

PubMed

Ohtana, Yuki; Abdullah, Azian Azamimi; Altaf-Ul-Amin, Md; Huang, Ming; Ono, Naoaki; Sato, Tetsuo; Sugiura, Tadao; Horai, Hisayuki; Nakamura, Yukiko; Morita Hirai, Aki; Lange, Klaus W; Kibinge, Nelson K; Katsuragi, Tetsuo; Shirai, Tsuyoshi; Kanaya, Shigehiko

2014-12-01

Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4). Applying this method to a data set consisting of 2072 secondary metabolites and 140 biological activities reported in KNApSAcK Metabolite Activity DB, we obtained 983 statistically significant structure group-biological activity pairs. As a whole, we systematically analyzed the relationship between 3D-chemical structures of metabolites and biological activities. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Marital assortment for genetic similarity.

PubMed

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

2002-10-01

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

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

PubMed

Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

2013-01-01

Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor

Marking Student Programs Using Graph Similarity

ERIC Educational Resources Information Center

Naude, Kevin A.; Greyling, Jean H.; Vogts, Dieter

2010-01-01

We present a novel approach to the automated marking of student programming assignments. Our technique quantifies the structural similarity between unmarked student submissions and marked solutions, and is the basis by which we assign marks. This is accomplished through an efficient novel graph similarity measure ("AssignSim"). Our experiments…

Correlation of predicted and measured thermal stresses on an advanced aircraft structure with similar materials

NASA Technical Reports Server (NTRS)

Jenkins, J. M.

1979-01-01

A laboratory heating test simulating hypersonic heating was conducted on a heat-sink type structure to provide basic thermal stress measurements. Six NASTRAN models utilizing various combinations of bar, shear panel, membrane, and plate elements were used to develop calculated thermal stresses. Thermal stresses were also calculated using a beam model. For a given temperature distribution there was very little variation in NASTRAN calculated thermal stresses when element types were interchanged for a given grid system. Thermal stresses calculated for the beam model compared similarly to the values obtained for the NASTRAN models. Calculated thermal stresses compared generally well to laboratory measured thermal stresses. A discrepancy of signifiance occurred between the measured and predicted thermal stresses in the skin areas. A minor anomaly in the laboratory skin heating uniformity resulted in inadequate temperature input data for the structural models.

Psychometric properties and factor structure of the Fertility Problem Inventory in a sample of infertile women undergoing fertility treatment.

PubMed

Gourounti, K; Anagnostopoulos, F; Vaslamatzis, G

2011-10-01

to examine the psychometric properties of the Fertility Problem Inventory (FPI) originally developed by Newton et al. (1999); as there are no data concerning the factorial structure of the FPI, a special focus is placed on construct validity through factor analysis. public hospital in Athens, Greece. a cross-sectional study. 108 women undergoing fertility treatment with in-vitro fertilisation. the FPI was 'forward-backward' translated from English to Greek. The translated instrument was then administered to a set of infertile women for pilot testing. Principal axis factoring with promax rotation was used to test the factor structure of the FPI. Measures of anxiety State Trait Anxiety Inventory, depression (Center for Epidemiologic Studies--Depression Scale) and mood states Profile of Mood States were used to assess the convergent validity of the FPI. Cronbach's α was used to measure internal consistency of the FPI scales. exploratory factor analysis suggested four factors. The majority of relationship and sexual concern items grouped into one solid factor, named 'spousal concern'. The original scales of social concern, need for parenthood and rejection of childfree lifestyle were reproduced after rearranging nine cross-loading items. Construct validity was confirmed by computing correlations between the derived FPI scales and conceptually similar constructions of anxiety, depression and mood states. Internal consistency reliability was satisfactory. the FPI was found to have a relatively stable factor structure and satisfactory reliability, and convergent and discriminant validity. The FPI may enable researchers and clinicians to apply a reliable measure that focuses on various/many dimensions of infertility-related stress. Copyright © 2010 Elsevier Ltd. All rights reserved.

The Structure of Musical Preferences: A Five-Factor Model

PubMed Central

Rentfrow, Peter J.; Goldberg, Lewis R.; Levitin, Daniel J.

2011-01-01

Music is a cross-cultural universal, a ubiquitous activity found in every known human culture. Individuals demonstrate manifestly different preferences in music, and yet relatively little is known about the underlying structure of those preferences. Here, we introduce a model of musical preferences based on listeners’ affective reactions to excerpts of music from a wide variety of musical genres. The findings from three independent studies converged to suggest that there exists a latent five-factor structure underlying music preferences that is genre-free, and reflects primarily emotional/affective responses to music. We have interpreted and labeled these factors as: 1) a Mellow factor comprising smooth and relaxing styles; 2) an Urban factor defined largely by rhythmic and percussive music, such as is found in rap, funk, and acid jazz; 3) a Sophisticated factor that includes classical, operatic, world, and jazz; 4) an Intense factor defined by loud, forceful, and energetic music; and 5) a Campestral factor comprising a variety of different styles of direct, and rootsy music such as is often found in country and singer-songwriter genres. The findings from a fourth study suggest that preferences for the MUSIC factors are affected by both the social and auditory characteristics of the music. PMID:21299309

The structure of musical preferences: a five-factor model.

PubMed

Rentfrow, Peter J; Goldberg, Lewis R; Levitin, Daniel J

2011-06-01

Music is a cross-cultural universal, a ubiquitous activity found in every known human culture. Individuals demonstrate manifestly different preferences in music, and yet relatively little is known about the underlying structure of those preferences. Here, we introduce a model of musical preferences based on listeners' affective reactions to excerpts of music from a wide variety of musical genres. The findings from 3 independent studies converged to suggest that there exists a latent 5-factor structure underlying music preferences that is genre free and reflects primarily emotional/affective responses to music. We have interpreted and labeled these factors as (a) a Mellow factor comprising smooth and relaxing styles; (b) an Unpretentious factor comprising a variety of different styles of sincere and rootsy music such as is often found in country and singer-songwriter genres; (c) a Sophisticated factor that includes classical, operatic, world, and jazz; (d) an Intense factor defined by loud, forceful, and energetic music; and (e) a Contemporary factor defined largely by rhythmic and percussive music, such as is found in rap, funk, and acid jazz. The findings from a fourth study suggest that preferences for the MUSIC factors are affected by both the social and the auditory characteristics of the music. 2011 APA, all rights reserved

Self-similar assemblies of globular whey proteins at the air-water interface: effect of the structure.

PubMed

Mahmoudi, Najet; Gaillard, Cédric; Boué, François; Axelos, Monique A V; Riaublanc, Alain

2010-05-01

We investigated the structure of heat-induced assemblies of whey globular proteins using small angle neutron scattering (SANS), static and dynamic light scattering (SLS and DLS), and cryogenic transmission electron microscopy (Cryo-TEM). Whey protein molecules self-assemble in fractal aggregates with a structure density depending on the electrostatic interactions. We determined the static and dynamic properties of interfacial layer formed by the protein assemblies, upon adsorption and spreading at the air-water interface using surface film balance and interfacial dilatational rheology. Upon spreading, all whey protein systems show a power-law scaling behavior of the surface pressure versus concentration in the semi-dilute surface concentration regime, with an exponent ranging from 5.5 to 9 depending on the electrostatic interactions and the aggregation state. The dilatational modulus derived from surface pressure isotherms shows a main peak at 6-8 mN/m, generally considered to be the onset of a conformational change in the monolayer, and a second peak or a shoulder at 15 mN/m. Long-time adsorption kinetics give similar results for both the native whey proteins and the corresponding self-similar assemblies, with a systematic effect of the ionic strength. Copyright 2010 Elsevier Inc. All rights reserved.

Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations.

PubMed

Gorai, Biswajit; Prabhavadhni, Arasu; Sivaraman, Thirunavukkarasu

2015-09-01

Unfolding stabilities of two homologous proteins, cardiotoxin III and short-neurotoxin (SNTX) belonging to three-finger toxin (TFT) superfamily, have been probed by means of molecular dynamics (MD) simulations. Combined analysis of data obtained from steered MD and all-atom MD simulations at various temperatures in near physiological conditions on the proteins suggested that overall structural stabilities of the two proteins were different from each other and the MD results are consistent with experimental data of the proteins reported in the literature. Rationalization for the differential structural stabilities of the structurally similar proteins has been chiefly attributed to the differences in the structural contacts between C- and N-termini regions in their three-dimensional structures, and the findings endorse the 'CN network' hypothesis proposed to qualitatively analyse the thermodynamic stabilities of proteins belonging to TFT superfamily of snake venoms. Moreover, the 'CN network' hypothesis has been revisited and the present study suggested that 'CN network' should be accounted in terms of 'structural contacts' and 'structural strengths' in order to precisely describe order of structural stabilities of TFTs.

Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity.

PubMed

Findlay, S; Sinsabaugh, R L

2006-10-01

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.

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

PubMed

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.

Factor Structure of the Piagetian Stage of Concrete Operations.

ERIC Educational Resources Information Center

Klausmeier, Herbert J.; Sipple, Thomas S.

1982-01-01

The Piagetian developmental stage of concrete operational thought and the theoretical groupement structures underlying children's performance of 12 concrete operations tasks are discussed. Tasks were shown to develop in five related sets. Three factor structures were found in this longitudinal study. (Author/CM)

Brief Symptom Inventory Factor Structure in Antisocial Adolescents: Implications for Juvenile Justice

ERIC Educational Resources Information Center

Whitt, Ahmed; Howard, Matthew O.

2012-01-01

Objectives: The Brief Symptom Inventory (BSI) is widely used in juvenile justice settings; however, little is known regarding its factor structure in antisocial youth. The authors evaluated the BSI factor structure in a state residential treatment population. Methods: 707 adolescents completed the BSI. Exploratory and confirmatory factor analyses…

Structure and dynamics of zymogen human blood coagulation factor X.

PubMed

Venkateswarlu, Divi; Perera, Lalith; Darden, Tom; Pedersen, Lee G

2002-03-01

The solution structure and dynamics of the human coagulation factor X (FX) have been investigated to understand the key structural elements in the zymogenic form that participates in the activation process. The model was constructed based on the 2.3-A-resolution x-ray crystallographic structure of active-site inhibited human FXa (PDB:1XKA). The missing gamma-carboxyglutamic acid (GLA) and part of epidermal growth factor 1 (EGF1) domains of the light chain were modeled based on the template of GLA-EGF1 domains of the tissue factor (TF)-bound FVIIa structure (PDB:1DAN). The activation peptide and other missing segments of FX were introduced using homology modeling. The full calcium-bound model of FX was subjected to 6.2 ns of molecular dynamics simulation in aqueous medium using the AMBER6.0 package. We observed significant reorientation of the serine-protease (SP) domain upon activation leading to a compact multi-domain structure. The solution structure of zymogen appears to be in a well-extended conformation with the distance between the calcium ions in the GLA domain and the catalytic residues estimated to be approximately 95 A in contrast to approximately 83 A in the activated form. The latter is in close agreement with fluorescence studies on FXa. The S1-specificity residues near the catalytic triad show significant differences between the zymogen and activated structures.

Phonological Similarity in American Sign Language.

ERIC Educational Resources Information Center

Hildebrandt, Ursula; Corina, David

2002-01-01

Investigates deaf and hearing subjects' ratings of American Sign Language (ASL) signs to assess whether linguistic experience shapes judgments of sign similarity. Findings are consistent with linguistic theories that posit movement and location as core structural elements of syllable structure in ASL. (Author/VWL)

Personality traits across countries: Support for similarities rather than differences

PubMed Central

Mac Giolla, Erik

2017-01-01

In the current climate of migration and globalization, personality characteristics of individuals from different countries have received a growing interest. Previous research has established reliable differences in personality traits across countries. The present study extends this research by examining 30 personality traits in 22 countries, based on an online survey in English with large national samples (NTotal = 130,602). The instrument used was a comprehensive, open-source measure of the Five Factor Model (FFM) (IPIP-NEO-120). We postulated that differences in personality traits between countries would be small, labeling this a Similarities Hypothesis. We found support for this in three stages. First, similarities across countries were observed for model fits for each of the five personality trait structures. Second, within-country sex differences for the five personality traits showed similar patterns across countries. Finally, the overall the contribution to personality traits from countries was less than 2%. In other words, the relationship between a country and an individual’s personality traits, however interesting, are small. We conclude that the most parsimonious explanation for the current and past findings is a cross-country personality Similarities Hypothesis. PMID:28622380

Personality traits across countries: Support for similarities rather than differences.

PubMed

Kajonius, Petri; Mac Giolla, Erik

2017-01-01

In the current climate of migration and globalization, personality characteristics of individuals from different countries have received a growing interest. Previous research has established reliable differences in personality traits across countries. The present study extends this research by examining 30 personality traits in 22 countries, based on an online survey in English with large national samples (NTotal = 130,602). The instrument used was a comprehensive, open-source measure of the Five Factor Model (FFM) (IPIP-NEO-120). We postulated that differences in personality traits between countries would be small, labeling this a Similarities Hypothesis. We found support for this in three stages. First, similarities across countries were observed for model fits for each of the five personality trait structures. Second, within-country sex differences for the five personality traits showed similar patterns across countries. Finally, the overall the contribution to personality traits from countries was less than 2%. In other words, the relationship between a country and an individual's personality traits, however interesting, are small. We conclude that the most parsimonious explanation for the current and past findings is a cross-country personality Similarities Hypothesis.

Factor Structure of ImPACT® in Adolescent Student Athletes.

PubMed

Gerrard, Paul B; Iverson, Grant L; Atkins, Joseph E; Maxwell, Bruce A; Zafonte, Ross; Schatz, Philip; Berkner, Paul D

2017-02-01

ImPACT ® (Immediate Post-Concussion Assessment and Cognitive Testing) is a computerized neuropsychological screening battery, which is widely used to measure the acute effects of sport-related concussion and to monitor recovery from injury. This study examined the factor structure of ImPACT ® in several samples of high school student athletes. We hypothesized that a 2-factor structure would be present in all samples. A sample of 4,809 adolescent student athletes was included, and subgroups with a history of treatment for headaches or a self-reported history of learning problems or attention-deficit hyperactivity disorder were analyzed separately. Exploratory principal axis factor analyses with Promax rotations were used. As hypothesized, both the combination of Verbal Memory and Visual Memory Composite scores loaded on one (Memory) factor, while Visual Motor Speed and Reaction Time loaded on a different (Speed) factor, in the total sample and in all subgroups. These results provide reasonably compelling evidence, across multiple samples, which ImPACT ® measures 2 distinct factors: memory and speed. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Scalar Similarity for Relaxed Eddy Accumulation Methods

NASA Astrophysics Data System (ADS)

Ruppert, Johannes; Thomas, Christoph; Foken, Thomas

2006-07-01

The relaxed eddy accumulation (REA) method allows the measurement of trace gas fluxes when no fast sensors are available for eddy covariance measurements. The flux parameterisation used in REA is based on the assumption of scalar similarity, i.e., similarity of the turbulent exchange of two scalar quantities. In this study changes in scalar similarity between carbon dioxide, sonic temperature and water vapour were assessed using scalar correlation coefficients and spectral analysis. The influence on REA measurements was assessed by simulation. The evaluation is based on observations over grassland, irrigated cotton plantation and spruce forest. Scalar similarity between carbon dioxide, sonic temperature and water vapour showed a distinct diurnal pattern and change within the day. Poor scalar similarity was found to be linked to dissimilarities in the energy contained in the low frequency part of the turbulent spectra ( < 0.01 Hz). The simulations of REA showed significant change in b-factors throughout the diurnal course. The b-factor is part of the REA parameterisation scheme and describes a relation between the concentration difference and the vertical flux of a trace gas. The diurnal course of b-factors for carbon dioxide, sonic temperature and water vapour matched well. Relative flux errors induced in REA by varying scalar similarity were generally below ± 10%. Systematic underestimation of the flux of up to - 40% was found for the use of REA applying a hyperbolic deadband (HREA). This underestimation was related to poor scalar similarity between the scalar of interest and the scalar used as proxy for the deadband definition.

Structure of Plasmodium falciparum ADP-ribosylation factor 1

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

Cook, William J.; Smith, Craig D.; Senkovich, Olga

Vesicular trafficking may play a crucial role in the pathogenesis and survival of the malaria parasite. ADP-ribosylation factors (ARFs) are among the major components of vesicular trafficking pathways in eukaryotes. The crystal structure of ARF1 GTPase from Plasmodium falciparum has been determined in the GDP-bound conformation at 2.5 {angstrom} resolution and is compared with the structures of mammalian ARF1s.

The Factor Structure of Effortful Control and Measurement Invariance Across Ethnicity and Sex in a High-Risk Sample

PubMed Central

Huerta, Snjezana; Zerr, Argero A.; Eisenberg, Nancy; Spinrad, Tracy L.; Valiente, Carlos; Di Giunta, Laura; Pina, Armando A.; Eggum, Natalie D.; Sallquist, Julie; Edwards, Alison; Kupfer, Anne; Lonigan, Christopher J.; Phillips, Beth M.; Wilson, Shauna B.; Clancy-Menchetti, Jeanine; Landry, Susan H.; Swank, Paul R.; Assel, Michael A.; Taylor, Heather B.

2010-01-01

Measurement invariance of a one-factor model of effortful control (EC) was tested for 853 low-income preschoolers (M age = 4.48 years). Using a teacher-report questionnaire and seven behavioral measures, configural invariance (same factor structure across groups), metric invariance (same pattern of factor loadings across groups), and partial scalar invariance (mostly the same intercepts across groups) were established across ethnicity (European Americans, African Americans and Hispanics) and across sex. These results suggest that the latent construct of EC behaved in a similar way across ethnic groups and sex, and that comparisons of mean levels of EC are valid across sex and probably valid across ethnicity, especially when larger numbers of tasks are used. The findings also support the use of diverse behavioral measures as indicators of a single latent EC construct. PMID:20593008

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

PubMed

Vaguine, A A; Richelle, J; Wodak, S J

1999-01-01

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Scoring of Side-Chain Packings: An Analysis of Weight Factors and Molecular Dynamics Structures.

PubMed

Colbes, Jose; Aguila, Sergio A; Brizuela, Carlos A

2018-02-26

The protein side-chain packing problem (PSCPP) is a central task in computational protein design. The problem is usually modeled as a combinatorial optimization problem, which consists of searching for a set of rotamers, from a given rotamer library, that minimizes a scoring function (SF). The SF is a weighted sum of terms, that can be decomposed in physics-based and knowledge-based terms. Although there are many methods to obtain approximate solutions for this problem, all of them have similar performances and there has not been a significant improvement in recent years. Studies on protein structure prediction and protein design revealed the limitations of current SFs to achieve further improvements for these two problems. In the same line, a recent work reported a similar result for the PSCPP. In this work, we ask whether or not this negative result regarding further improvements in performance is due to (i) an incorrect weighting of the SFs terms or (ii) the constrained conformation resulting from the protein crystallization process. To analyze these questions, we (i) model the PSCPP as a bi-objective combinatorial optimization problem, optimizing, at the same time, the two most important terms of two SFs of state-of-the-art algorithms and (ii) performed a preprocessing relaxation of the crystal structure through molecular dynamics to simulate the protein in the solvent and evaluated the performance of these two state-of-the-art SFs under these conditions. Our results indicate that (i) no matter what combination of weight factors we use the current SFs will not lead to better performances and (ii) the evaluated SFs will not be able to improve performance on relaxed structures. Furthermore, the experiments revealed that the SFs and the methods are biased toward crystallized structures.

A plasma membrane sucrose-binding protein that mediates sucrose uptake shares structural and sequence similarity with seed storage proteins but remains functionally distinct.

PubMed

Overvoorde, P J; Chao, W S; Grimes, H D

1997-06-20

Photoaffinity labeling of a soybean cotyledon membrane fraction identified a sucrose-binding protein (SBP). Subsequent studies have shown that the SBP is a unique plasma membrane protein that mediates the linear uptake of sucrose in the presence of up to 30 mM external sucrose when ectopically expressed in yeast. Analysis of the SBP-deduced amino acid sequence indicates it lacks sequence similarity with other known transport proteins. Data presented here, however, indicate that the SBP shares significant sequence and structural homology with the vicilin-like seed storage proteins that organize into homotrimers. These similarities include a repeated sequence that forms the basis of the reiterated domain structure characteristic of the vicilin-like protein family. In addition, analytical ultracentrifugation and nonreducing SDS-polyacrylamide gel electrophoresis demonstrate that the SBP appears to be organized into oligomeric complexes with a Mr indicative of the existence of SBP homotrimers and homodimers. The structural similarity shared by the SBP and vicilin-like proteins provides a novel framework to explore the mechanistic basis of SBP-mediated sucrose uptake. Expression of the maize Glb protein (a vicilin-like protein closely related to the SBP) in yeast demonstrates that a closely related vicilin-like protein is unable to mediate sucrose uptake. Thus, despite sequence and structural similarities shared by the SBP and the vicilin-like protein family, the SBP is functionally divergent from other members of this group.

Peplau's Theory of Interpersonal Relations: An Alternate Factor Structure for Patient Experience Data?

PubMed

Hagerty, Thomas A; Samuels, William; Norcini-Pala, Andrea; Gigliotti, Eileen

2017-04-01

A confirmatory factor analysis of data from the responses of 12,436 patients to 16 items on the Consumer Assessment of Healthcare Providers and Systems-Hospital survey was used to test a latent factor structure based on Peplau's middle-range theory of interpersonal relations. A two-factor model based on Peplau's theory fit these data well, whereas a three-factor model also based on Peplau's theory fit them excellently and provided a suitable alternate factor structure for the data. Though neither the two- nor three-factor model fit as well as the original factor structure, these results support using Peplau's theory to demonstrate nursing's extensive contribution to the experiences of hospitalized patients.

Structural similarities in tetraaryltins described by virtual non-crystallographic rotations or translations: Kitaigorodskii's morphotropism is revisited.

PubMed

Kálmán, Alajos; Fábián, László

2007-06-01

Recently Kálmán [(2005), Acta Cryst. B61, 536-547] revealed that semirigid molecules or their patterns held together e.g. by hydrogen bonds may perform non-crystallographic rotations (through 180, 90 degrees etc.) around themselves whenever a substitution, ring enlargement or isomerization destroys the existing close packing, i.e. the novel substituent or the enlarged ring can no longer fit in the hollows formed between the molecules. In other words, the old and new arrangements of such chemically similar molecules can be converted into each other by virtual rotations. However, when a semirigid molecule without substitution, but under the influence of solvents, temperature etc., is fully or partly rearranged in the solid state, the corresponding non-crystallographic rotation (hereinafter ncr) is real and gives rise to polymorphism. Such polymorphs are hallmarked by full or partial isostructurality and show that ncrs always occur together with isostructurality. First Kitaigorodskii [(1961), Organic Chemical Crystallography, New York: Consultants Bureau] reported on the structural similarity of three tetraaryltins, (p-RC(6)H(4))(4)Sn, R = H, CH(3), CH(3)O, which is terminated by the larger C(2)H(5)O group. A revisit to these structures revealed that the tetragonal --> monoclinic conversion termed by Kitaigorodskii as a ;morphotropic step' is also performed by an ncr. Similarly, other tetraaryltins in the literature are related by ncrs or the nc translation of the semirigid tetrahedra, or they remain isostructural. Since one of the definitions of morphotropism, a word of Greek origin, is 'turn of form', the ncrs of semirigid molecules can be denoted--following Kitaigorodskii--by this word, whereas its alternative definition in the morphological crystallography of ;unidirectional changes' [applied by Groth (1870). Ber. Chem. Ges. 3, 449-457] covers the non-crystallographic translations described first in this work.

Exploring the factor structure of the Food Cravings Questionnaire-Trait in Cuban adults

PubMed Central

Rodríguez-Martín, Boris C.; Molerio-Pérez, Osana

2014-01-01

Food cravings refer to an intense desire to eat specific foods. The Food Cravings Questionnaire-Trait (FCQ-T) is the most commonly used instrument to assess food cravings as a multidimensional construct. Its 39 items have an underlying nine-factor structure for both the original English and Spanish version; but subsequent studies yielded fewer factors. As a result, a 15-item version of the FCQ-T with one-factor structure has been proposed (FCQ-T-reduced; see this Research Topic). The current study aimed to explore the factor structure of the Spanish version for both the FCQ-T and FCQ-T-reduced in a sample of 1241 Cuban adults. Results showed a four-factor structure for the FCQ-T, which explained 55% of the variance. Factors were highly correlated. Using the items of the FCQ-T-reduced only showed a one-factor structure, which explained 52% of the variance. Both versions of the FCQ-T were positively correlated with body mass index (BMI), scores on the Food Thoughts Suppression Inventory and weight cycling. In addition, women had higher scores than men and restrained eaters had higher scores than unrestrained eaters. To summarize, results showed that (1) the FCQ-T factor structure was significantly reduced in Cuban adults and (2) the FCQ-T-reduced may represent a good alternative to efficiently assess food craving on a trait level. PMID:24672503

Factor Structure, Internal Consistency, and Screening Sensitivity of the GARS-2 in a Developmental Disabilities Sample

PubMed Central

Volker, Martin A.; Dua, Elissa H.; Lopata, Christopher; Thomeer, Marcus L.; Toomey, Jennifer A.; Smerbeck, Audrey M.; Rodgers, Jonathan D.; Popkin, Joshua R.; Nelson, Andrew T.; Lee, Gloria K.

2016-01-01

The Gilliam Autism Rating Scale-Second Edition (GARS-2) is a widely used screening instrument that assists in the identification and diagnosis of autism. The purpose of this study was to examine the factor structure, internal consistency, and screening sensitivity of the GARS-2 using ratings from special education teaching staff for a sample of 240 individuals with autism or other significant developmental disabilities. Exploratory factor analysis yielded a correlated three-factor solution similar to that found in 2005 by Lecavalier for the original GARS. Though the three factors appeared to be reasonably consistent with the intended constructs of the three GARS-2 subscales, the analysis indicated that more than a third of the GARS-2 items were assigned to the wrong subscale. Internal consistency estimates met or exceeded standards for screening and were generally higher than those in previous studies. Screening sensitivity was .65 and specificity was .81 for the Autism Index using a cut score of 85. Based on these findings, recommendations are made for instrument revision. PMID:26981279

Clustering biomolecular complexes by residue contacts similarity.

PubMed

Rodrigues, João P G L M; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J

2012-07-01

Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions. Albeit widely used, these measures suffer from several theoretical and technical limitations (e.g., choice of regions for fitting) that impair their application in multicomponent systems (N > 2), large-scale studies (e.g., interactomes), and other time-critical scenarios. We present here a simple similarity measure for structural clustering based on atomic contacts--the fraction of common contacts--and compare it with the most used similarity measure of the protein docking community--interface backbone RMSD. We show that this method produces very compact clusters in remarkably short time when applied to a collection of binary and multicomponent protein-protein and protein-DNA complexes. Furthermore, it allows easy clustering of similar conformations of multicomponent symmetrical assemblies in which chain permutations can occur. Simple contact-based metrics should be applicable to other structural biology clustering problems, in particular for time-critical or large-scale endeavors. Copyright © 2012 Wiley Periodicals, Inc.

Molecular characterization and in situ mRNA localization of the neural recognition molecule J1-160/180: a modular structure similar to tenascin

PubMed Central

1993-01-01

The oligodendrocyte-derived extracellular matrix glycoprotein J1- 160/180 is a recognition molecule expressed exclusively in the central nervous system. J1-160/180 has been shown to be adhesive for astrocytes and repellent towards neurons and growth cones. We report here the complete nucleotide sequence of J1-160/180 in the rat. The predicted amino acid sequence showed a structural architecture very similar to tenascin: a cysteine-rich amino terminal region is followed by 4.5 epidermal growth factor-like repeats, 9 fibronectin type III homologous repeats and a domain homologous to fibrinogen. Sequence comparison analysis revealed highest homology of rat J1-160/180 to mouse tenascin and chicken restrictin with a similarity of 66% and 85%, respectively. The J1-160/180-coding mRNA is derived from a single copy gene. Using the polymerase chain reaction we could show that two J1-160/180 isoforms are generated by alternative splicing of the sixth fibronectin type III homologous repeat. Localization of J1-160/180 mRNA by in situ hybridization in the cerebellum, hippocampus and olfactory bulb confirmed the expression of J1-160/180 by oligodendrocytes with a peak of transcription at 7-14 d after birth, indicating a functional role during myelination. In addition, J1-160/180-specific RNA was found in a small subset of neurons in all three structures of the CNS analyzed. These neurons continue to express J1-160/180 in the adult. PMID:7679676

Factor Structure and Psychometric Properties of the Injection Phobia Scale-Anxiety

ERIC Educational Resources Information Center

Olatunji, Bunmi O.; Sawchuk, Craig N.; Moretz, Melanie W.; David, Bieke; Armstrong, Thomas; Ciesielski, Bethany G.

2010-01-01

The present investigation examined the factor structure and psychometric properties of the Injection Phobia Scale-Anxiety (IPS-Anx). Principal components analysis of IPS-Anx items in Study 1 (n = 498) revealed a 2-factor structure consisting of Distal Fear and Contact Fear. However, CFA results in Study 2 (n = 567) suggest that a 1-factor…

The factor structure of the Alcohol Use Disorders Identification Test (AUDIT).

PubMed

Doyle, Suzanne R; Donovan, Dennis M; Kivlahan, Daniel R

2007-05-01

Past research assessing the factor structure of the Alcohol Use Disorders Identification Test (AUDIT) with various exploratory and confirmatory factor analytic techniques has identified one-, two-, and three-factor solutions. Because different factor analytic procedures may result in dissimilar findings, we examined the factor structure of the AUDIT using the same factor analytic technique on two new large clinical samples and on archival data from six samples studied in previous reports. Responses to the AUDIT were obtained from participants who met Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), criteria for alcohol dependence in two large randomized clinical trials: the COMBINE (Combining Medications and Behavioral Interventions) Study (N = 1,337; 69% men) and Project MATCH (Matching Alcoholism Treatments to Client Heterogeneity; N = 1,711; 76% men). Supplementary analyses involved six correlation matrices of AUDIT data obtained from five previously published articles. Confirmatory factor analyses based on one-, two-, and three-factor models were conducted on the eight correlation matrices to assess the factor structure of the AUDIT. Across samples, analyses supported a correlated, two-factor solution representing alcohol consumption and alcohol-related consequences. The three-factor solution fit the data equally well, but two factors (alcohol dependence and harmful alcohol use) were highly correlated. The one-factor solution did not provide a good fit to the data. These findings support a two-factor solution for the AUDIT (alcohol consumption and alcohol-related consequences). The results contradict the original three-factor design of the AUDIT and the prevalent use of the AUDIT as a one-factor screening instrument with a single cutoff score.

Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

PubMed

Ray, Sumanta; Maulik, Ujjwal

2016-12-20

Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

Investigating Pharmacological Similarity by Charting Chemical Space.

PubMed

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

2015-11-23

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

Identification challenges for large space structures

NASA Technical Reports Server (NTRS)

Pappa, Richard S.

1990-01-01

The paper examines the on-orbit modal identification of large space structures, stressing the importance of planning and experience, in preparation for the Space Station Structural Characterization Experiment (SSSCE) for the Space Station Freedom. The necessary information to foresee and overcome practical difficulties is considered in connection with seven key factors, including test objectives, dynamic complexity of the structure, data quality, extent of exploratory studies, availability and understanding of software tools, experience with similar problems, and pretest analytical conditions. These factors affect identification success in ground tests. Comparisons with similar ground tests of assembled systems are discussed, showing that the constraints of space tests make these factors more significant. The absence of data and experiences relating to on-orbit modal identification testing is shown to make identification a uniquely mathematical problem, although all spacecraft are constructed and verified by proven engineering methods.

Factor structure and validation of the Attentional Control Scale.

PubMed

Judah, Matt R; Grant, DeMond M; Mills, Adam C; Lechner, William V

2014-04-01

The Attentional Control Scale (ACS; Derryberry & Reed, 2002) has been used to assess executive control over attention in numerous studies, but no published data have examined the factor structure of the English version. The current studies addressed this need and tested the predictive and convergent validity of the ACS subscales. In Study 1, exploratory factor analysis yielded a two-factor model with Focusing and Shifting subscales. In Study 2, confirmatory factor analysis supported this model and suggested superior fit compared to the factor structure of the Icelandic version (Ólafsson et al., 2011). Study 3 examined correlations between the ACS subscales and measures of working memory, anxiety, and cognitive control. Study 4 examined correlations between the subscales and reaction times on a mixed-antisaccade task, revealing positive correlations for antisaccade performance and prosaccade latency with Focusing scores and between switch trial performance and Shifting scores. Additionally, the findings partially supported unique relationships between Focusing and trait anxiety and between Shifting and depression that have been noted in recent research. Although the results generally support the validity of the ACS, additional research using performance-based tasks is needed.

The influence of phylogeny, social style, and sociodemographic factors on macaque social network structure.

PubMed

Balasubramaniam, Krishna N; Beisner, Brianne A; Berman, Carol M; De Marco, Arianna; Duboscq, Julie; Koirala, Sabina; Majolo, Bonaventura; MacIntosh, Andrew J; McFarland, Richard; Molesti, Sandra; Ogawa, Hideshi; Petit, Odile; Schino, Gabriele; Sosa, Sebastian; Sueur, Cédric; Thierry, Bernard; de Waal, Frans B M; McCowan, Brenda

2018-01-01

Among nonhuman primates, the evolutionary underpinnings of variation in social structure remain debated, with both ancestral relationships and adaptation to current conditions hypothesized to play determining roles. Here we assess whether interspecific variation in higher-order aspects of female macaque (genus: Macaca) dominance and grooming social structure show phylogenetic signals, that is, greater similarity among more closely-related species. We use a social network approach to describe higher-order characteristics of social structure, based on both direct interactions and secondary pathways that connect group members. We also ask whether network traits covary with each other, with species-typical social style grades, and/or with sociodemographic characteristics, specifically group size, sex-ratio, and current living condition (captive vs. free-living). We assembled 34-38 datasets of female-female dyadic aggression and allogrooming among captive and free-living macaques representing 10 species. We calculated dominance (transitivity, certainty), and grooming (centrality coefficient, Newman's modularity, clustering coefficient) network traits as aspects of social structure. Computations of K statistics and randomization tests on multiple phylogenies revealed moderate-strong phylogenetic signals in dominance traits, but moderate-weak signals in grooming traits. GLMMs showed that grooming traits did not covary with dominance traits and/or social style grade. Rather, modularity and clustering coefficient, but not centrality coefficient, were strongly predicted by group size and current living condition. Specifically, larger groups showed more modular networks with sparsely-connected clusters than smaller groups. Further, this effect was independent of variation in living condition, and/or sampling effort. In summary, our results reveal that female dominance networks were more phylogenetically conserved across macaque species than grooming networks, which were more

The factor structure of the illness attitude scales in a German population.

PubMed

Weck, Florian; Bleichhardt, Gaby; Hiller, Wolfgang

2009-01-01

The illness attitudes scales (IAS) were developed to identify different dimensions of hypochondrical attitudes, fears, beliefs, and abnormal illness behavior (Kellner 1986). Although there are several studies which focus on the scale structure of the IAS, the factor structure has not yet been made quite clear. Therefore, the aim of this study was to investigate the factor structure of the IAS on a large representative sample. Participants (N = 1,575) comparable with the general German population regarding sex, age, and education level completed the IAS. For the data analyses, a principal components analyses with subsequent oblique rotations was used. The minimum average partial method suggested a three-factor solution. The three factors were named (1) health anxiety, (2) health behavior, and (3) health habits. Internal consistency (Cronbach's alpha) for the three scales were (1) alpha = 0.88, (2) alpha = 0.75, and (3) alpha = 0.56. The results support previous findings, namely that the IAS factor structure appears to be less complex than originally suggested by the author. For a sample of the general German population, a three-factor solution fit best. Further items should be added to improve the internal consistency, especially for the third scale (health habits).

On a fast calculation of structure factors at a subatomic resolution.

PubMed

Afonine, P V; Urzhumtsev, A

2004-01-01

In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9 A. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high-quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for 'small-molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re-examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst. 4, 362-367; Ten Eyck (1977). Acta Cryst. A33, 486-492] may be much more computationally efficient, but contains some parameters (grid step, 'effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct-formulae calculations. The impact of the different parameters on the computer efficiency of structure-factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required

Three-factor structure for Epistemic Belief Inventory: A cross-validation study

PubMed Central

2017-01-01

Research on epistemic beliefs has been hampered by lack of validated models and measurement instruments. The most widely used instrument is the Epistemological Questionnaire, which has been criticized for validity, and it has been proposed a new instrument based in the Epistemological Questionnaire: the Epistemic Belief Inventory. The Spanish-language version of Epistemic Belief Inventory was applied to 1,785 Chilean high school students. Exploratory and confirmatory factor analyses in independent subsamples were performed. A three factor structure emerged and was confirmed. Reliability was comparable to other studies, and the factor structure was invariant among randomized subsamples. The structure that was found does not replicate the one proposed originally, but results are interpreted in light of embedded systemic model of epistemological beliefs. PMID:28278258

The Sla2p/HIP1/HIP1R family: similar structure, similar function in endocytosis?

PubMed

Gottfried, Irit; Ehrlich, Marcelo; Ashery, Uri

2010-02-01

HIP1 (huntingtin interacting protein 1) has two close relatives: HIP1R (HIP1-related) and yeast Sla2p. All three members of the family have a conserved domain structure, suggesting a common function. Over the past decade, a number of studies have characterized these proteins using a combination of biochemical, imaging, structural and genetic techniques. These studies provide valuable information on binding partners, structure and dynamics of HIP1/HIP1R/Sla2p. In general, all suggest a role in CME (clathrin-mediated endocytosis) for the three proteins, though some differences have emerged. In this mini-review we summarize the current views on the roles of these proteins, while emphasizing the unique attributes of each family member.

Hardware-Based Non-Optimum Factors for Launch Vehicle Structural Design

NASA Technical Reports Server (NTRS)

Wu, K. Chauncey; Cerro, Jeffrey A.

2010-01-01

During aerospace vehicle conceptual and preliminary design, empirical non-optimum factors are typically applied to predicted structural component weights to account for undefined manufacturing and design details. Non-optimum factors are developed here for 32 aluminum-lithium 2195 orthogrid panels comprising the liquid hydrogen tank barrel of the Space Shuttle External Tank using measured panel weights and manufacturing drawings. Minimum values for skin thickness, axial and circumferential blade stiffener thickness and spacing, and overall panel thickness are used to estimate individual panel weights. Panel non-optimum factors computed using a coarse weights model range from 1.21 to 1.77, and a refined weights model (including weld lands and skin and stiffener transition details) yields non-optimum factors of between 1.02 and 1.54. Acreage panels have an average 1.24 non-optimum factor using the coarse model, and 1.03 with the refined version. The observed consistency of these acreage non-optimum factors suggests that relatively simple models can be used to accurately predict large structural component weights for future launch vehicles.

STRUCTURAL AND FUNCTIONAL BASES OF CARDIAC FIBRILLATION. DIFFERENCES AND SIMILARITIES BETWEEN ATRIA AND VENTRICLES

PubMed Central

Filgueiras-Rama, David; Jalife, José

2016-01-01

Evidence accumulated over the last 25 years suggests that, whether in the atria or ventricles, fibrillation may be explained by the self-organization of the cardiac electrical activity into rapidly spinning rotors giving way to spiral waves that break intermittently and result in fibrillatory conduction. The dynamics and frequency of such rotors depend on the ion channel composition, excitability and refractory properties of the tissues involved, as well as on the thickness and respective three-dimensional fiber structure of the atrial and ventricular chambers. Therefore, improving the understanding of fibrillation has required the use of multidisciplinary research approaches, including optical mapping, patch clamping and molecular biology, and the application of concepts derived from the theory of wave propagation in excitable media. Moreover, translation of such concepts to the clinic has recently opened new opportunities to apply novel mechanistic approaches to therapy, particularly during atrial fibrillation ablation. Here we review the current understanding of the manner in which the underlying myocardial structure and function influence rotor initiation and maintenance during cardiac fibrillation. We also examine relevant underlying differences and similarities between atrial fibrillation and ventricular fibrillation and evaluate the latest clinical mapping technologies used to identify rotors in either arrhythmia. Altogether, the data being discussed have significantly improved our understanding of the cellular and structural bases of cardiac fibrillation and pointed toward potentially exciting new avenues for more efficient and effective identification and therapy of the most complex cardiac arrhythmias. PMID:27042693

Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia

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

Buchko, Garry W.; Abendroth, Jan; Robinson, Howard

2013-06-15

Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with twomore » anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two “gate-keeper” residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y==>R) and 100 (V==>D) and for Gl-MIF it is at position 100 (V==>R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins.« less

26 CFR 157.5891-1 - Imposition of excise tax on structured settlement factoring transactions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... settlement factoring transactions. 157.5891-1 Section 157.5891-1 Internal Revenue INTERNAL REVENUE SERVICE... SETTLEMENT FACTORING TRANSACTIONS Tax on Structured Settlement Factoring Transactions § 157.5891-1 Imposition of excise tax on structured settlement factoring transactions. (a) In general. Section 5891 imposes...

A guide to structural factors for advanced composites used on spacecraft

NASA Technical Reports Server (NTRS)

Vanwagenen, Robert

1989-01-01

The use of composite materials in spacecraft systems is constantly increasing. Although the areas of composite design and fabrication are maturing, they remain distinct from the same activities performed using conventional materials and processes. This has led to some confusion regarding the precise meaning of the term 'factor of safety' as it applies to these structures. In addition, composite engineering introduces terms such as 'knock-down factors' to further modify material properties for design purposes. This guide is intended to clarify these terms as well as their use in the design of composite structures for spacecraft. It is particularly intended to be used by the engineering community not involved in the day-to-day composites design process. An attempt is also made to explain the wide range of factors of safety encountered in composite designs as well as their relationship to the 1.4 factor of safety conventionally applied to metallic structures.

Similarities and differences in borderline and organic personality disorder.

PubMed

Mathiesen, Birgit B; Simonsen, Erik; Soegaard, Ulf; Kvist, Kajsa

2014-01-01

Previous research has shown that brain injury patients with Organic Personality Disorder (OPD) may display "borderline" traits due to prefrontal damage, and their personality structure may be unstable and close to a borderline personality organisation. They may have few general neuropsychological dysfunctions but specific executive deficits. Similar deficits have been found in patients with Borderline Personality Disorder (BPD). The objective of this study was to identify differences and similarities between the neuropsychological and personality profiles of BPD and OPD patients. Twenty BPD patients and 24 OPD patients were assessed with the Structured Clinical Interview for DSM-IV Axis II Disorders (SCID-II), the Karolinska Psychodynamic Profile (KAPP), and a comprehensive neuropsychological test battery. Very few neuropsychological differences were found between the two patient groups. However, the verbal fluency, verbal intelligence, verbal memory, and immediate auditory memory/attention of the BPD patients were significantly poorer than the OPD patients'. The KAPP profiles of the BPD patients showed significantly poorer functioning in three areas: frustration tolerance, the body as a factor of self-esteem, and overall personality organisation. These results support our clinical experience and expectations concerning the severity of symptoms of both patient groups. We suggest considering in depth assessments of both neuropsychological and personality-related problems for each of these patients in order to inform treatment.

Relations between structural and dynamic thermal characteristics of building walls

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

Kossecka, E.; Kosny, J.

1996-10-01

The effect of internal thermal structure on dynamic characteristics of walls is analyzed. The concept of structure factors is introduced and the conditions they impose on response factors are given. Simple examples of multilayer walls, representing different types of thermal resistance and capacity distribution, are analyzed to illustrate general relations between structure factors and response factors. The idea of the ``thermally equivalent wall``, a plane multilayer structure, with dynamic characteristics similar to those of a complex structure, in which three-dimensional heat flow occurs, is presented.

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

PubMed

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

A New Approach to Diagnose Parkinson's Disease Using a Structural Cooccurrence Matrix for a Similarity Analysis.

PubMed

de Souza, João W M; Alves, Shara S A; Rebouças, Elizângela de S; Almeida, Jefferson S; Rebouças Filho, Pedro P

2018-01-01

Parkinson's disease affects millions of people around the world and consequently various approaches have emerged to help diagnose this disease, among which we can highlight handwriting exams. Extracting features from handwriting exams is an important contribution of the computational field for the diagnosis of this disease. In this paper, we propose an approach that measures the similarity between the exam template and the handwritten trace of the patient following the exam template. This similarity was measured using the Structural Cooccurrence Matrix to calculate how close the handwritten trace of the patient is to the exam template. The proposed approach was evaluated using various exam templates and the handwritten traces of the patient. Each of these variations was used together with the Naïve Bayes, OPF, and SVM classifiers. In conclusion the proposed approach was proven to be better than the existing methods found in the literature and is therefore a promising tool for the diagnosis of Parkinson's disease.

2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib.

PubMed

Gohlke, Bjoern-Oliver; Overkamp, Tim; Richter, Anja; Richter, Antje; Daniel, Peter T; Gillissen, Bernd; Preissner, Robert

2015-09-24

Searching for two-dimensional (2D) structural similarities is a useful tool to identify new active compounds in drug-discovery programs. However, as 2D similarity measures neglect important structural and functional features, similarity by 2D might be underestimated. In the present study, we used combined 2D and three-dimensional (3D) similarity comparisons to reveal possible new functions and/or side-effects of known bioactive compounds. We utilised more than 10,000 compounds from the SuperTarget database with known inhibition values for twelve different anti-cancer targets. We performed all-against-all comparisons resulting in 2D similarity landscapes. Among the regions with low 2D similarity scores are inhibitors of vascular endothelial growth factor receptor (VEGFR) and inhibitors of poly ADP-ribose polymerase (PARP). To demonstrate that 3D landscape comparison can identify similarities, which are untraceable in 2D similarity comparisons, we analysed this region in more detail. This 3D analysis showed the unexpected structural similarity between inhibitors of VEGFR and inhibitors of PARP. Among the VEGFR inhibitors that show similarities to PARP inhibitors was Vatalanib, an oral "multi-targeted" small molecule protein kinase inhibitor being studied in phase-III clinical trials in cancer therapy. An in silico docking simulation and an in vitro HT universal colorimetric PARP assay confirmed that the VEGFR inhibitor Vatalanib exhibits off-target activity as a PARP inhibitor, broadening its mode of action. In contrast to the 2D-similarity search, the 3D-similarity landscape comparison identifies new functions and side effects of the known VEGFR inhibitor Vatalanib.

A Profile-Based Framework for Factorial Similarity and the Congruence Coefficient.

PubMed

Hartley, Anselma G; Furr, R Michael

2017-01-01

We present a novel profile-based framework for understanding factorial similarity in the context of exploratory factor analysis in general, and for understanding the congruence coefficient (a commonly used index of factor similarity) specifically. First, we introduce the profile-based framework articulating factorial similarity in terms of 3 intuitive components: general saturation similarity, differential saturation similarity, and configural similarity. We then articulate the congruence coefficient in terms of these components, along with 2 additional profile-based components, and we explain how these components resolve ambiguities that can be-and are-found when using the congruence coefficient. Finally, we present secondary analyses revealing that profile-based components of factorial are indeed linked to experts' actual evaluations of factorial similarity. Overall, the profile-based approach we present offers new insights into the ways in which researchers can examine factor similarity and holds the potential to enhance researchers' ability to understand the congruence coefficient.

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

USDA-ARS?s Scientific Manuscript database

The effects of a processive pectin-methylesterase treatment on two different pectins, both possessing a high degree of methylesterification, were investigated. While the starting samples were purportedly very similar in fine structure, and even though the sample-averaged degree of methylesterificati...

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

PubMed Central

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

2009-01-01

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

Risk of maltreatment for siblings: Factors associated with similar and different childhood experiences in a dyadic sample of adult siblings.

PubMed

Witte, Susanne; Fegert, Jörg M; Walper, Sabine

2018-02-01

Siblings share the same environment and thus potentially a substantial number of risk factors for child maltreatment. Furthermore, the number of siblings and the sibling constellation itself might pose a risk for child maltreatment. Little is known about the likelihood that more than one child in a family is maltreated and which factors increase the risk. This study sought to investigate similarities and differences in maltreatment in siblings and risk factors associated with the maltreatment of more than one child from the same family. Data on maltreatment during childhood and adolescence, family background, and sibling constellation were collected from 870 pairs of siblings. In the dyadic analyses, siblings reported similar maltreatment experiences, especially when any type of maltreatment was considered. Parents' mental health problems were significant predictors for maltreatment of at least one sibling. Father's mental health problems were predictive of maltreatment of both or only the younger sibling, mother's mental health problems of both or only the older sibling. Closeness in age and same gender of siblings did not emerge as a consistent predictor. The increasing number of siblings was a risk factor for any type of maltreatment of both siblings. The results highlight the need for preventive measures for families with a large number of children and with parents with mental health problems as well as a repeated risk assessment of all siblings in a family when one sibling was maltreated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Moving Aerospace Structural Design Practice to a Load and Resistance Factor Approach

NASA Technical Reports Server (NTRS)

Larsen, Curtis E.; Raju, Ivatury S.

2016-01-01

Aerospace structures are traditionally designed using the factor of safety (FOS) approach. The limit load on the structure is determined and the structure is then designed for FOS times the limit load - the ultimate load. Probabilistic approaches utilize distributions for loads and strengths. Failures are predicted to occur in the region of intersection of the two distributions. The load and resistance factor design (LRFD) approach judiciously combines these two approaches by intensive calibration studies on loads and strength to result in structures that are efficient and reliable. This paper discusses these three approaches.

Evaluating WAIS-IV structure through a different psychometric lens: structural causal model discovery as an alternative to confirmatory factor analysis.

PubMed

van Dijk, Marjolein J A M; Claassen, Tom; Suwartono, Christiany; van der Veld, William M; van der Heijden, Paul T; Hendriks, Marc P H

Since the publication of the WAIS-IV in the U.S. in 2008, efforts have been made to explore the structural validity by applying factor analysis to various samples. This study aims to achieve a more fine-grained understanding of the structure of the Dutch language version of the WAIS-IV (WAIS-IV-NL) by applying an alternative analysis based on causal modeling in addition to confirmatory factor analysis (CFA). The Bayesian Constraint-based Causal Discovery (BCCD) algorithm learns underlying network structures directly from data and assesses more complex structures than is possible with factor analysis. WAIS-IV-NL profiles of two clinical samples of 202 patients (i.e. patients with temporal lobe epilepsy and a mixed psychiatric outpatient group) were analyzed and contrasted with a matched control group (N = 202) selected from the Dutch standardization sample of the WAIS-IV-NL to investigate internal structure by means of CFA and BCCD. With CFA, the four-factor structure as proposed by Wechsler demonstrates acceptable fit in all three subsamples. However, BCCD revealed three consistent clusters (verbal comprehension, visual processing, and processing speed) in all three subsamples. The combination of Arithmetic and Digit Span as a coherent working memory factor could not be verified, and Matrix Reasoning appeared to be isolated. With BCCD, some discrepancies from the proposed four-factor structure are exemplified. Furthermore, these results fit CHC theory of intelligence more clearly. Consistent clustering patterns indicate these results are robust. The structural causal discovery approach may be helpful in better interpreting existing tests, the development of new tests, and aid in diagnostic instruments.

Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine

PubMed Central

Hew, Kelly; Dahlroth, Sue-Li; Veerappan, Saranya; Pan, Lucy Xin; Cornvik, Tobias; Nordlund, Pär

2015-01-01

Varicella zoster virus (VZV) is a highly infectious human herpesvirus that is the causative agent for chicken pox and shingles. VZV encodes a functional thymidylate synthase (TS), which is the sole enzyme that produces dTMP from dUMP de novo. To study substrate binding, the complex structure of TSVZV with dUMP was determined to a resolution of 2.9 Å. In the absence of a folate co-substrate, dUMP binds in the conserved TS active site and is coordinated similarly as in the human encoded TS (TSHS) in an open conformation. The interactions between TSVZV with dUMP and a cofactor analog, raltitrexed, were also studied using differential scanning fluorimetry (DSF), suggesting that TSVZV binds dUMP and raltitrexed in a sequential binding mode like other TS. The DSF also revealed interactions between TSVZV and in vitro phosphorylated brivudine (BVDUP), a highly potent anti-herpesvirus drug against VZV infections. The binding of BVDUP to TSVZV was further confirmed by the complex structure of TSVZV and BVDUP solved at a resolution of 2.9 Å. BVDUP binds similarly as dUMP in the TSHS but it induces a closed conformation of the active site. The structure supports that the 5-bromovinyl substituent on BVDUP is likely to inhibit TSVZV by preventing the transfer of a methylene group from its cofactor and the subsequent formation of dTMP. The interactions between TSVZV and BVDUP are consistent with that TSVZV is indeed a target of brivudine in vivo. The work also provided the structural basis for rational design of more specific TSVZV inhibitors. PMID:26630264

Using Multilevel Factor Analysis with Clustered Data: Investigating the Factor Structure of the Positive Values Scale

ERIC Educational Resources Information Center

Huang, Francis L.; Cornell, Dewey G.

2016-01-01

Advances in multilevel modeling techniques now make it possible to investigate the psychometric properties of instruments using clustered data. Factor models that overlook the clustering effect can lead to underestimated standard errors, incorrect parameter estimates, and model fit indices. In addition, factor structures may differ depending on…

A combination of 2D similarity search, pharmacophore, and molecular docking techniques for the identification of vascular endothelial growth factor receptor-2 inhibitors.

PubMed

Ai, Guanhua; Tian, Caiping; Deng, Dawei; Fida, Guissi; Chen, Haiyan; Ma, Yuxiang; Ding, Li; Gu, Yueqing

2015-04-01

The human vascular endothelial growth factor receptor-2 (VEGFR-2) has been an attractive target for the inhibition of angiogenesis. In the current study, we used a hybrid protocol of virtual screening methods to retrieve new VEGFR-2 inhibitors from the Zinc-Specs Database (441 574 compounds). The hybrid protocol included the initial screening of candidates by comparing the 2D similarity to five reported top active inhibitors of 13 VEGFR-2 X-ray crystallography structures, followed by the pharmacophore modeling of virtual screening on the basis of receptor-ligand interactions and further narrowing by LibDOCK to obtain the final hits. Two compounds (AN-919/41439526 and AK-968/40939851) with a high libscore were selected as the final hits for a subsequent cell cytotoxicity study. The two compounds screened exerted significant inhibitory effects on the proliferation of cancer cells (U87 and MCF-7). The results indicated that the hybrid procedure is an effective approach for screening specific receptor inhibitors.

Do homologous thermophilic-mesophilic proteins exhibit similar structures and dynamics at optimal growth temperatures? A molecular dynamics simulation study.

PubMed

Basu, Sohini; Sen, Srikanta

2013-02-25

Structure and dynamics both are known to be important for the activity of a protein. A fundamental question is whether a thermophilic protein and its mesophilic homologue exhibit similar dynamics at their respective optimal growth temperatures. We have addressed this question by performing molecular dynamics (MD) simulations of a natural mesophilic-thermophilic homologue pair at their respective optimal growth temperatures to compare their structural, dynamical, and solvent properties. The MD simulations were done in explicit aqueous solvent under periodic boundary and constant pressure and temperature (CPT) conditions and continued for 10.0 ns using the same protocol for the two proteins, excepting the temperatures. The trajectories were analyzed to compare the properties of the two proteins. Results indicated that the dynamical behaviors of the two proteins at the respective optimal growth temperatures were remarkably similar. For the common residues in the thermophilic protein, the rms fluctuations have a general trend to be slightly higher compared to that in the mesophilic counterpart. Lindemann parameter values indicated that only a few residues exhibited solid-like dynamics while the protein as a whole appeared as a molten globule in each case. Interestingly, the water-water interaction was found to be strikingly similar in spite of the difference in temperatures while, the protein-water interaction was significantly different in the two simulations.

Differences in within- and between-person factor structure of positive and negative affect: analysis of two intensive measurement studies using multilevel structural equation modeling.

PubMed

Rush, Jonathan; Hofer, Scott M

2014-06-01

The Positive and Negative Affect Schedule (PANAS) is a widely used measure of emotional experience. The factor structure of the PANAS has been examined predominantly with cross-sectional designs, which fails to disaggregate within-person variation from between-person differences. There is still uncertainty as to the factor structure of positive and negative affect and whether they constitute 2 distinct independent factors. The present study examined the within-person and between-person factor structure of the PANAS in 2 independent samples that reported daily affect over 7 and 14 occasions, respectively. Results from multilevel confirmatory factor analyses revealed that a 2-factor structure at both the within-person and between-person levels, with correlated specific factors for overlapping items, provided good model fit. The best-fitting solution was one where within-person factors of positive and negative affect were inversely correlated, but between-person factors were independent. The structure was further validated through multilevel structural equation modeling examining the effects of cognitive interference, daily stress, physical symptoms, and physical activity on positive and negative affect factors.

Examining the Factor Structure and Hierarchical Nature of the Quality of Life Construct

ERIC Educational Resources Information Center

Wang, Mian; Schalock, Robert L.; Verdugo, Miguel A.; Jenaro, Christina

2010-01-01

There is considerable debate in the area of individual quality of life research regarding the factor structure and hierarchical nature of the quality of life construct. Our purpose in this study was to test via structural equation modeling an a priori quality of life model consisting of eight first-order factors and one second-order factor. Data…

WISC-R Factor Structures of Younger and Older Youth with Low IQs.

ERIC Educational Resources Information Center

Groff, M.; Hubble, L.

1982-01-01

Factor analyzed Wechsler Intelligence Scale for Children-Revised scores of low-IQ youths aged 9-11 and 14-16. Extracted Verbal Comprehension, Perceptual Organization and Freedom From Distractibility dimensions for each group. Coefficients of congruence indicated the two age groups were not similar on the Freedom From Distractibility factor.…

Regional factors rather than forest type drive the community structure of soil living oribatid mites (Acari, Oribatida).

PubMed

Erdmann, Georgia; Scheu, Stefan; Maraun, Mark

2012-06-01

Most European forests are managed by humans. However, the manner and intensity of management vary. While the effect of forest management on above-ground communities has been investigated in detail, effects on the below-ground fauna remain poorly understood. Oribatid mites are abundant microarthropods in forest soil and important decomposers in terrestrial ecosystems. Here, we investigated the effect of four forest types (i.e., managed coniferous forests; 30 and 70 years old managed beech forests; natural beech forests) on the density, diversity and community structure of oribatid mites (Acari). The study was replicated at three regions in Germany: the Swabian Alb, the Hainich and the Schorfheide. To relate changes in oribatid mite community structure to environmental factors, litter mass, pH, C and N content of litter, fine roots and C content of soil were measured. Density of oribatid mites was highest in the coniferous forests and decreased in the order 30 years old, 70 years old, and natural beech forests. Mass of the litter layer and density of oribatid mites were strongly correlated indicating that the litter layer is an important factor regulating oribatid mite densities. Diversity of oribatid mites was little affected by forest type indicating that they harbor similar numbers of niches. Species composition differed between the forest types, suggesting different types of niches. The community structure of oribatid mites differed more strongly between the three regions than between the forest types indicating that regional factors are more important than effects associated with forest type.

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

PubMed

Diykh, Mohammed; Li, Yan; Wen, Peng

2016-11-01

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

HIV and influenza share a similar structural blueprint

Cancer.gov

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

Structure of rapidity divergences in multi-parton scattering soft factors

NASA Astrophysics Data System (ADS)

Vladimirov, Alexey

2018-04-01

We discuss the structure of rapidity divergences that are presented in the soft factors of transverse momentum dependent (TMD) factorization theorems. To provide the discussion on the most general level we consider soft factors for multi-parton scattering. We show that the rapidity divergences are result of the gluon exchanges with the distant transverse plane, and are structurally equivalent to the ultraviolet divergences. It allows to formulate and to prove the renormalization theorem for rapidity divergences. The proof is made with the help the conformal transformation which maps rapidity divergences to ultraviolet divergences. The theorem is the systematic form of the factorization of rapidity divergences, which is required for the definition of TMD parton distributions. In particular, the definition of multi parton distributions is presented. The equivalence of ultraviolet and rapidity divergences leads to the exact relation between soft and rapidity anomalous dimensions. Using this relation we derive the rapidity anomalous dimension at the three-loop order.

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

PubMed

Valles, Steven M; Bell, Susanne; Firth, Andrew E

2014-01-01

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.

Social cognition in schizophrenia: Factor structure of emotion processing and theory of mind

PubMed Central

Browne, Julia; Penn, David L.; Raykov, Tenko; Pinkham, Amy E.; Kelsven, Skylar; Buck, Benjamin; Harvey, Philip D.

2018-01-01

Factor analytic studies examining social cognition in schizophrenia have yielded inconsistent results most likely due to the varying number and quality of measures. With the recent conclusion of Phase 3 of the Social Cognition Psychometric Evaluation (SCOPE) Study, the most psychometrically sound measures of social cognition have been identified. Therefore, the aims of the present study were to: 1) examine the factor structure of social cognition in schizophrenia through the utilization of psychometrically sound measures, 2) examine the stability of the factor structure across two study visits, 3) compare the factor structure of social cognition in schizophrenia to that in healthy controls, and 4) examine the relationship between the factors and relevant outcome measures including social functioning and symptoms. Results supported a one-factor model for the patient and healthy control samples at both visits. This single factor was significantly associated with negative symptoms in the schizophrenia sample and with social functioning in both groups at both study visits. PMID:27280525

Structure-function relationships of curaremimetic neurotoxin loop 2 and of a structurally similar segment of rabies virus glycoprotein in their interaction with the nicotinic acetylcholine receptor

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

Lentz, T.L.

1991-11-12

Peptides corresponding to portions of curaremimetic neurotoxin loop 2 and to a structurally similar segment of rabies virus glycoprotein were synthetically modified in order to gain information on structure-function relationships of neurotoxin loop 2 interactions with the acetylcholine receptor. Binding of synthetic peptides to the acetylcholine receptor of Torpedo electric organ membranes was assessed by measuring their ability to inhibit the binding of {sup 125}I-{alpha}-bungarotoxin to the receptor. The peptides showing the highest affinity for the receptor were a peptide corresponding to the sequence of loop 2 (residues 25-44) of Ophiophagus hannah (king cobra) toxin b and the structurally similarmore » segment of CVS rabies virus glycoprotein. These affinities were comparable to those of d-tubocurarine and suberyldicholine. These results demonstrate the importance of loop 2 in the neurotoxin interaction with the receptor. N- and C-terminal deletions of the loop 2 peptides and substitution of residues invariant or highly conserved among neurotoxins were performed in order to determine the role of individual residues in binding. Residues 25-40 are the most crucial in the interaction with the acetylcholine receptor. Since this region of the glycoprotein contains residues corresponding to all of the functionally invariant neurotoxin residues, it may interact with the acetylcholine receptor through a mechanism similar to that of the neurotoxins.« less

Structural similarity and distribution of small cryptic plasmids of Lactobacillus curvatus and L. sake.

PubMed

Vogel, R F; Lohmann, M; Weller, A N; Hugas, M; Hammes, W P

1991-11-15

Plasmid profiles of strains of Lactobacillus curvatus and L. sake isolated from meat or sauerkraut were analysed to investigate plasmid homology and distribution in relation to the ecology of these organisms in fermenting foods. A hybridisation probe was constructed by cloning of pLc2, a cryptic, 2.6-kbp plasmid from L. curvatus LTH683, into the Escherichia coli plasmid pRV50. In Southern hybridisations with the digoxygenine labeled pLc2 probe, pLc2-related small plasmids were frequently detected in meat-borne strains of L. casei subsp. pseudoplantarum, L. curvatus, L. sake, L. alimentarius, L. farciminis and L. halotolerans and in L. curvatus and L. sake isolated from sauerkraut. Among 27 Lactobacillus type strains originally isolated from habitats other than meat this type of homology was detected only with plasmids of L. buchneri and L. mali. Restriction-enzyme mapping of six small cryptic plasmids from L. curvatus and L. sake revealed strong structural homology but no similarity to previously characterized plasmids of lactobacilli. The presence of a variable region in addition to a conserved one and the occurrence of deletions during cloning of pLc2 suggest that vectors derived from these plasmids are likely to be structurally unstable.

Factor Structure of the Social Appearance Anxiety Scale in Turkish Early Adolescents

ERIC Educational Resources Information Center

Sahin, Ertugrul; Topkaya, Nursel

2015-01-01

Although the Social Appearance Anxiety Scale (SAAS) is most often validated with the use of confirmatory factor analysis (CFA) on undergraduate students, exploratory factor analysis and multiple factor retention decision criteria necessitate the analysis of underlying factor structure to prevent over and under factoring as well as to reveal…

[Fine stereo structure for natural organic molecules, a preliminary study. II. Melting point influenced by structure factors].

PubMed

Lu, Y; Zheng, Q; Lu, D; Ma, P; Chen, Y

1995-06-01

Crystal structures of two compounds from Tripterygium wilfordii Hook f. have been determined by X-ray diffraction method. Structure factors influencing melting point of solid state have been analysed. Crystal class (or space group), recrystallization solvent, force between molecules and fine changes of molecular structures will all cause melting point changes of crystal substance.

The Network Structure of Human Personality According to the NEO-PI-R: Matching Network Community Structure to Factor Structure

PubMed Central

Goekoop, Rutger; Goekoop, Jaap G.; Scholte, H. Steven

2012-01-01

Introduction Human personality is described preferentially in terms of factors (dimensions) found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. Aim To directly compare the ability of network community detection (NCD) and principal component factor analysis (PCA) to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R). Methods 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS) of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS) of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. Results At facet level, NCS showed a best match (96.2%) with a ‘confirmatory’ 5-FS. At item level, NCS showed a best match (80%) with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with ‘confirmatory’ 5-FS and ‘exploratory’ 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. Conclusion We present the first optimized network graph of personality traits according to the NEO-PI-R: a ‘Personality Web’. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network. PMID:23284713

The network structure of human personality according to the NEO-PI-R: matching network community structure to factor structure.

PubMed

Goekoop, Rutger; Goekoop, Jaap G; Scholte, H Steven

2012-01-01

Human personality is described preferentially in terms of factors (dimensions) found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. To directly compare the ability of network community detection (NCD) and principal component factor analysis (PCA) to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R). 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS) of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS) of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. At facet level, NCS showed a best match (96.2%) with a 'confirmatory' 5-FS. At item level, NCS showed a best match (80%) with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with 'confirmatory' 5-FS and 'exploratory' 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. We present the first optimized network graph of personality traits according to the NEO-PI-R: a 'Personality Web'. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network.

What Difference Reveals about Similarity

ERIC Educational Resources Information Center

Sagi, Eyal; Gentner, Dedre; Lovett, Andrew

2012-01-01

Detecting that two images are different is faster for highly dissimilar images than for highly similar images. Paradoxically, we showed that the reverse occurs when people are asked to describe "how" two images differ--that is, to state a difference between two images. Following structure-mapping theory, we propose that this…

Identification of the underlying factor structure of the Derriford Appearance Scale 24

PubMed Central

Lawson, Victoria; White, Paul

2015-01-01

Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker’s Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale. PMID:26157633

Identification of the underlying factor structure of the Derriford Appearance Scale 24.

PubMed

Moss, Timothy P; Lawson, Victoria; White, Paul

2015-01-01

Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker's Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale.

Probabilistic simulation of the human factor in structural reliability

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1993-01-01

A formal approach is described in an attempt to computationally simulate the probable ranges of uncertainties of the human factor in structural probabilistic assessments. A multi-factor interaction equation (MFIE) model has been adopted for this purpose. Human factors such as marital status, professional status, home life, job satisfaction, work load and health, are considered to demonstrate the concept. Parametric studies in conjunction with judgment are used to select reasonable values for the participating factors (primitive variables). Suitability of the MFIE in the subsequently probabilistic sensitivity studies are performed to assess the validity of the whole approach. Results obtained show that the uncertainties for no error range from five to thirty percent for the most optimistic case.

Factor structure of the Korean version of illness intrusiveness rating scale: cross-cultural implications.

PubMed

Kim, Daeho; Kim, Kwang-iel; Lee, Haewon; Choi, Joonho; Park, Yong-Chon

2005-04-01

The Illness Intrusiveness Rating Scale (IIRS) measures illness-induced disruptions to 13 domains of lifestyles, activities, and interests. A stable three-factor structure has been well documented; however, the cross-cultural validity of this scale needs to be tested. This study investigated the factor structure of the Korean version of IIRS in 712 outpatients at a university medical center. A predominant diagnosis of the patients was rheumatoid arthritis (47%). The Center for Epidemiological Studies-Depression Scale (CES-D), and Health Assessment Questionnaire (HAQ) were also administered. Exploratory Principal Component Analysis identified a two-factor structure, "Relationships and Personal Development (RPD)" and "Instrumental", accounting for 57% of the variance. Confirmatory analyses extracted an identical factor structure. However, a goodness-of-the fit test failed to support two-factor solution (chi(2)=138.2, df=43, p<.001). Two factors had high internal consistency (RPD, alpha=.89; Instrumental, alpha=.75) and significantly correlated with scores of HAQ (RPD, r=.53, p<.001; Instrumental, .r=44, p<.001) and CES-D (RPD, .r=55, p<.001; Instrumental, .r=43, p<.001). These findings supported construct validity of the Korean version of IIRS, but did not support cross-cultural equivalence of the factor structure.

Factor Structure of the Korean Version of Illness Intrusiveness Rating Scale: Cross-cultural Implications

PubMed Central

Kim, Kwang-iel; Lee, Haewon; Choi, Joonho; Park, Yong-Chon

2005-01-01

The Illness Intrusiveness Rating Scale (IIRS) measures illness-induced disruptions to 13 domains of lifestyles, activities, and interests. A stable three-factor structure has been well documented; however, the cross-cultural validity of this scale needs to be tested. This study investigated the factor structure of the Korean version of IIRS in 712 outpatients at a university medical center. A predominant diagnosis of the patients was rheumatoid arthritis (47%). The Center for Epidemiological Studies-Depression Scale (CES-D), and Health Assessment Questionnaire (HAQ) were also administered. Exploratory Principal Component Analysis identified a two-factor structure, "Relationships and Personal Development (RPD)" and "Instrumental", accounting for 57% of the variance. Confirmatory analyses extracted an identical factor structure. However, a goodness-of-the fit test failed to support two-factor solution (χ2=138.2, df=43, p<.001). Two factors had high internal consistency (RPD, α=.89; Instrumental, α=.75) and significantly correlated with scores of HAQ (RPD, r=.53, p<.001; Instrumental, .r=44, p<.001) and CES-D (RPD, .r=55, p<.001; Instrumental, .r=43, p<.001). These findings supported construct validity of the Korean version of IIRS, but did not support cross-cultural equivalence of the factor structure. PMID:15832005

The p Factor: One General Psychopathology Factor in the Structure of Psychiatric Disorders?

PubMed Central

Caspi, Avshalom; Houts, Renate M.; Belsky, Daniel W.; Goldman-Mellor, Sidra J.; Harrington, HonaLee; Israel, Salomon; Meier, Madeline H.; Ramrakha, Sandhya; Shalev, Idan; Poulton, Richie; Moffitt, Terrie E.

2013-01-01

Mental disorders traditionally have been viewed as distinct, episodic, and categorical conditions. This view has been challenged by evidence that many disorders are sequentially comorbid, recurrent/chronic, and exist on a continuum. Using the Dunedin Multidisciplinary Health and Development Study, we examined the structure of psychopathology, taking into account dimensionality, persistence, co-occurrence, and sequential comorbidity of mental disorders across 20 years, from adolescence to midlife. Psychiatric disorders were initially explained by three higher-order factors (Internalizing, Externalizing, and Thought Disorder) but explained even better with one General Psychopathology dimension. We have called this dimension the p factor because it conceptually parallels a familiar dimension in psychological science: the g factor of general intelligence. Higher p scores are associated with more life impairment, greater familiality, worse developmental histories, and more compromised early-life brain function. The p factor explains why it is challenging to find causes, consequences, biomarkers, and treatments with specificity to individual mental disorders. Transdiagnostic approaches may improve research. PMID:25360393

The Recruitment of Social Movement Leaders: Structural Factors.

ERIC Educational Resources Information Center

Himes, Joseph S.

1979-01-01

A review of pertinent literature indicates that social movements produce their leaders by transforming and transferring some followers into the roles of leadership. A case study of the recruitment of social movement leaders in Rhodesia supports this hypothesis and illustrates some of the structural factors which condition the process. (EB)

Social cognition in schizophrenia: Factor structure of emotion processing and theory of mind.

PubMed

Browne, Julia; Penn, David L; Raykov, Tenko; Pinkham, Amy E; Kelsven, Skylar; Buck, Benjamin; Harvey, Philip D

2016-08-30

Factor analytic studies examining social cognition in schizophrenia have yielded inconsistent results most likely due to the varying number and quality of measures. With the recent conclusion of Phase 3 of the Social Cognition Psychometric Evaluation (SCOPE) Study, the most psychometrically sound measures of social cognition have been identified. Therefore, the aims of the present study were to: 1) examine the factor structure of social cognition in schizophrenia through the utilization of psychometrically sound measures, 2) examine the stability of the factor structure across two study visits, 3) compare the factor structure of social cognition in schizophrenia to that in healthy controls, and 4) examine the relationship between the factors and relevant outcome measures including social functioning and symptoms. Results supported a one-factor model for the patient and healthy control samples at both visits. This single factor was significantly associated with negative symptoms in the schizophrenia sample and with social functioning in both groups at both study visits. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Unequal density effect on static structure factor of coupled electron layers

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

Saini, L. K., E-mail: lks@ashd.svnit.ac.in; Nayak, Mukesh G., E-mail: lks@ashd.svnit.ac.in

In order to understand the ordered phase, if any, in a real coupled electron layers (CEL), there is a need to take into account the effect of unequal layer density. Such phase is confirmed by a strong peak in a static structure factor. With the aid of quantum/dynamical version of Singwi, Tosi, Land and Sjölander (so-called qSTLS) approximation, we have calculated the intra- and interlayer static structure factors, S{sub ll}(q) and S{sub 12}(q), over a wide range of density parameter r{sub sl} and interlayer spacing d. In our present study, the sharp peak in S{sub 22}(q) has been found atmore » critical density with sufficiently lower interlayer spacing. Further, to find the resultant effect of unequal density on intra- and interlayer static structure factors, we have compared our results with that of the recent CEL system with equal layer density and isolated single electron layer.« less

Structure and Measurement of Acculturation/Enculturation for Asian Americans Using the ARSMA-II

ERIC Educational Resources Information Center

Lee, Richard M.; Yoon, Eunju; Liu-Tom, Hsin-Tine Tina

2006-01-01

The structure and measurement of acculturation/enculturation was investigated on 2 Asian American samples. Factor analyses revealed similar 2-factor structures for both acculturation and enculturation. The factor-analytic-derived measure yielded scores with adequate reliability and marginal construct validity. Acculturation/enculturation…

Factor analysis of the Mayo-Portland Adaptability Inventory: structure and validity.

PubMed

Bohac, D L; Malec, J F; Moessner, A M

1997-07-01

Principal-components (PC) factor analysis of the Mayo-Portland Adaptability Inventory (MPAI) was conducted using a sample of outpatients (n = 189) with acquired brain injury (ABI) to evaluate whether outcome after ABI is multifactorial or unifactorial in nature. An eight-factor model was derived which explained 64-4% of the total variance. The eight factors were interpreted as representing Activities of Daily Living, Social Initiation, Cognition, Impaired-Self-awareness/Distress, Social Skills/ Support, Independence, Visuoperceptual, and Psychiatric, respectively. Validation of the Cognition factor was supported when factor scores were correlated with various neuropsychological measures. In addition, 117 patient self-rating total scores were used to evaluate the Impaired Self-awareness/Distress factor. An inverse relationship was observed, supporting this factor's ability to capture the two-dimensional phenomena of diminished self-awareness or enhanced emotional distress. A new subscale structure is suggested, that may allow greater clinical utility in understanding how ABI manifests in patients, and may provide clinicians with a better structure for implementing treatment strategies to address specific areas of impairment and disability for specific patients. Additionally, more precise measurement of treatment outcomes may be afforded by this reorganization.

SAR and X-ray Structures of Enantiopure 1,2-cis-(1R,2S)-cyclopentyldiamine and Cyclohexyldiamine Derivativies as Inhibitors of Coagulation Factor Xa

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

Qiao,J.; Chang, C.; Cheney, D.

In the search of Factor Xa (FXa) inhibitors structurally different from the pyrazole-based series, we identified a viable series of enantiopure cis-(1R,2S)-cycloalkyldiamine derivatives as potent and selective inhibitors of FXa. Among them, cyclohexyldiamide 7 and cyclopentyldiamide 9 were the most potent neutral compounds, and had good anticoagulant activity comparable to the pyrazole-based analogs. Crystal structures of 7-FXa and 9-FXa illustrate binding similarities and differences between the five- and the six-membered core systems, and provide rationales for the observed SAR of P1 and linker moieties.

Factor Structure of the Children's Behavior Questionnaire in Children with Williams Syndrome

ERIC Educational Resources Information Center

Leyfer, Ovsanna; John, Angela E.; Woodruff-Borden, Janet; Mervis, Carolyn B.

2012-01-01

To examine the factor structure of temperament in 5-10-year-olds with Williams syndrome, an exploratory factor analysis was conducted on the responses of parents of 192 children on the children's behavior questionnaire. Four factors were identified. Two corresponded to factors reported for typically developing children: effortful control and…

Measuring Sense of Community: A Methodological Interpretation of the Factor Structure Debate

ERIC Educational Resources Information Center

Peterson, N. Andrew; Speer, Paul W.; Hughey, Joseph

2006-01-01

Instability in the factor structure of the Sense of Community Index (SCI) was tested as a methodological artifact. Confirmatory factor analyses, tested with two data sets, supported neither the proposed one-factor nor the four-factor (needs fulfillment, group membership, influence, and emotional connection) SCI. Results demonstrated that the SCI…

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives.

PubMed

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q (2) values of 0.753 and 0.770, and r (2) values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2'-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure-property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature.

Examination of the factor structure of the Schizotypal Personality Questionnaire among British and Trinidadian adults.

PubMed

Barron, David; Swami, Viren; Towell, Tony; Hutchinson, Gerard; Morgan, Kevin D

2015-01-01

Much debate in schizotypal research has centred on the factor structure of the Schizotypal Personality Questionnaire (SPQ), with research variously showing higher-order dimensionality consisting of two to seven dimensions. In addition, cross-cultural support for the stability of those factors remains limited. Here, we examined the factor structure of the SPQ among British and Trinidadian adults. Participants from a White British subsample (n = 351) resident in the UK and from an African Caribbean subsample (n = 284) resident in Trinidad completed the SPQ. The higher-order factor structure of the SPQ was analysed through confirmatory factor analysis, followed by multiple-group analysis for the model of best fit. Between-group differences for sex and ethnicity were investigated using multivariate analysis of variance in relation to the higher-order domains. The model of best-fit was the four-factor structure, which demonstrated measurement invariance across groups. Additionally, these data had an adequate fit for two alternative models: (a) 3-factor and (b) modified 4-factor model. The British subsample had significantly higher scores across all domains than the Trinidadian group, and men scored significantly higher on the disorganised domain than women. The four-factor structure received confirmatory support and, importantly, support for use with populations varying in ethnicity and culture.

Similarity-based Regularized Latent Feature Model for Link Prediction in Bipartite Networks.

PubMed

Wang, Wenjun; Chen, Xue; Jiao, Pengfei; Jin, Di

2017-12-05

Link prediction is an attractive research topic in the field of data mining and has significant applications in improving performance of recommendation system and exploring evolving mechanisms of the complex networks. A variety of complex systems in real world should be abstractly represented as bipartite networks, in which there are two types of nodes and no links connect nodes of the same type. In this paper, we propose a framework for link prediction in bipartite networks by combining the similarity based structure and the latent feature model from a new perspective. The framework is called Similarity Regularized Nonnegative Matrix Factorization (SRNMF), which explicitly takes the local characteristics into consideration and encodes the geometrical information of the networks by constructing a similarity based matrix. We also develop an iterative scheme to solve the objective function based on gradient descent. Extensive experiments on a variety of real world bipartite networks show that the proposed framework of link prediction has a more competitive, preferable and stable performance in comparison with the state-of-art methods.

Factor structure of the Japanese Interpersonal Competence Scale.

PubMed

Matsudaira, Tomomi; Fukuhara, Taihei; Kitamura, Toshinori

2008-04-01

Assessing social competence is important for clinical and preventive interventions of depression. The aim of the present paper was to examine the factor structure of the Japanese Interpersonal Competence Scale (JICS). Exploratory and confirmatory factor analysis was performed on the survey responses of 730 participants. Simultaneous multigroup analyses were conducted to confirm factor stability across psychological health status and sex differences. Two factors, which represent Perceptive Ability and Self-Restraint, were confirmed to show a moderate correlation. Perceptive Ability involves a more cognitive aspect of social competence, while Self-Restraint involves a more behavioral aspect, both of which are considered to reflect the emotion-based relating style specific to the Japanese people: indulgent dependence (amae) and harmony (wa). In addition, Self-Restraint may be linked to social functioning. Both constructs may confound a respondent's perceived confidence. Despite its shortcomings, the JICS is a unique measure of social competence in the Japanese cultural context.

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

PubMed

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, M N V Prasad

2016-10-01

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Factors affecting strategic plan implementation using interpretive structural modeling (ISM).

PubMed

Bahadori, Mohammadkarim; Teymourzadeh, Ehsan; Tajik, Hamidreza; Ravangard, Ramin; Raadabadi, Mehdi; Hosseini, Seyed Mojtaba

2018-06-11

Purpose Strategic planning is the best tool for managers seeking an informed presence and participation in the market without surrendering to changes. Strategic planning enables managers to achieve their organizational goals and objectives. Hospital goals, such as improving service quality and increasing patient satisfaction cannot be achieved if agreed strategies are not implemented. The purpose of this paper is to investigate the factors affecting strategic plan implementation in one teaching hospital using interpretive structural modeling (ISM). Design/methodology/approach The authors used a descriptive study involving experts and senior managers; 16 were selected as the study sample using a purposive sampling method. Data were collected using a questionnaire designed and prepared based on previous studies. Data were analyzed using ISM. Findings Five main factors affected strategic plan implementation. Although all five variables and factors are top level, "senior manager awareness and participation in the strategic planning process" and "creating and maintaining team participation in the strategic planning process" had maximum drive power. "Organizational structure effects on the strategic planning process" and "Organizational culture effects on the strategic planning process" had maximum dependence power. Practical implications Identifying factors affecting strategic plan implementation is a basis for healthcare quality improvement by analyzing the relationship among factors and overcoming the barriers. Originality/value The authors used ISM to analyze the relationship between factors affecting strategic plan implementation.

Similarity Measures for Protein Ensembles

PubMed Central

Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

2009-01-01

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

Evaluation of Structural Factors Potentially Implicated in Acute Lymphoblastic Leukemia: A report of the MIGICCL.

PubMed

López-Sánchez, Dulce María; Méndez-Tenorio, Alfonso; Roacho-Pérez, Jorge Alberto; Rangel-López, Angélica

2016-10-01

Acute lymphoblastic leukemia (ALL) is the most common cancer in the pediatric population; ∼80% of the cases show some translocation. Translocations that result in ALL are due to chromosome breaks. However, the exact mechanisms that cause these breaks have not been well studied. A detailed search of the breakpoints associated with ALL reported in the NCBI database shows that some are concentrated in limited regions of the chromosome, whereas others are scattered throughout. Therefore, the objective of this study was to identify the structural factors involved in chromosomal breaks in ALL. We performed several bioinformatic studies on the sequences where chromosomal breakpoints have been reported in search of rearrangements: areas of high similarity, thermodynamic stability, composition and conformation of the DNA. Certain factors may influence chromosome breaks and are capable of predicting the propensity towards these types of events. These findings may be useful in the design of molecular techniques able to detect these changes in ALL. Copyright © 2016 IMSS. Published by Elsevier Inc. All rights reserved.

Investigating the Crystallization Propensity of Structurally Similar Organic Molecules From Amorphous State

NASA Astrophysics Data System (ADS)

Kalra, Arjun

Combinatorial chemistry and high-throughput screening approaches utilized during drug discovery have resulted in many potent pharmacologically active molecules with low aqueous solubility and consequently poor bioavailability. Enabling technologies, such as amorphous solid dispersions (ASD's), can obviate these challenges and provide an efficient route to formulate the drug as an oral solid dosage form. However, high-energy amorphous materials have an inherent tendency to crystallize and in doing so can negate the apparent solubility advantage achieved by using such formulations. Crystallization can occur during (1) cooling the drug molecule from the melt state (such as during hot melt extrusion); (2) during storage of an amorphous formulation; (3) during pharmaceutical processing unit operations such as compression, granulation etc. Current knowledge with regards to the relationship between crystallization propensity of an active pharmaceutical ingredient (API) from the amorphous state (supercooled liquid and glass) and its thermodynamic, kinetic and molecular properties is limited. Furthermore, examining the mechanistic steps involved in crystallization of organic molecules under conditions of supercooling provides an opportunity to examine supramolecular aggregation events occurring during early stages of crystallization. Studying crystallization mechanism from amorphous state is important for pharmaceutical formulation development because a molecular-level understanding of the crystallization process would provide clues regarding the intermolecular interactions at the early stages of nucleation and help in rational selection of polymeric excipients to hinder such events. The primary goal of this research is to develop an understanding of phase transition from amorphous pharmaceuticals, specifically focusing on the role of thermodynamic, kinetic and molecular properties of a series of structurally similar compounds. It is hypothesized that the there exists a

Factor Structure and Internal Validity of the Functional Movement Screen in Adults.

PubMed

Koehle, Michael S; Saffer, Boaz Y; Sinnen, Nadine M; MacInnis, Martin J

2016-02-01

The factor structure and internal consistency of the Functional Movement Screen (FMS) have not been examined in a general healthcare population. Replicating the factor structure of the FMS is important because it illustrates the interdependence between each of the subtests, enabling the strength and conditioning professional to better interpret and act on an individual's FMS score. Anthropometric data and FMS scores were collected from 1,113 clients of a multidisciplinary healthcare clinic in Vancouver, BC The mean (SD) ages were 53.4 (11.1) for men (n = 656) and 49.3 (12.3) for women (n = 457). The mean FMS Summary Score was 13.7 (2.9) and was significantly negatively correlated with both age (r = -0.25; p < 0.001) and body mass index (r = -0.37; p < 0.001). The internal consistency of the FMS scale, which was assessed with both ordinal and Cronbach's alpha, was 0.73 and 0.64, respectively. Polychoric correlations between individual movements ranged from 0.03 to 0.59. Exploratory and confirmatory factor analyses (CFA) revealed that the FMS showed 2 main factors, a basic movement factor (shoulder mobility and active straight leg raise) and a complex movement factor (squat, hurdle step, inline lunge, and the trunk stability push-up). Rotary stability loaded onto both factors in the CFA, and its exclusion from the model had little effect. The findings of this study broadly replicated the intended factor structure of the FMS, as the individual movements aligned well with the intended factors.

Zeroing In on Mindfulness Facets: Similarities, Validity, and Dimensionality across Three Independent Measures.

PubMed

Siegling, Alex B; Petrides, K V

2016-01-01

The field of mindfulness has seen a proliferation of psychometric measures, characterised by differences in operationalisation and conceptualisation. To illuminate the scope of, and offer insights into, the diversity apparent in the burgeoning literature, two distinct samples were used to examine the similarities, validity, and dimensionality of mindfulness facets and subscales across three independent measures: the Five Facet Mindfulness Questionnaire (FFMQ), Philadelphia Mindfulness Scale (PHLMS), and Toronto Mindfulness Scale (TMS). Results revealed problematic associations of FFMQ Observe with the other FFMQ facets and supported a four-factor structure (omitting this facet), while disputing the originally envisaged five-factor model; thus, solidifying a pattern in the literature. Results also confirmed the bidimensional nature of the PHLMS and TMS subscales, respectively. A joint Confirmatory Factor Analysis showed that PHLMS Acceptance could be assimilated within the FFMQ's four-factor model (as a distinct factor). The study offers a way of understanding interrelationships between the available mindfulness scales, so as to help practitioners and researchers make a more informed choice when conceptualising and operationalising mindfulness.

Zeroing In on Mindfulness Facets: Similarities, Validity, and Dimensionality across Three Independent Measures

PubMed Central

Siegling, Alex B.; Petrides, K. V.

2016-01-01

The field of mindfulness has seen a proliferation of psychometric measures, characterised by differences in operationalisation and conceptualisation. To illuminate the scope of, and offer insights into, the diversity apparent in the burgeoning literature, two distinct samples were used to examine the similarities, validity, and dimensionality of mindfulness facets and subscales across three independent measures: the Five Facet Mindfulness Questionnaire (FFMQ), Philadelphia Mindfulness Scale (PHLMS), and Toronto Mindfulness Scale (TMS). Results revealed problematic associations of FFMQ Observe with the other FFMQ facets and supported a four-factor structure (omitting this facet), while disputing the originally envisaged five-factor model; thus, solidifying a pattern in the literature. Results also confirmed the bidimensional nature of the PHLMS and TMS subscales, respectively. A joint Confirmatory Factor Analysis showed that PHLMS Acceptance could be assimilated within the FFMQ’s four-factor model (as a distinct factor). The study offers a way of understanding interrelationships between the available mindfulness scales, so as to help practitioners and researchers make a more informed choice when conceptualising and operationalising mindfulness. PMID:27055017

Similar Fracture Patterns in Human Nose and Gothic Cathedral.

PubMed

Lee, Shu Jin; Tse, Kwong Ming; Lee, Heow Pueh

2015-10-01

This study proposes that the bony anatomy of the human nose and masonry structure of the Gothic cathedral are geometrically similar, and have common fracture patterns. We also aim to correlate the fracture patterns observed in patients' midface structures with those seen in the Gothic cathedral using computational approach. CT scans of 33 patients with facial fractures were examined and compared with computer simulations of both the Gothic cathedral and human nose. Three similar patterns were found: (1) Cracks of the nasal arch with crumpling of the vertical buttresses akin to the damage seen during minor earthquakes; (2) lateral deviation of the central nasal arch and collapse of the vertical buttresses akin to those due to lateral forces from wind and in major earthquakes; and (3) Central arch collapse seen as a result of collapse under excessive dead weight. Interestingly, the finding of occult nasal and septal fractures in the mandible fractures with absence of direct nasal trauma highlights the possibility of transmission of forces from the foundation to the arch leading to structural failure. It was also found that the structural buttresses of the Gothic cathedral delineate the vertical buttresses in the human midface structure. These morphologic similarities between the human nose and Gothic cathedral will serve as a basis to study the biomechanics of nasal fractures. Identification of structural buttresses in a skeletal structure has important implications for reconstruction as reestablishment of structural continuity restores normal anatomy and architectural stability of the human midface structure. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Community detection in sequence similarity networks based on attribute clustering

DOE PAGES

Chowdhary, Janamejaya; Loeffler, Frank E.; Smith, Jeremy C.

2017-07-24

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs,more » for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments« less

Community detection in sequence similarity networks based on attribute clustering

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

Chowdhary, Janamejaya; Loeffler, Frank E.; Smith, Jeremy C.

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs,more » for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments« less

Depression Anxiety Stress Scales (DASS-21): Factor Structure in Traumatic Brain Injury Rehabilitation.

PubMed

Randall, Diane; Thomas, Matt; Whiting, Diane; McGrath, Andrew

To confirm the construct validity of the Depression Anxiety Stress Scales-21 (DASS-21) by investigating the fit of published factor structures in a sample of adults with moderate to severe traumatic brain injury (posttraumatic amnesia > 24 hours). Archival data from 504 patient records at the Brain Injury Rehabilitation Unit at Liverpool Hospital, Australia. Participants were aged between 16 and 71 years and were engaged in a specialist rehabilitation program. The DASS-21. Two of the 6 models had adequate fit using structural equation modeling. The data best fit Henry and Crawford's quadripartite model, which comprised a Depression, Anxiety and Stress factor, as well as a General Distress factor. The data also adequately fit Lovibond and Lovibond's original 3-factor model, and the internal consistencies of each factor were very good (α = 0.82-0.90). This study confirms the structure and construct validity of the DASS-21 and provides support for its use as a screening tool in traumatic brain injury rehabilitation.

The structure of the nucleon: Elastic electromagnetic form factors

DOE PAGES

Punjabi, V.; Perdrisat, C. F.; Jones, M. K.; ...

2015-07-10

Precise proton and neutron form factor measurements at Jefferson Lab, using spin observables, have recently made a significant contribution to the unraveling of the internal structure of the nucleon. Accurate experimental measurements of the nucleon form factors are a test-bed for understanding how the nucleon's static properties and dynamical behavior emerge from QCD, the theory of the strong interactions between quarks. There has been enormous theoretical progress, since the publication of the Jefferson Lab proton form factor ratio data, aiming at reevaluating the picture of the nucleon. We will review the experimental and theoretical developments in this field and discussmore » the outlook for the future.« less

Graph-based similarity concepts in virtual screening.

PubMed

Hutter, Michael C

2011-03-01

Applying similarity for finding new promising compounds is a key issue in drug design. Conversely, quantifying similarity between molecules has remained a difficult task despite the numerous approaches. Here, some general aspects along with recent developments regarding similarity criteria are collected. For the purpose of virtual screening, the compounds have to be encoded into a computer-readable format that permits a comparison, according to given similarity criteria, comprising the use of the 3D structure, fingerprints, graph-based and alignment-based approaches. Whereas finding the most common substructures is the most obvious method, more recent approaches take into account chemical modifications that appear throughout existing drugs, from various therapeutic categories and targets.

Latent Factor Structure of DSM-5 Posttraumatic Stress Disorder

PubMed Central

Gentes, Emily; Dennis, Paul A.; Kimbrel, Nathan A.; Kirby, Angela C.; Hair, Lauren P.; Beckham, Jean C.; Calhoun, Patrick S.

2015-01-01

The current study examined the latent factor structure of posttraumatic stress disorder (PTSD) based on DSM-5 criteria in a sample of participants (N = 374) recruited for studies on trauma and health. Confirmatory factor analyses (CFA) were used to compare the fit of the previous 3-factor DSM-IV model of PTSD to the 4-factor model specified in DSM-5 as well as to a competing 4-factor “dysphoria” model (Simms, Watson, & Doebbeling, 2002) and a 5-factor (Elhai et al., 2011) model of PTSD. Results indicated that the Elhai 5-factor model (re-experiencing, active avoidance, emotional numbing, dysphoric arousal, anxious arousal) provided the best fit to the data, although substantial support was demonstrated for the DSM-5 4-factor model. Low factor loadings were noted for two of the symptoms in the DSM-5 model (psychogenic amnesia and reckless/self-destructive behavior), which raises questions regarding the adequacy of fit of these symptoms with other core features of the disorder. Overall, the findings from the present research suggest the DSM-5 model of PTSD is a significant improvement over the previous DSM-IV model of PTSD. PMID:26366290

A study of concept-based similarity approaches for recommending program examples

NASA Astrophysics Data System (ADS)

Hosseini, Roya; Brusilovsky, Peter

2017-07-01

This paper investigates a range of concept-based example recommendation approaches that we developed to provide example-based problem-solving support in the domain of programming. The goal of these approaches is to offer students a set of most relevant remedial examples when they have trouble solving a code comprehension problem where students examine a program code to determine its output or the final value of a variable. In this paper, we use the ideas of semantic-level similarity-based linking developed in the area of intelligent hypertext to generate examples for the given problem. To determine the best-performing approach, we explored two groups of similarity approaches for selecting examples: non-structural approaches focusing on examples that are similar to the problem in terms of concept coverage and structural approaches focusing on examples that are similar to the problem by the structure of the content. We also explored the value of personalized example recommendation based on student's knowledge levels and learning goal of the exercise. The paper presents concept-based similarity approaches that we developed, explains the data collection studies and reports the result of comparative analysis. The results of our analysis showed better ranking performance of the personalized structural variant of cosine similarity approach.

The Swedish WAIS-R Factor Structure and Cognitive Profiles for Adults with Dyslexia.

ERIC Educational Resources Information Center

Alm, Jan; Kaufman, Alan S.

2002-01-01

Factor analysis of the Swedish version of the Wechsler Adult Intelligence Scale-Revised on 88 adults with dyslexia showed a three-factor structure: a verbal comprehension (VC) factor, a perceptual organization (PO) factor, and a freedom from distractibility (FD) factor. The PO factor had the highest scores and the FD the lowest. (Contains…

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Factor structure and longitudinal measurement invariance of PHQ-9 for specialist mental health care patients with persistent major depressive disorder: Exploratory Structural Equation Modelling.

PubMed

Guo, Boliang; Kaylor-Hughes, Catherine; Garland, Anne; Nixon, Neil; Sweeney, Tim; Simpson, Sandra; Dalgleish, Tim; Ramana, Rajini; Yang, Min; Morriss, Richard

2017-09-01

The Patient Health Questionnaire-9 (PHQ-9) is a widely used instrument for measuring levels of depression in patients in clinical practice and academic research; its factor structure has been investigated in various samples, with limited evidence of measurement equivalence/invariance (ME/I) but not in patients with more severe depression of long duration. This study aims to explore the factor structure of the PHQ-9 and the ME/I between treatment groups over time for these patients. 187 secondary care patients with persistent major depressive disorder (PMDD) were recruited to a randomised controlled trial (RCT) with allocation to either a specialist depression team arm or a general mental health arm; their PHQ-9 score was measured at baseline, 3, 6, 9 and 12 months. Exploratory Structural Equational Modelling (ESEM) was performed to examine the factor structure for this specific patient group. ME/I between treatment arm at and across follow-up time were further explored by means of multiple-group ESEM approach using the best-fitted factor structure. A two-factor structure was evidenced (somatic and affective factor). This two-factor structure had strong factorial invariance between the treatment groups at and across follow up times. Participants were largely white British in a RCT with 40% attrition potentially limiting the study's generalisability. Not all two-factor modelling criteria were met at every time-point. PHQ-9 has a two-factor structure for PMDD patients, with strong measurement invariance between treatment groups at and across follow-up time, demonstrating its validity for RCTs and prospective longitudinal studies in chronic moderate to severe depression. Copyright © 2017. Published by Elsevier B.V.

A Confirmatory Factor Analysis of the Structure of Abbreviated Math Anxiety Scale

PubMed Central

Farrokhi, Farahman

2011-01-01

Objective The aim of this study is to explore the confirmatory factor analysis results of the Persian adaptation of Abbreviated Math Anxiety Scale (AMAS), proposed by Hopko, Mahadevan, Bare & Hunt. Method The validity and reliability assessments of the scale were performed on 298 college students chosen randomly from Tabriz University in Iran. The confirmatory factor analysis (CFA) was carried out to determine the factor structures of the Persian version of AMAS. Results As expected, the two-factor solution provided a better fit to the data than a single factor. Moreover, multi-group analyses showed that this two-factor structure was invariant across sex. Hence, AMAS provides an equally valid measure for use among college students. Conclusions Brief AMAS demonstrates adequate reliability and validity. The AMAS scores can be used to compare symptoms of math anxiety between male and female students. The study both expands and adds support to the existing body of math anxiety literature. PMID:22952521

33 CFR 157.147 - Similar tank design: Inspections on foreign tank vessels.

Code of Federal Regulations, 2012 CFR

2012-07-01

... tanks similar in dimensions and internal structure, the owner or operator may submit a written request... tanks similar in dimensions and internal structure is inspected under § 157.140(a)(1), if the Commandant...

33 CFR 157.147 - Similar tank design: Inspections on foreign tank vessels.

Code of Federal Regulations, 2014 CFR

2014-07-01

... tanks similar in dimensions and internal structure, the owner or operator may submit a written request... tanks similar in dimensions and internal structure is inspected under § 157.140(a)(1), if the Commandant...

33 CFR 157.147 - Similar tank design: Inspections on foreign tank vessels.

Code of Federal Regulations, 2013 CFR

2013-07-01

... tanks similar in dimensions and internal structure, the owner or operator may submit a written request... tanks similar in dimensions and internal structure is inspected under § 157.140(a)(1), if the Commandant...

Factor structure of the Liebowitz Social Anxiety Scale for Children and Adolescents.

PubMed

Storch, Eric A; Masia-Warner, Carrie; Heidgerken, Amanda D; Fisher, Paige H; Pincus, Donna B; Liebowitz, Michael R

2006-01-01

The purpose of this study was to evaluate the factor structure of the Liebowitz Social Anxiety Scale for Children and Adolescents (LSAS-CA). The LSAS-CA was administered to 225 children and adolescents as a component of various clinical studies. In addition, other measures of psychopathology and impairment were administered to a subgroup of the sample. Confirmatory factor analyses of the social interaction and performance subscales for the anxiety and avoidance ratings yielded poor fit indices. Exploratory factor analysis supported a two-factor solution with a higher order factor for the LSAS-CA anxiety and avoidance ratings. Based on item content, factors were named Social and School Performance. The internal consistency of the factors was high and the convergent and divergent validity was supported vis-à-vis correlations with measures of depression and social anxiety, and clinician ratings of impairment and functioning. Findings suggest that the anxiety and avoidance ratings are best explained by a two-factor solution that measures social anxiety and avoidance in social and school performance interactions. This factor structure appears to be a reliable and valid framework for assessing childhood social phobia.

Structure of p-shell nuclei using three-nucleon interactions evolved with the similarity renormalization group

DOE PAGES

Jurgenson, E. D.; Maris, P.; Furnstahl, R. J.; ...

2013-05-13

The similarity renormalization group (SRG) is used to soften interactions for ab initio nuclear structure calculations by decoupling low- and high-energy Hamiltonian matrix elements. The substantial contribution of both initial and SRG-induced three-nucleon forces requires their consistent evolution in a three-particle basis space before applying them to larger nuclei. While, in principle, the evolved Hamiltonians are unitarily equivalent, in practice the need for basis truncation introduces deviations, which must be monitored. Here we present benchmark no-core full configuration calculations with SRG-evolved interactions in p-shell nuclei over a wide range of softening. As a result, these calculations are used to assessmore » convergence properties, extrapolation techniques, and the dependence of energies, including four-body contributions, on the SRG resolution scale.« less