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Sample records for accurate scoring functions

  1. MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

    PubMed

    Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

    2012-09-11

    An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

  2. An accurate metalloprotein-specific scoring function and molecular docking program devised by a dynamic sampling and iteration optimization strategy.

    PubMed

    Bai, Fang; Liao, Sha; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin

    2015-04-27

    Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal-ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, multiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloprotein-specific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDockZn, an extensive comparison was performed against six universal, popular docking programs: Glide XP mode, Glide SP mode, Gold, AutoDock, AutoDock4Zn, and EADock DSS. The zinc metalloprotein-specific knowledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDockZn had a competitive ability to sample and identify native binding poses with a higher success rate than the other six docking programs.

  3. Classification of current scoring functions.

    PubMed

    Liu, Jie; Wang, Renxiao

    2015-03-23

    Scoring functions are a class of computational methods widely applied in structure-based drug design for evaluating protein-ligand interactions. Dozens of scoring functions have been published since the early 1990s. In literature, scoring functions are typically classified as force-field-based, empirical, and knowledge-based. This classification scheme has been quoted for more than a decade and is still repeatedly quoted by some recent publications. Unfortunately, it does not reflect the recent progress in this field. Besides, the naming convention used for describing different types of scoring functions has been somewhat jumbled in literature, which could be confusing for newcomers to this field. Here, we express our viewpoint on an up-to-date classification scheme and appropriate naming convention for current scoring functions. We propose that they can be classified into physics-based methods, empirical scoring functions, knowledge-based potentials, and descriptor-based scoring functions. We also outline the major difference and connections between different categories of scoring functions. PMID:25647463

  4. Classification of current scoring functions.

    PubMed

    Liu, Jie; Wang, Renxiao

    2015-03-23

    Scoring functions are a class of computational methods widely applied in structure-based drug design for evaluating protein-ligand interactions. Dozens of scoring functions have been published since the early 1990s. In literature, scoring functions are typically classified as force-field-based, empirical, and knowledge-based. This classification scheme has been quoted for more than a decade and is still repeatedly quoted by some recent publications. Unfortunately, it does not reflect the recent progress in this field. Besides, the naming convention used for describing different types of scoring functions has been somewhat jumbled in literature, which could be confusing for newcomers to this field. Here, we express our viewpoint on an up-to-date classification scheme and appropriate naming convention for current scoring functions. We propose that they can be classified into physics-based methods, empirical scoring functions, knowledge-based potentials, and descriptor-based scoring functions. We also outline the major difference and connections between different categories of scoring functions.

  5. Baseline adjustment increases accurate interpretation of posturographic sway scores.

    PubMed

    Tietäväinen, A; Corander, J; Hæggström, E

    2015-09-01

    Postural steadiness may be quantified using posturographic sway measures. These measures are commonly used to differentiate between a person's baseline balance and balance related to some physiological condition. However, the difference in sway scores between the two conditions may be difficult to detect due to large inter-subject variation. We compared detection accuracy provided by three models that linearly regress a sway measure (mean distance, velocity, or frequency) on the effect of eye closure on balance (eyes open (EO) vs. eyes closed (EC)). In Model 1 the dependent variable is a single sway score (EO or EC), whereas in Models 2 and 3 it is a change score (EO-EO or EC-EO). The independent variable is always the group (group=0: EO or group=1: EC). Model 3 also accounts for the regression to the mean effect (RTM), by considering the baseline value (EO) as a covariate. When differentiating between EO and EC conditions, 94% accuracy can be achieved when using mean velocity as sway measure and either Model 2 or 3. Thus by adjusting for baseline score one increases the accurate interpretation of posturographic sway scores.

  6. Accurate density functional thermochemistry for larger molecules.

    SciTech Connect

    Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.

    1997-06-20

    Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).

  7. Threshold adjusted calcium scoring using CT is less susceptible to cardiac motion and more accurate.

    PubMed

    Groen, J M; Dijkstra, H; Greuter, M J W; Oudkerk, M

    2009-02-01

    The purpose of this paper is to investigate calcium scoring on computed tomography (CT) using an adjusted threshold depending on the maximum Hounsfield value within the calcification (HU(peak)). The volume of 19 calcifications was retrospectively determined on 64-slice multidetector CT and dual source CT (DSCT) at different thresholds and the threshold associated with the physical volume was determined. In addition, approximately 10 000 computer simulations were done simulating the same process for calcifications with mixed density. Using these data a relation between the HU(peak) and the threshold could be established. Hereafter, this relation was assessed by scanning six calcifications in a phantom at 40-110 beats per minute using DSCT. The influence of motion was determined and the measured calcium scores were compared to the physical volumes and mass. A positive linear correlation was found between the scoring threshold and the HU(peak) of the calcifications both for the phantom measurements as for the computer simulations. Using this relation the individual threshold for each calcification could be calculated. Calcium scores of the moving calcifications determined with an adjusted threshold were approximately 30% less susceptible to cardiac motion compared to standard calcium scoring. Furthermore, these scores approximated the physical volume and mass at least 10% better than the standard calcium scores. The threshold in calcium scoring should be adjusted for each individual calcification based on the HU(peak) of the calcification. Calcium scoring using an adjusted threshold is less susceptible to cardiac motion and more accurate compared to the physical values. PMID:19291982

  8. Missing gene identification using functional coherence scores

    PubMed Central

    Chitale, Meghana; Khan, Ishita K.; Kihara, Daisuke

    2016-01-01

    Reconstructing metabolic and signaling pathways is an effective way of interpreting a genome sequence. A challenge in a pathway reconstruction is that often genes in a pathway cannot be easily found, reflecting current imperfect information of the target organism. In this work, we developed a new method for finding missing genes, which integrates multiple features, including gene expression, phylogenetic profile, and function association scores. Particularly, for considering function association between candidate genes and neighboring proteins to the target missing gene in the network, we used Co-occurrence Association Score (CAS) and PubMed Association Score (PAS), which are designed for capturing functional coherence of proteins. We showed that adding CAS and PAS substantially improve the accuracy of identifying missing genes in the yeast enzyme-enzyme network compared to the cases when only the conventional features, gene expression, phylogenetic profile, were used. Finally, it was also demonstrated that the accuracy improves by considering indirect neighbors to the target enzyme position in the network using a proper network-topology-based weighting scheme. PMID:27552989

  9. Chain functions and scoring functions in genetic networks.

    PubMed

    Gat-Viks, I; Shamir, R

    2003-01-01

    One of the grand challenges of system biology is to reconstruct the network of regulatory control among genes and proteins. High throughput data, particularly from expression experiments, may gradually make this possible in the future. Here we address two key ingredients in any such 'reverse engineering' effort: The choice of a biologically relevant, yet restricted, set of potential regulation functions, and the appropriate score to evaluate candidate regulatory relations. We propose a set of regulation functions which we call chain functions, and argue for their ubiquity in biological networks. We analyze their complexity and show that their number is exponentially smaller than all boolean functions of the same dimension. We define two new scores: one evaluating the fitness of a candidate set of regulators of a particular gene, and the other evaluating a candidate function. Both scores use established statistical methods. Finally, we test our methods on experimental gene expression data from the yeast galactose pathway. We show the utility of using chain functions and the improved inference using our scores in comparison to several extant scores. We demonstrate that the combined use of the two scores gives an extra advantage. We expect both chain functions and the new scores to be helpful in future attempts to infer regulatory networks. PMID:12855446

  10. Scoring function to predict solubility mutagenesis

    PubMed Central

    2010-01-01

    Background Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to mutations. The scoring function captures both sequence and structure information. By exploring the literature, we have assembled a substantial database of 137 single- and multiple-point solubility mutations. Our database is the largest such collection with structural information known so far. We optimize the scoring function using linear programming (LP) methods to derive its weights based on training. Starting with default values of 1, we find weights in the range [0,2] so that predictions of increase or decrease in solubility are optimized. We compare the LP method to the standard machine learning techniques of support vector machines (SVM) and the Lasso. Using statistics for leave-one-out (LOO), 10-fold, and 3-fold cross validations (CV) for training and prediction, we demonstrate that the LP method performs the best overall. For the LOOCV, the LP method has an overall accuracy of 81%. Availability Executables of programs, tables of weights, and datasets of mutants are available from the following web page: http://www.wsu.edu/~kbala/OptSolMut.html. PMID:20929563

  11. Accurate scoring of non-uniform sampling schemes for quantitative NMR

    PubMed Central

    Aoto, Phillip C.; Fenwick, R. Bryn; Kroon, Gerard J. A.; Wright, Peter E.

    2014-01-01

    Non-uniform sampling (NUS) in NMR spectroscopy is a recognized and powerful tool to minimize acquisition time. Recent advances in reconstruction methodologies are paving the way for the use of NUS in quantitative applications, where accurate measurement of peak intensities is crucial. The presence or absence of NUS artifacts in reconstructed spectra ultimately determines the success of NUS in quantitative NMR. The quality of reconstructed spectra from NUS acquired data is dependent upon the quality of the sampling scheme. Here we demonstrate that the best performing sampling schemes make up a very small percentage of the total randomly generated schemes. A scoring method is found to accurately predict the quantitative similarity between reconstructed NUS spectra and those of fully sampled spectra. We present an easy-to-use protocol to batch generate and rank optimal Poisson-gap NUS schedules for use with 2D NMR with minimized noise and accurate signal reproduction, without the need for the creation of synthetic spectra. PMID:25063954

  12. Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening

    PubMed Central

    Villarreal, Marcos A.

    2016-01-01

    Autodock Vina is a very popular, and highly cited, open source docking program. Here we present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based on Vina, and was trained through a novel approach, on state of the art datasets. We show that the traditional approach to train empirical scoring functions, using linear regression to optimize the correlation of predicted and experimental binding affinities, does not result in a function with optimal docking capabilities. On the other hand, a combination of scoring, minimization, and re-docking on carefully curated training datasets allowed us to develop a simplified scoring function with optimum docking performance. This article provides an overview of the development of the Vinardo scoring function, highlights its differences with Vina, and compares the performance of the two scoring functions in scoring, docking and virtual screening applications. Vinardo outperforms Vina in all tests performed, for all datasets analyzed. The Vinardo scoring function is available as an option within Smina, a fork of Vina, which is freely available under the GNU Public License v2.0 from http://smina.sf.net. Precompiled binaries, source code, documentation and a tutorial for using Smina to run the Vinardo scoring function are available at the same address. PMID:27171006

  13. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  14. What's Normal? Accurately and Efficiently Assessing Menstrual Function.

    PubMed

    Takemoto, Darcie M; Beharry, Meera S

    2015-09-01

    Many young women are unsure of what constitutes normal menses. By asking focused questions, pediatric providers can quickly and accurately assess menstrual function and dispel anxiety and myths. In this article, we review signs and symptoms of normal versus pathologic menstrual functioning and provide suggestions to improve menstrual history taking.

  15. Are Medical Students Assigning Proper Global Assessment of Functioning Scores?

    ERIC Educational Resources Information Center

    Warsi, Mustafa K.; Sattar, S. Pirzada; Din, Amad U.; Petty, Frederick; Padala, Prasad R.

    2007-01-01

    Objective: This article seeks to determine whether medical students can estimate the appropriate score for the Global Assessment of Functioning (GAF) compared with psychiatry residents and staff psychiatrists. The authors hypothesized that medical students' estimations of GAF scores for patients in clinical vignettes would differ from those…

  16. Validity and Reliability of Scores Obtained on Multiple-Choice Questions: Why Functioning Distractors Matter

    ERIC Educational Resources Information Center

    Ali, Syed Haris; Carr, Patrick A.; Ruit, Kenneth G.

    2016-01-01

    Plausible distractors are important for accurate measurement of knowledge via multiple-choice questions (MCQs). This study demonstrates the impact of higher distractor functioning on validity and reliability of scores obtained on MCQs. Freeresponse (FR) and MCQ versions of a neurohistology practice exam were given to four cohorts of Year 1 medical…

  17. Drug efficiency indices for improvement of molecular docking scoring functions.

    PubMed

    García-Sosa, Alfonso T; Hetényi, Csaba; Maran, Uko

    2010-01-15

    A dataset of protein-drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as DeltaG/W (Wiener index), DeltaG/NoC (number of carbons), and DeltaG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening.

  18. Evaluation of molecular docking using polynomial empirical scoring functions.

    PubMed

    Dias, Raquel; Timmers, Luis Fernando Saraiva Macedo; Caceres, Rafael Andrade; de Azevedo, Walter Filgueira

    2008-12-01

    Molecular docking simulations are of pivotal importance for analysis of protein-ligand interactions and also an essential resource for virtual-screening initiatives. In molecular docking simulations several possible docked structures are generated, which create an ensemble of structures representing binary complexes. Therefore, it is crucial to find the best solution for the simulation. One approach to this problem is to employ empirical scoring function to identify the best docked structure. It is expected that scoring functions show a descriptive funnel-shaped energy surface without many false minima to impair the efficiency of conformational sampling. We employed this methodology against a test set with 300 docked structures. Docking simulations of these ligands against enzyme binding pocket indicated a funnel-shaped behavior of the complexation for this system. This review compares a set of recently proposed polynomial empirical scoring functions, implemented in a program called POLSCORE, with two popular scoring function programs (XSCORE and DrugScore). Overall comparison indicated that POLSCORE works better to predict the correct docked position, for the ensemble of docked structures analyzed in the present work.

  19. Force fields and scoring functions for carbohydrate simulation.

    PubMed

    Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

    2015-01-12

    Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design.

  20. Functional movement screen scores in a group of running athletes.

    PubMed

    Loudon, Janice K; Parkerson-Mitchell, Amy J; Hildebrand, Laurie D; Teague, Connie

    2014-04-01

    The purpose of this study was to determine the mean values of the functional movement screen (FMS) in a group of long-distance runners. The secondary aims were to investigate whether the FMS performance differed between sexes and between young and older runners. Forty-three runners, 16 women (mean age = 33.5 years, height = 165.2 cm, weight = 56.3 kg, and body mass index [BMI] = 20.6) and 27 men (mean age = 39.3 years, height = 177.6 cm, weight = 75.8 kg, and BMI = 24.2) performed the FMS. All the runners were injury-free and ran >30 km·wk. Independent t-tests were performed on the composite scores to examine the differences between men and women and also between young (<40 years) and older runners (>40 years). Contingency tables (2 × 2) were developed for each of the 7 screening tests to further look at the differences in groups for each single test. The χ values were calculated to determine significant differences. Statistical significance was set at p ≤ 0.05. There was no significant difference in the composite score between women and men. There were significant differences between the sexes in the push-up and straight leg test scores, with the women scoring better on each test. A significant difference was found in the composite scores between younger and older runners (p < 0.000). Additional score differences were found for the squat, hurdle step, and in-line lunge tests with the younger runners scoring better. This study provided mean values for the FMS in a cohort of long-distance runners. These values can be used as a reference for comparing FMST scores in other runners who are screened with this tool.

  1. A new scoring function for top-down spectral deconvolution

    DOE PAGES

    Kou, Qiang; Wu, Si; Liu, Xiaowen

    2014-12-18

    Background: Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results: In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showedmore » that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions: L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.« less

  2. A new scoring function for top-down spectral deconvolution

    SciTech Connect

    Kou, Qiang; Wu, Si; Liu, Xiaowen

    2014-12-18

    Background: Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results: In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showed that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions: L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.

  3. Optimizing an emperical scoring function for transmembrane protein structure determination.

    SciTech Connect

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson

    2003-10-01

    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  4. RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics.

    PubMed

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2010-11-16

    Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic E-value reported by any method into the textbook-defined E-value, which may serve as the universal statistical standard. This protocol, although robust, may lose spectrum-specific statistics and might require a new calibration when changes in experimental setup occur. To mitigate these issues, we developed a new MS/MS search tool, RAId_aPS, that is able to provide spectrum-specific-values for additive scoring functions. Given a selection of scoring functions out of RAId score, K-score, Hyperscore and XCorr, RAId_aPS generates the corresponding score histograms of all possible peptides using dynamic programming. Using these score histograms to assign E-values enables a calibration-free protocol for accurate significance assignment for each scoring function. RAId_aPS features four different modes: (i) compute the total number of possible peptides for a given molecular mass range, (ii) generate the score histogram given a MS/MS spectrum and a scoring function, (iii) reassign E-values for a list of candidate peptides given a MS/MS spectrum and the scoring functions chosen, and (iv) perform database searches using selected scoring functions. In modes (iii) and (iv), RAId_aPS is also capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page.

  5. Accurate ionization potential of semiconductors from efficient density functional calculations

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2016-07-01

    Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.

  6. Deep Learning for Cerebellar Ataxia Classification and Functional Score Regression

    PubMed Central

    Yang, Zhen; Zhong, Shenghua; Carass, Aaron; Ying, Sarah H.; Prince, Jerry L.

    2014-01-01

    Cerebellar ataxia is a progressive neuro-degenerative disease that has multiple genetic versions, each with a characteristic pattern of anatomical degeneration that yields distinctive motor and cognitive problems. Studying this pattern of degeneration can help with the diagnosis of disease subtypes, evaluation of disease stage, and treatment planning. In this work, we propose a learning framework using MR image data for discriminating a set of cerebellar ataxia types and predicting a disease related functional score. We address the difficulty in analyzing high-dimensional image data with limited training subjects by: 1) training weak classifiers/regressors on a set of image subdomains separately, and combining the weak classifier/regressor outputs to make the decision; 2) perturbing the image subdomain to increase the training samples; 3) using a deep learning technique called the stacked auto-encoder to develop highly representative feature vectors of the input data. Experiments show that our approach can reliably classify between one of four categories (healthy control and three types of ataxia), and predict the functional staging score for ataxia. PMID:25553339

  7. Reformulating the entropic contribution in molecular docking scoring functions.

    PubMed

    Procacci, Piero

    2016-07-15

    We have derived, in the context of the Rigid Rotor Harmonic Approximation (RRHO), a general mass and Planck's constant h independent expression for the dissociation free energy in ligand-receptor systems, featuring a systematically (anti-binding) additive negative entropic term depending on readily available ligand-receptor quantities. The proposed RRHO expression allows to straightforwardly compute the absolute standard dissociation free energy without resorting to expensive normal mode analysis or other dynamical matrix-based techniques for evaluating the entropic contribution, hence providing an effective scoring function for assessing docking poses with no adjustable parameters. Our RRHO formula was tested on a set of 55 ligand-receptor systems obtaining correlation coefficients and unsigned mean errors comparable to or better than those obtained with computationally demanding techniques for the dissociation entropy assessment. The proposed compact reformulation of the RRHO entropy term could constitute the basis for new and more effective scoring functions in molecular docking-based high-throughput virtual screening for drug discovery. © 2016 Wiley Periodicals, Inc. PMID:27231844

  8. On the Variance of the Optimal Alignments Score for Binary Random Words and an Asymmetric Scoring Function

    NASA Astrophysics Data System (ADS)

    Houdré, Christian; Matzinger, Heinrich

    2016-08-01

    We investigate the order of the variance of the optimal alignments (OA) score of two independent iid binary random words having the same length. The letters are equiprobable, but the scoring function is such that one letter has a larger score than the other. In this setting, we prove that the order of variance is linear in the common length. OAs constitute a generalization of longest common subsequences, they can be represented as optimal paths in a two-dimensional last passage percolation setting with dependent weights.

  9. Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

    PubMed Central

    Yan, Zhiqiang; Wang, Jin

    2013-01-01

    Protein-nucleic acid (protein-DNA and protein-RNA) recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions) for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions. PMID:24098651

  10. Prognostic models and risk scores: can we accurately predict postoperative nausea and vomiting in children after craniotomy?

    PubMed

    Neufeld, Susan M; Newburn-Cook, Christine V; Drummond, Jane E

    2008-10-01

    Postoperative nausea and vomiting (PONV) is a problem for many children after craniotomy. Prognostic models and risk scores help identify who is at risk for an adverse event such as PONV to help guide clinical care. The purpose of this article is to assess whether an existing prognostic model or risk score can predict PONV in children after craniotomy. The concepts of transportability, calibration, and discrimination are presented to identify what is required to have a valid tool for clinical use. Although previous work may inform clinical practice and guide future research, existing prognostic models and risk scores do not appear to be options for predicting PONV in children undergoing craniotomy. However, until risk factors are further delineated, followed by the development and validation of prognostic models and risk scores that include children after craniotomy, clinical judgment in the context of current research may serve as a guide for clinical care in this population. PMID:18939320

  11. Exponentially accurate approximations to piece-wise smooth periodic functions

    NASA Technical Reports Server (NTRS)

    Greer, James; Banerjee, Saheb

    1995-01-01

    A family of simple, periodic basis functions with 'built-in' discontinuities are introduced, and their properties are analyzed and discussed. Some of their potential usefulness is illustrated in conjunction with the Fourier series representations of functions with discontinuities. In particular, it is demonstrated how they can be used to construct a sequence of approximations which converges exponentially in the maximum norm to a piece-wise smooth function. The theory is illustrated with several examples and the results are discussed in the context of other sequences of functions which can be used to approximate discontinuous functions.

  12. Survival outcomes scores (SOFT, BAR, and Pedi-SOFT) are accurate in predicting post-liver transplant survival in adolescents.

    PubMed

    Conjeevaram Selvakumar, Praveen Kumar; Maksimak, Brian; Hanouneh, Ibrahim; Youssef, Dalia H; Lopez, Rocio; Alkhouri, Naim

    2016-09-01

    SOFT and BAR scores utilize recipient, donor, and graft factors to predict the 3-month survival after LT in adults (≥18 years). Recently, Pedi-SOFT score was developed to predict 3-month survival after LT in young children (≤12 years). These scoring systems have not been studied in adolescent patients (13-17 years). We evaluated the accuracy of these scoring systems in predicting the 3-month post-LT survival in adolescents through a retrospective analysis of data from UNOS of patients aged 13-17 years who received LT between 03/01/2002 and 12/31/2012. Recipients of combined organ transplants, donation after cardiac death, or living donor graft were excluded. A total of 711 adolescent LT recipients were included with a mean age of 15.2±1.4 years. A total of 100 patients died post-LT including 33 within 3 months. SOFT, BAR, and Pedi-SOFT scores were all found to be good predictors of 3-month post-transplant survival outcome with areas under the ROC curve of 0.81, 0.80, and 0.81, respectively. All three scores provided good accuracy for predicting 3-month survival post-LT in adolescents and may help clinical decision making to optimize survival rate and organ utilization. PMID:27478012

  13. Accurate estimators of correlation functions in Fourier space

    NASA Astrophysics Data System (ADS)

    Sefusatti, E.; Crocce, M.; Scoccimarro, R.; Couchman, H. M. P.

    2016-08-01

    Efficient estimators of Fourier-space statistics for large number of objects rely on fast Fourier transforms (FFTs), which are affected by aliasing from unresolved small-scale modes due to the finite FFT grid. Aliasing takes the form of a sum over images, each of them corresponding to the Fourier content displaced by increasing multiples of the sampling frequency of the grid. These spurious contributions limit the accuracy in the estimation of Fourier-space statistics, and are typically ameliorated by simultaneously increasing grid size and discarding high-frequency modes. This results in inefficient estimates for e.g. the power spectrum when desired systematic biases are well under per cent level. We show that using interlaced grids removes odd images, which include the dominant contribution to aliasing. In addition, we discuss the choice of interpolation kernel used to define density perturbations on the FFT grid and demonstrate that using higher order interpolation kernels than the standard Cloud-In-Cell algorithm results in significant reduction of the remaining images. We show that combining fourth-order interpolation with interlacing gives very accurate Fourier amplitudes and phases of density perturbations. This results in power spectrum and bispectrum estimates that have systematic biases below 0.01 per cent all the way to the Nyquist frequency of the grid, thus maximizing the use of unbiased Fourier coefficients for a given grid size and greatly reducing systematics for applications to large cosmological data sets.

  14. Functional group based Ligand binding affinity scoring function at atomic environmental level

    PubMed Central

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2009-01-01

    Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure. PMID:19255647

  15. Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions.

    PubMed

    Pencheva, Tania; Soumana, Oumarou Samna; Pajeva, Ilza; Miteva, Maria A

    2010-06-01

    Most of the benchmark studies on docking-scoring methods reported in the last decade conclude that no single scoring function performs well across different protein targets. In this study a comparison of thirteen commonly used force field and empirical scoring functions as implemented in DOCK, AMMOS, X-Score and FRED is carried out on five proteins with diverse binding pockets. The performance is analyzed in relation to the physicochemical properties of the binding sites. The solvation effects are considered via the Generalized Born/Surface Area (GBSA) solvation method for one of the assessed scoring functions. We examined the ability of these scoring functions to discriminate between active and inactive compounds over receptor-based focused libraries. Our results demonstrated that the employed here empirical scoring functions were more appropriate for the pocket of predominant hydrophobic nature while the force field scoring functions performed better on the mixed or polar pockets.

  16. A New Scoring Function for Molecular Docking Based on AutoDock and AutoDock Vina.

    PubMed

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2015-01-01

    Molecular docking of small molecules in the protein binding sites is the most widely used computational technique in modern structure-based drug discovery. Although accurate prediction of binding modes of small molecules can be achieved in most cases, estimation of their binding affinities remains mediocre at best. As an attempt to improve the correlation between the inhibitory constants, pKi, and scoring, we created a new, hybrid scoring function. The new function is a linear combination of the terms of the scoring functions of AutoDock and AutoDock Vina. It was trained on 2,412 protein-ligand complexes from the PDBbind database (www.pdbbind.org.cn, version 2012) and validated on a set of 313 complexes released in the 2013 version as a test set. The new function was included in a modified version of AutoDock. The hybrid scoring function showed a statistically significant improvement in both training and test sets in terms of correlation with and root mean square and mean absolute errors in prediction of pKi values. It was also tested on the CSAR 2014 Benchmark Exercise dataset (team T) and produced reasonably good results.

  17. A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions.

    PubMed

    Yang, Zhuo; Liu, Yingtao; Chen, Zhaoqiang; Xu, Zhijian; Shi, Jiye; Chen, Kaixian; Zhu, Weiliang

    2015-06-01

    A quantum mechanics-based scoring function for halogen bonding interaction, namely XBScore(QM), is developed based on 18,135 sets of geometrical and energetical parameters optimized at M06-2X/aug-cc-pVDZ level. Applying the function on typical halogen bonding systems from Protein Data Bank demonstrates its strong ability of predicting halogen bonding as attractive interaction with strength up to -4 kcal mol(-1). With a diverse set of proteins complexed with halogenated ligands, a systematic evaluation demonstrates the integrative advantage of XBScore(QM) over 12 other scoring functions on halogen bonding in four aspects, viz. pseudo docking power, ranking power, scoring power, and genuine docking power. Thus, this study not only provides a practicable scoring function of halogen bonding for high throughput virtual screening, but also serves as a benchmark for evaluating the performance of current scoring functions on characterizing halogen bonding.

  18. PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements

    PubMed Central

    Tang, Yat T.; Marshall, Garland R.

    2011-01-01

    Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r2pred) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind “refined set” (n = 1612) resulted in a Pearson correlation coefficient (Rp) of 0.575 and a mean error (ME) of 1.41 pKd. Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable

  19. IQ Scores among Homeless Older Adolescents: Characteristics of Intellectual Performance and Associations with Psychosocial Functioning.

    ERIC Educational Resources Information Center

    Rohde, Paul; Noell, John; Ochs, Linda

    1999-01-01

    Study showed IQ scores of homeless adolescents (N=50) were comparable to population means, and unrelated to the duration of homelessness. Higher scores were significantly correlated with only a minority of the measures of psychosocial functioning, including less self-reported depression, lower reported delinquency, and less self-control in…

  20. dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.

    PubMed

    Spiliotopoulos, Dimitrios; Kastritis, Panagiotis L; Melquiond, Adrien S J; Bonvin, Alexandre M J J; Musco, Giovanna; Rocchia, Walter; Spitaleri, Andrea

    2016-01-01

    Molecular-docking programs coupled with suitable scoring functions are now established and very useful tools enabling computational chemists to rapidly screen large chemical databases and thereby to identify promising candidate compounds for further experimental processing. In a broader scenario, predicting binding affinity is one of the most critical and challenging components of computer-aided structure-based drug design. The development of a molecular docking scoring function which in principle could combine both features, namely ranking putative poses and predicting complex affinity, would be of paramount importance. Here, we systematically investigated the performance of the MM-PBSA approach, using two different Poisson-Boltzmann solvers (APBS and DelPhi), in the currently rising field of protein-peptide interactions (PPIs), identifying the correct binding conformations of 19 different protein-peptide complexes and predicting their binding free energies. First, we scored the decoy structures from HADDOCK calculation via the MM-PBSA approach in order to assess the capability of retrieving near-native poses in the best-scoring clusters and of evaluating the corresponding free energies of binding. MM-PBSA behaves well in finding the poses corresponding to the lowest binding free energy, however the built-in HADDOCK score shows a better performance. In order to improve the MM-PBSA-based scoring function, we dampened the MM-PBSA solvation and coulombic terms by 0.2, as proposed in the HADDOCK score and LIE approaches. The new dampened MM-PBSA (dMM-PBSA) outperforms the original MM-PBSA and ranks the decoys structures as the HADDOCK score does. Second, we found a good correlation between the dMM-PBSA and HADDOCK scores for the near-native clusters of each system and the experimental binding energies, respectively. Therefore, we propose a new scoring function, dMM-PBSA, to be used together with the built-in HADDOCK score in the context of protein-peptide docking

  1. dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

    PubMed Central

    Spiliotopoulos, Dimitrios; Kastritis, Panagiotis L.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.; Musco, Giovanna; Rocchia, Walter; Spitaleri, Andrea

    2016-01-01

    Molecular-docking programs coupled with suitable scoring functions are now established and very useful tools enabling computational chemists to rapidly screen large chemical databases and thereby to identify promising candidate compounds for further experimental processing. In a broader scenario, predicting binding affinity is one of the most critical and challenging components of computer-aided structure-based drug design. The development of a molecular docking scoring function which in principle could combine both features, namely ranking putative poses and predicting complex affinity, would be of paramount importance. Here, we systematically investigated the performance of the MM-PBSA approach, using two different Poisson–Boltzmann solvers (APBS and DelPhi), in the currently rising field of protein-peptide interactions (PPIs), identifying the correct binding conformations of 19 different protein-peptide complexes and predicting their binding free energies. First, we scored the decoy structures from HADDOCK calculation via the MM-PBSA approach in order to assess the capability of retrieving near-native poses in the best-scoring clusters and of evaluating the corresponding free energies of binding. MM-PBSA behaves well in finding the poses corresponding to the lowest binding free energy, however the built-in HADDOCK score shows a better performance. In order to improve the MM-PBSA-based scoring function, we dampened the MM-PBSA solvation and coulombic terms by 0.2, as proposed in the HADDOCK score and LIE approaches. The new dampened MM-PBSA (dMM-PBSA) outperforms the original MM-PBSA and ranks the decoys structures as the HADDOCK score does. Second, we found a good correlation between the dMM-PBSA and HADDOCK scores for the near-native clusters of each system and the experimental binding energies, respectively. Therefore, we propose a new scoring function, dMM-PBSA, to be used together with the built-in HADDOCK score in the context of protein-peptide docking

  2. dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

    PubMed Central

    Spiliotopoulos, Dimitrios; Kastritis, Panagiotis L.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.; Musco, Giovanna; Rocchia, Walter; Spitaleri, Andrea

    2016-01-01

    Molecular-docking programs coupled with suitable scoring functions are now established and very useful tools enabling computational chemists to rapidly screen large chemical databases and thereby to identify promising candidate compounds for further experimental processing. In a broader scenario, predicting binding affinity is one of the most critical and challenging components of computer-aided structure-based drug design. The development of a molecular docking scoring function which in principle could combine both features, namely ranking putative poses and predicting complex affinity, would be of paramount importance. Here, we systematically investigated the performance of the MM-PBSA approach, using two different Poisson–Boltzmann solvers (APBS and DelPhi), in the currently rising field of protein-peptide interactions (PPIs), identifying the correct binding conformations of 19 different protein-peptide complexes and predicting their binding free energies. First, we scored the decoy structures from HADDOCK calculation via the MM-PBSA approach in order to assess the capability of retrieving near-native poses in the best-scoring clusters and of evaluating the corresponding free energies of binding. MM-PBSA behaves well in finding the poses corresponding to the lowest binding free energy, however the built-in HADDOCK score shows a better performance. In order to improve the MM-PBSA-based scoring function, we dampened the MM-PBSA solvation and coulombic terms by 0.2, as proposed in the HADDOCK score and LIE approaches. The new dampened MM-PBSA (dMM-PBSA) outperforms the original MM-PBSA and ranks the decoys structures as the HADDOCK score does. Second, we found a good correlation between the dMM-PBSA and HADDOCK scores for the near-native clusters of each system and the experimental binding energies, respectively. Therefore, we propose a new scoring function, dMM-PBSA, to be used together with the built-in HADDOCK score in the context of protein-peptide docking

  3. A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina.

    PubMed

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2016-04-01

    Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock.

  4. Evaluation of ligand-binding affinity using polynomial empirical scoring functions.

    PubMed

    de Azevedo, Walter Filgueira; Dias, Raquel

    2008-10-15

    Assessing protein-ligand interaction is of great importance for virtual screening initiatives in order to discover new drugs. The present work describes a set of empirical scoring functions to assess the binding affinity, involving terms for intermolecular hydrogen bonds and contact surface. The results show that our methodology works better to predict protein-ligand affinity when compared with XSCORE, a popular empirical scoring function.

  5. Global optimum protein threading with gapped alignment and empirical pair score functions.

    PubMed

    Lathrop, R H; Smith, T F

    1996-02-01

    We describe a branch-and-bound search algorithm for finding the exact global optimum gapped sequence-structure alignment ("threading") between a protein sequence and a protein core or structural model, using an arbitrary amino acid pair score function (e.g. contact potentials, knowledge-based potentials, potentials of mean force, etc.). The search method imposes minimal conditions on how structural environments are defined or the form of the score function, and allows arbitrary sequence-specific functions for scoring loops and active site residues. Consequently the search method can be used with many different score functions and threading methodologies; this paper illustrates five from the literature. On a desktop workstation running LISP, we have found the global optimum protein sequence-structure alignment in NP-hard search spaces as large as 9.6 x 10(31), at rates ranging as high as 6.8 x 10(28) equivalent threadings per second (most of which are pruned before they ever are examined explicitly). Continuing the procedure past the global optimum enumerates successive candidate threadings in monotonically increasing score order. We give efficient algorithms for search space size, uniform random sampling, segment placement probabilities, mean, standard deviation and partition function. The method should prove useful for structure prediction, as well as for critical evaluation of new pair score functions. PMID:8568903

  6. Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry

    NASA Astrophysics Data System (ADS)

    Tao, Jianmin; Mo, Yuxiang

    2016-08-01

    Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

  7. Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

    PubMed

    Tao, Jianmin; Mo, Yuxiang

    2016-08-12

    Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

  8. Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

    PubMed

    Tao, Jianmin; Mo, Yuxiang

    2016-08-12

    Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals. PMID:27563956

  9. Accurate FDTD modelling for dispersive media using rational function and particle swarm optimisation

    NASA Astrophysics Data System (ADS)

    Chung, Haejun; Ha, Sang-Gyu; Choi, Jaehoon; Jung, Kyung-Young

    2015-07-01

    This article presents an accurate finite-difference time domain (FDTD) dispersive modelling suitable for complex dispersive media. A quadratic complex rational function (QCRF) is used to characterise their dispersive relations. To obtain accurate coefficients of QCRF, in this work, we use an analytical approach and a particle swarm optimisation (PSO) simultaneously. In specific, an analytical approach is used to obtain the QCRF matrix-solving equation and PSO is applied to adjust a weighting function of this equation. Numerical examples are used to illustrate the validity of the proposed FDTD dispersion model.

  10. More accurate fitting of {sup 125}I and {sup 103}Pd radial dose functions

    SciTech Connect

    Taylor, R. E. P.; Rogers, D. W. O.

    2008-09-15

    In this study an improved functional form for fitting the radial dose functions, g(r), of {sup 125}I and {sup 103}Pd brachytherapy seeds is presented. The new function is capable of accurately fitting radial dose functions over ranges as large as 0.05 cm{<=}r{<=}10 cm for {sup 125}I seeds and 0.10 cm{<=}r{<=}10 cm for {sup 103}Pd seeds. The average discrepancies between fit and calculated data are less than 0.5% over the full range of fit and maximum discrepancies are 2% or less. The fitting function is also capable of accounting for the sharp increase in g(r) (upturn) seen for some sources for r<0.1 cm. This upturn has previously been attributed to the breakdown of the approximation of the sources as a line, however, in this study we demonstrate that another contributing factor is the 4.5 keV characteristic x-rays emitted from the Ti seed casing. Radial dose functions are calculated for 18 {sup 125}I seeds and 9 {sup 103}Pd seeds using the EGSnrc Monte Carlo user-code BrachyDose. Fitting coefficients of the new function are tabulated for all 27 seeds. Extrapolation characteristics of the function are also investigated. The new functional form is an improvement over currently used fitting functions with its main strength being the ability to accurately fit the rapidly varying radial dose function at small distances. The new function is an excellent candidate for fitting the radial dose function of all {sup 103}Pd and {sup 125}I brachytherapy seeds and will increase the accuracy of dose distributions calculated around brachytherapy seeds using the TG-43 protocol over a wider range of data. More accurate values of g(r) for r<0.5 cm may be particularly important in the treatment of ocular melanoma.

  11. Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.

    PubMed

    Sharma, Ashok K; Gupta, Ankit; Kumar, Sanjiv; Dhakan, Darshan B; Sharma, Vineet K

    2015-07-01

    Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annotate and classify proteins are extremely slow. Therefore, to achieve faster and accurate functional annotation, we have developed an orthology-based functional classifier 'Woods' by using a combination of machine learning and similarity-based approaches. Woods displayed a precision of 98.79% on independent genomic dataset, 96.66% on simulated metagenomic dataset and >97% on two real metagenomic datasets. In addition, it performed >87 times faster than BLAST on the two real metagenomic datasets. Woods can be used as a highly efficient and accurate classifier with high-throughput capability which facilitates its usability on large metagenomic datasets. PMID:25863333

  12. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  13. A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry

    PubMed Central

    Hong, Sun Pyo; Ji, Seung Il; Rhee, Hwanseok; Shin, Soo Kyeong; Hwang, Sun Young; Lee, Seung Hwan; Lee, Soong Deok; Oh, Heung-Bum; Yoo, Wangdon; Kim, Soo-Ok

    2008-01-01

    Background We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate, and high-throughput manner. The assay is based on polymerase chain reaction (PCR) amplification and mass measurement of oligonucleotides containing a polymorphic base, to which a typeIIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products leads to excision of oligonucleotide fragments representing base variation of the polymorphic site whose masses were determined by MALDI-TOF MS. Results The assay represents an improvement over previous methods because it relies on the direct mass determination of PCR products rather than on an indirect analysis, where a base-extended or fluorescent report tag is interpreted. The RFMP strategy is simple and straightforward, requiring one restriction digestion reaction following target amplification in a single vessel. With this technology, genotypes are generated with a high call rate (99.6%) and high accuracy (99.8%) as determined by independent sequencing. Conclusion The simplicity, accuracy and amenability to high-throughput screening analysis should make the RFMP assay suitable for large-scale genotype association study as well as clinical genotyping in laboratories. PMID:18538037

  14. Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

    PubMed

    Liebeschuetz, John W; Cole, Jason C; Korb, Oliver

    2012-06-01

    The performance of all four GOLD scoring functions has been evaluated for pose prediction and virtual screening under the standardized conditions of the comparative docking and scoring experiment reported in this Edition. Excellent pose prediction and good virtual screening performance was demonstrated using unmodified protein models and default parameter settings. The best performing scoring function for both pose prediction and virtual screening was demonstrated to be the recently introduced scoring function ChemPLP. We conclude that existing docking programs already perform close to optimally in the cognate pose prediction experiments currently carried out and that more stringent pose prediction tests should be used in the future. These should employ cross-docking sets. Evaluation of virtual screening performance remains problematic and much remains to be done to improve the usefulness of publically available active and decoy sets for virtual screening. Finally we suggest that, for certain target/scoring function combinations, good enrichment may sometimes be a consequence of 2D property recognition rather than a modelling of the correct 3D interactions.

  15. Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

    PubMed

    Liebeschuetz, John W; Cole, Jason C; Korb, Oliver

    2012-06-01

    The performance of all four GOLD scoring functions has been evaluated for pose prediction and virtual screening under the standardized conditions of the comparative docking and scoring experiment reported in this Edition. Excellent pose prediction and good virtual screening performance was demonstrated using unmodified protein models and default parameter settings. The best performing scoring function for both pose prediction and virtual screening was demonstrated to be the recently introduced scoring function ChemPLP. We conclude that existing docking programs already perform close to optimally in the cognate pose prediction experiments currently carried out and that more stringent pose prediction tests should be used in the future. These should employ cross-docking sets. Evaluation of virtual screening performance remains problematic and much remains to be done to improve the usefulness of publically available active and decoy sets for virtual screening. Finally we suggest that, for certain target/scoring function combinations, good enrichment may sometimes be a consequence of 2D property recognition rather than a modelling of the correct 3D interactions. PMID:22371207

  16. In Lumbar Fusion Patients, How Does Establishing a Comfort Function Goal Preoperatively Impact Postoperative Pain Scores?

    PubMed

    Hennessy, Winnie; Wagner, Elizabeth; Dumas, Bonnie P; Handley, Patricia

    2015-12-01

    The purpose of this feasibility study was to determine the impact of establishing a comfort function goal preoperatively on postoperative pain scores and opiate requirements in lumbar fusion patients. A comfort function goal is defined as the pain score identified by the patient describing the level of pain tolerance to participate in healing activities such as deep breathing, ambulation and participation in activities of daily living. The design was prospective, nonrandomized, intervention group (n = 30) compared with retrospective chart review as control group (n = 30). Sample included patients scheduled for routine lumbar fusion in an urban southeastern hospital. The study intervention established a comfort function goal during a routine preoperative patient education class. No significant difference in pain score or opiate requirement was found for these data. However, a fundamental clinical question arose surrounding opiate requirements and dosing management. In our hospital, the norm for postoperative pain management is to categorize pain scores as mild (1-3), moderate (4-6), and severe (7-10) pain. Physician orders commonly use this differential to order opiate dose ranges. In this sample, the mean pain score for the intervention group at home is 5.8 and the mean comfort function goal is 4.9. Based on normative categories of pain scores, if a patient's baseline of tolerable pain is 4.9, this has potential impact on clinician responses to managing pain, as 4.9-5.8 is, for this patient, perhaps a mild range of pain, not moderate. If a patient reports a pain score of 7, and their norm is 5.8, the delta is only 1.2. Does this imply that the patient is experiencing mild or severe pain? Does the nurse deliver a dose of pain medication that is in the mild or severe dose range? PMID:26293197

  17. Function-specific virtual screening for GPCR ligands using a combined scoring method

    PubMed Central

    Kooistra, Albert J.; Vischer, Henry F.; McNaught-Flores, Daniel; Leurs, Rob; de Esch, Iwan J. P.; de Graaf, Chris

    2016-01-01

    The ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H1 receptor (H1R) antagonists/inverse agonists, 2) the selective structure-based identification of ß2-adrenoceptor (ß2R) agonists, and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H1R and ß2R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß2R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß2R and 73% of the H1R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß2R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information. PMID:27339552

  18. Function-specific virtual screening for GPCR ligands using a combined scoring method.

    PubMed

    Kooistra, Albert J; Vischer, Henry F; McNaught-Flores, Daniel; Leurs, Rob; de Esch, Iwan J P; de Graaf, Chris

    2016-01-01

    The ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H1 receptor (H1R) antagonists/inverse agonists, 2) the selective structure-based identification of ß2-adrenoceptor (ß2R) agonists, and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H1R and ß2R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß2R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß2R and 73% of the H1R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß2R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information. PMID:27339552

  19. Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation

    PubMed Central

    Wu, Chia-Chou; Lin, Che

    2015-01-01

    The induction of stem cells toward a desired differentiation direction is required for the advancement of stem cell-based therapies. Despite successful demonstrations of the control of differentiation direction, the effective use of stem cell-based therapies suffers from a lack of systematic knowledge regarding the mechanisms underlying directed differentiation. Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. A proposed relevance score identified the essential components in the directed differentiation. Inspection of well-known proteins and functional modules in the directed differentiation showed the plausibility of the proposed relevance score, with the higher scores of several proteins and function modules indicating their essential roles in the directed differentiation. During the differentiation process, the proteins and functional modules with higher relevance scores also became more specific to the neuronal identity. Ultimately, the essential components revealed by the relevance scores may play a role in controlling the direction of differentiation. In addition, these components may serve as a starting point for understanding the systematic mechanisms of directed differentiation and for increasing the efficiency of stem cell-based therapies. PMID:25977693

  20. A machine learning based method to improve docking scoring functions and its application to drug repurposing

    PubMed Central

    Kinnings, Sarah L.; Liu, Nina; Tonge, Peter J.; Jackson, Richard M.; Xie, Lei; Bourne, Philip E.

    2011-01-01

    Docking scoring functions are notoriously weak predictors of binding affinity. They typically assign a common set of weights to the individual energy terms that contribute to the overall energy score, however, these weights should be gene family-dependent. In addition, they incorrectly assume that individual interactions contribute towards the total binding affinity in an additive manner. In reality, noncovalent interactions often depend on one another in a nonlinear manner. In this paper we show how the use of support vector machines (SVMs), trained by associating sets of individual energy terms retrieved from molecular docking with the known binding affinity of each compound from high-throughput screening experiments, can be used to improve the correlation between known binding affinities and those predicted by the docking program eHiTS. We construct two prediction models; a regression model trained using IC50 values from BindingDB, and a classification model trained using active and decoy compounds from the Directory of Useful Decoys (DUD). Moreover, to address the issue of overrepresentation of negative data in high-throughput screening data sets, we have designed a multiple-planar SVM training procedure for the classification model. The increased performance that both SVMs give when compared with the original eHiTS scoring function highlights the potential for using nonlinear methods when deriving overall energy scores from their individual components. We apply the above methodology to train a new scoring function for direct inhibitors of M.tuberculosis (M.tb) InhA. By combining ligand binding site comparison with the new scoring function, we propose that phosphodiesterase inhibitors can potentially be repurposed to target M.tb InhA. Our methodology may be applied to other gene families for which target structures and activity data are available, as demonstrated in the work presented here. PMID:21291174

  1. An accurate Fortran code for computing hydrogenic continuum wave functions at a wide range of parameters

    NASA Astrophysics Data System (ADS)

    Peng, Liang-You; Gong, Qihuang

    2010-12-01

    The accurate computations of hydrogenic continuum wave functions are very important in many branches of physics such as electron-atom collisions, cold atom physics, and atomic ionization in strong laser fields, etc. Although there already exist various algorithms and codes, most of them are only reliable in a certain ranges of parameters. In some practical applications, accurate continuum wave functions need to be calculated at extremely low energies, large radial distances and/or large angular momentum number. Here we provide such a code, which can generate accurate hydrogenic continuum wave functions and corresponding Coulomb phase shifts at a wide range of parameters. Without any essential restrict to angular momentum number, the present code is able to give reliable results at the electron energy range [10,10] eV for radial distances of [10,10] a.u. We also find the present code is very efficient, which should find numerous applications in many fields such as strong field physics. Program summaryProgram title: HContinuumGautchi Catalogue identifier: AEHD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1233 No. of bytes in distributed program, including test data, etc.: 7405 Distribution format: tar.gz Programming language: Fortran90 in fixed format Computer: AMD Processors Operating system: Linux RAM: 20 MBytes Classification: 2.7, 4.5 Nature of problem: The accurate computation of atomic continuum wave functions is very important in many research fields such as strong field physics and cold atom physics. Although there have already existed various algorithms and codes, most of them can only be applicable and reliable in a certain range of parameters. We present here an accurate FORTRAN program for

  2. Changes in functional movement screen scores over a season in collegiate soccer and volleyball athletes.

    PubMed

    Sprague, Peter A; Mokha, G Monique; Gatens, Dustin R

    2014-11-01

    Changes in many aspects of physical capacity and athletic performance have been documented through the course of a competitive season in collegiate athletes. Movement pattern quality as measured by the functional movement screen (FMS) has recently been linked to performance and injury risk. The purpose of this study was to document the changes in functional movement patterns over a competitive season. Fifty-seven National Collegiate Athletic Association Division II athletes were screened using the FMS as part of the pre and post participation examination for their competitive seasons in 2012. Composite and individual FMS test scores for the preseason and postseason were compared with identified significant changes. The scores were also analyzed for changes in the number of asymmetries present and the frequency of a score of 1 in any of the tests. There were no significant interactions in the main effects for time or sport in the composite FMS scores. However, 4 individual tests did show significant change. The deep squat (Z = -3.260, p = 0.001) and in-line lunge scores (Z = -3.498, p < 0.001) improved across all athletes, and the active straight leg raise (Z = -2.496, p = 0.013) and rotary stability scores (Z = -2.530, p = 0.011) worsened across all athletes. A reduction in the number of asymmetries (χ = 4.258, p = 0.039) and scores of 1 (χ = 26.148, p < 0.001) were also found. Changes in individual fundamental movement patterns occur through the course of a competitive season.

  3. Quantitative Structure-Property Relationship Modeling of Electronic Properties of Graphene Using Atomic Radial Distribution Function Scores.

    PubMed

    Fernandez, Michael; Shi, Hongqing; Barnard, Amanda S

    2015-12-28

    The intrinsic relationships between nanoscale features and electronic properties of nanomaterials remain poorly investigated. In this work, electronic properties of 622 computationally optimized graphene structures were mapped to their structures using partial-least-squares regression and radial distributions function (RDF) scores. Quantitative structure-property relationship (QSPR) models were calibrated with 70% of a virtual data set of 622 passivated and nonpassivated graphenes, and we predicted the properties of the remaining 30% of the structures. The analysis of the optimum QSPR models revealed that the most relevant RDF scores appear at interatomic distances in the range of 2.0 to 10.0 Å for the energy of the Fermi level and the electron affinity, while the electronic band gap and the ionization potential correlate to RDF scores in a wider range from 3.0 to 30.0 Å. The predictions were more accurate for the energy of the Fermi level and the ionization potential, with more than 83% of explained data variance, while the electron affinity exhibits a value of ∼80% and the energy of the band gap a lower 70%. QSPR models have tremendous potential to rapidly identify hypothetical nanomaterials with desired electronic properties that could be experimentally prepared in the near future.

  4. Logistic Discriminant Function Analysis for DIF Identification of Polytomously Scored Items.

    ERIC Educational Resources Information Center

    Miller, Timothy R.; Spray, Judith A.

    1993-01-01

    Presents logistic discriminant analysis as a means of detecting differential item functioning (DIF) in items that are polytomously scored. Provides examples of DIF detection using a 27-item mathematics test with 1,977 examinees. The proposed method is simpler and more practical than polytomous extensions of the logistic regression DIF procedure.…

  5. Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics

    PubMed Central

    Zhang, Ying; Xu, Xin; Goddard, William A.

    2009-01-01

    We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling–Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn–Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size. PMID:19276116

  6. WAIS-IV reliable digit span is no more accurate than age corrected scaled score as an indicator of invalid performance in a veteran sample undergoing evaluation for mTBI.

    PubMed

    Spencer, Robert J; Axelrod, Bradley N; Drag, Lauren L; Waldron-Perrine, Brigid; Pangilinan, Percival H; Bieliauskas, Linas A

    2013-01-01

    Reliable Digit Span (RDS) is a measure of effort derived from the Digit Span subtest of the Wechsler intelligence scales. Some authors have suggested that the age-corrected scaled score provides a more accurate measure of effort than RDS. This study examined the relative diagnostic accuracy of the traditional RDS, an extended RDS including the new Sequencing task from the Wechsler Adult Intelligence Scale-IV, and the age-corrected scaled score, relative to performance validity as determined by the Test of Memory Malingering. Data were collected from 138 Veterans seen in a traumatic brain injury clinic. The traditional RDS (≤ 7), revised RDS (≤ 11), and Digit Span age-corrected scaled score ( ≤ 6) had respective sensitivities of 39%, 39%, and 33%, and respective specificities of 82%, 89%, and 91%. Of these indices, revised RDS and the Digit Span age-corrected scaled score provide the most accurate measure of performance validity among the three measures.

  7. A comparison of depression scores between aesthetic and functional rhinoplasty patients.

    PubMed

    Naraghi, Mohsen; Atari, Mohammad

    2015-04-01

    Depression is a mood state of sadness, gloom, and pessimistic ideation with loss of interest or pleasure in normal activities. This mood disorder has been reported to occur more frequently among cosmetic surgery patients. The purpose of the current study was to compare the score of depression among aesthetic rhinoplasty candidates and functional rhinoplasty patients as control group. The Beck Depression Inventory (BDI) and Depression (DE) subscale of Symptom Check List-90-Revised (SCL-90-R) were administered on a sample of aesthetic rhinoplasty patients (n=21) as well as a sample of functional rhinoplasty patients (n=21). Those with both cosmetic and functional purposes were categorized regarding their primary objective. Questionnaires were given to patients preoperatively. Cohen's d was also calculated as a measure of Effect Size (ES). BDI and SCL-90-R-DE scores were analyzed using t-test for independent groups. Statistical analyses suggested that the mean BDI and SCL-90-R-DE scores of aesthetic surgery patients were significantly higher than those of functional surgery patients (P<0.05). The results showed that age, sex, and Socio-Economic Status (SES) were not significantly different between the two groups as they can be capable of influencing the depression score. Effect size was above the moderate level: d=0.51, d=0.72 for BDI and SCL-90-R-DE, respectively. Using two different depression instruments, the findings of this study showed that aesthetic rhinoplasty patients were more depressed in comparison with functional rhinoplasty patients. The measures of ES also supported the hypothesis that aesthetic rhinoplasty candidates had higher scores in depression. PMID:25701068

  8. Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set.

    PubMed

    Li, Yan; Liu, Zhihai; Li, Jie; Han, Li; Liu, Jie; Zhao, Zhixiong; Wang, Renxiao

    2014-06-23

    Scoring functions are often applied in combination with molecular docking methods to predict ligand binding poses and ligand binding affinities or to identify active compounds through virtual screening. An objective benchmark for assessing the performance of current scoring functions is expected to provide practical guidance for the users to make smart choices among available methods. It can also elucidate the common weakness in current methods for future improvements. The primary goal of our comparative assessment of scoring functions (CASF) project is to provide a high-standard, publicly accessible benchmark of this type. Our latest study, i.e., CASF-2013, evaluated 20 popular scoring functions on an updated set of protein-ligand complexes. This data set was selected out of 8302 protein-ligand complexes recorded in the PDBbind database (version 2013) through a fairly complicated process. Sample selection was made by considering the quality of complex structures as well as binding data. Finally, qualified complexes were clustered by 90% similarity in protein sequences. Three representative complexes were chosen from each cluster to control sample redundancy. The final outcome, namely, the PDBbind core set (version 2013), consists of 195 protein-ligand complexes in 65 clusters with binding constants spanning nearly 10 orders of magnitude. In this data set, 82% of the ligand molecules are "druglike" and 78% of the protein molecules are validated or potential drug targets. Correlation between binding constants and several key properties of ligands are discussed. Methods and results of the scoring function evaluation will be described in a companion work in this issue (doi: 10.1021/ci500081m ). PMID:24716849

  9. A comparison of depression scores between aesthetic and functional rhinoplasty patients.

    PubMed

    Naraghi, Mohsen; Atari, Mohammad

    2015-04-01

    Depression is a mood state of sadness, gloom, and pessimistic ideation with loss of interest or pleasure in normal activities. This mood disorder has been reported to occur more frequently among cosmetic surgery patients. The purpose of the current study was to compare the score of depression among aesthetic rhinoplasty candidates and functional rhinoplasty patients as control group. The Beck Depression Inventory (BDI) and Depression (DE) subscale of Symptom Check List-90-Revised (SCL-90-R) were administered on a sample of aesthetic rhinoplasty patients (n=21) as well as a sample of functional rhinoplasty patients (n=21). Those with both cosmetic and functional purposes were categorized regarding their primary objective. Questionnaires were given to patients preoperatively. Cohen's d was also calculated as a measure of Effect Size (ES). BDI and SCL-90-R-DE scores were analyzed using t-test for independent groups. Statistical analyses suggested that the mean BDI and SCL-90-R-DE scores of aesthetic surgery patients were significantly higher than those of functional surgery patients (P<0.05). The results showed that age, sex, and Socio-Economic Status (SES) were not significantly different between the two groups as they can be capable of influencing the depression score. Effect size was above the moderate level: d=0.51, d=0.72 for BDI and SCL-90-R-DE, respectively. Using two different depression instruments, the findings of this study showed that aesthetic rhinoplasty patients were more depressed in comparison with functional rhinoplasty patients. The measures of ES also supported the hypothesis that aesthetic rhinoplasty candidates had higher scores in depression.

  10. SIFTER search: a web server for accurate phylogeny-based protein function prediction.

    PubMed

    Sahraeian, Sayed M; Luo, Kevin R; Brenner, Steven E

    2015-07-01

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

  11. The development and validation of a questionnaire for rotator cuff disorders: The Functional Shoulder Score

    PubMed Central

    Ibrahim, Edward F; Petrou, Charalambos; Galanos, Antonis

    2015-01-01

    Background The purpose of the present study was to validate the Functional Shoulder Score (FSS), a new patient-reported outcome score specifically designed to evaluate patients with rotator cuff disorders. Methods One hundred and nineteen patients were assessed using two shoulder scoring systems [the FSS and the Constant–Murley Score (CMS)] at 3 weeks pre- and 6 months post-arthroscopic rotator cuff surgery. The reliability, validity, responsiveness and interpretability of the FSS were evaluated. Results Reliability analysis (test–retest) showed an intraclass correlation coefficient value of 0.96 [95% confidence interval (CI) = 0.92 to 0.98]. Internal consistency analysis revealed a Cronbach's alpha coefficient of 0.93. The Pearson correlation coefficient FSS-CMS was 0.782 pre-operatively and 0.737 postoperatively (p < 0.0005). There was a statistically significant increase in FSS scores postoperatively, an effect size of 3.06 and standardized response mean of 2.80. The value for minimal detectable change was ±8.38 scale points (based on a 90% CI) and the minimal clinically important difference for improvement was 24.7 ± 5.4 points. Conclusions The FSS is a patient-reported outcome measure that can easily be incorporated into clinical practice, providing a quick, reliable, valid and practical measure for rotator cuff problems. The questionnaire is highly sensitive to clinical change. PMID:27582986

  12. Multiple-Resonance Local Wave Functions for Accurate Excited States in Quantum Monte Carlo.

    PubMed

    Zulfikri, Habiburrahman; Amovilli, Claudio; Filippi, Claudia

    2016-03-01

    We introduce a novel class of local multideterminant Jastrow-Slater wave functions for the efficient and accurate treatment of excited states in quantum Monte Carlo. The wave function is expanded as a linear combination of excitations built from multiple sets of localized orbitals that correspond to the bonding patterns of the different Lewis resonance structures of the molecule. We capitalize on the concept of orbital domains of local coupled-cluster methods, which is here applied to the active space to select the orbitals to correlate and construct the important transitions. The excitations are further grouped into classes, which are ordered in importance and can be systematically included in the Jastrow-Slater wave function to ensure a balanced description of all states of interest. We assess the performance of the proposed wave function in the calculation of vertical excitation energies and excited-state geometry optimization of retinal models whose π → π* state has a strong intramolecular charge-transfer character. We find that our multiresonance wave functions recover the reference values of the total energies of the ground and excited states with only a small number of excitations and that the same expansion can be flexibly used at very different geometries. Furthermore, significant computational saving can also be gained in the orbital optimization step by selectively mixing occupied and virtual orbitals based on spatial considerations without loss of accuracy on the excitation energy. Our multiresonance wave functions are therefore compact, accurate, and very promising for the calculation of multiple excited states of different character in large molecules.

  13. Accurate evaluation of the angular-dependent direct correlation function of water

    NASA Astrophysics Data System (ADS)

    Zhao, Shuangliang; Liu, Honglai; Ramirez, Rosa; Borgis, Daniel

    2013-07-01

    The direct correlation function (DCF) plays a pivotal role in addressing the thermodynamic properties with non-mean-field statistical theories of liquid state. This work provides an accurate yet efficient calculation procedure for evaluating the angular-dependent DCF of bulk SPC/E water. The DCF here represented in a discrete angles basis is computed with two typical steps: the first step involves solving the molecular Ornstein-Zernike equation with the input of total correlation function extracted from simulation; the resultant DCF is then polished in second step at small wavelength for all orientations in order to match correct thermodynamic properties. This function is also discussed in terms of its rotational invariant components. In particular, we show that the component c112(r) that accounts for dipolar symmetry reaches already its long-range asymptotic behavior at a short distance of 4 Å. With the knowledge of DCF, the angular-dependent bridge function of bulk water is thereafter computed and discussed in comparison with referenced hard-sphere bridge functions. We conclude that, even though such hard-sphere bridge functions may be relevant to improve the calculation of Helmholtz free energies in integral equations or density functional theory, they are doomed to fail at a structural level.

  14. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L.; Perdew, John P.

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  15. Do Bond Functions Help for the Calculation of Accurate Bond Energies?

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

    1998-01-01

    The bond energies of 8 chemically bound diatomics are computed using several basis sets with and without bond functions (BF). The bond energies obtained using the aug-pVnZ+BF basis sets (with a correction for basis set superposition error, BSSE) tend to be slightly smaller that the results obtained using the aug-pV(n+I)Z basis sets, but slightly larger than the BSSE corrected aug-pV(n+I)Z results. The aug-cc-pVDZ+BF and aug-cc-pVTZ+BF basis sets yield reasonable estimates of bond energies, but, in most cases, these results cannot be considered highly accurate. Extrapolation of the results obtained with basis sets including bond functions appears to be inferior to the results obtained by extrapolation using atom-centered basis sets. Therefore bond functions do not appear to offer a path for obtaining highly accurate results for chemically bound systems at a lower computational cost than atom centered basis sets.

  16. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

    PubMed

    Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science. PMID:27554409

  17. Tests of executive functioning predict scores on the MacAndrew Alcoholism Scale.

    PubMed

    Deckel, A W

    1999-02-01

    1. Previous work reported that tests of executive functioning (EF) predict the risk of alcoholism in subject populations selected for a "high density" of a family history of alcoholism and/or the presence of sociopathic traits. The current experiment examined the ability of EF tests to predict the risk of alcoholism, as measured by the MacAndrew Alcoholism Scale (MAC), in outpatient subjects referred to a general neuropsychological testing service. 2. Sixty-eight male and female subjects referred for neuropsychological testing were assessed for their past drinking histories and administered the Wisconsin Card Sorting Test, the Wechsler Adult Intelligence Scale-Revised, the Trails (Part B) Test, and the MAC. Principal Components analysis (PCA) reduced the number of EF tests to two measures, including one that loaded on the WCST, and one that loaded on the Similarities, Picture Arrangement, and Trails tests. Multiple hierarchical regression first removed the variance from demographic variables, alcohol consumption, and verbal (i.e., Vocabulary) and non-verbal (i.e., Block Design) IQ, and then entered the executive functioning factors into the prediction of the MAC. 3. Seventy-six percent of the subjects were classified as either light, infrequent, or non-drinkers on the Quantity-Frequency-Variability scale. The factor derived from the WCST on PCA significantly added to the prediction of risk on the MAC (p = .0063), as did scores on Block Design (p = .033). Relatively more impaired scores on the WCST factor and Block Design were predictive of higher scores on the MAC. The other factors were not associated with MAC scores. 4. These results support the hypothesis that decrements in EF are associated with risk factors for alcoholism, even in populations where the density of alcoholic behaviors are not unusually high. When taken in conjunction with other findings, these results implicate EF test scores, and prefrontal brain functioning, in the neurobiology of the risk for

  18. Effect of Mindfulness Meditation on Perceived Stress Scores and Autonomic Function Tests of Pregnant Indian Women

    PubMed Central

    Jain, Reena; Kohli, Sangeeta; Batra, Swaraj

    2016-01-01

    Introduction Various pregnancy complications like hypertension, preeclampsia have been strongly correlated with maternal stress. One of the connecting links between pregnancy complications and maternal stress is mind-body intervention which can be part of Complementary and Alternative Medicine (CAM). Biologic measures of stress during pregnancy may get reduced by such interventions. Aim To evaluate the effect of Mindfulness meditation on perceived stress scores and autonomic function tests of pregnant Indian women. Materials and Methods Pregnant Indian women of 12 weeks gestation were randomised to two treatment groups: Test group with Mindfulness meditation and control group with their usual obstetric care. The effect of Mindfulness meditation on perceived stress scores and cardiac sympathetic functions and parasympathetic functions (Heart rate variation with respiration, lying to standing ratio, standing to lying ratio and respiratory rate) were evaluated on pregnant Indian women. Results There was a significant decrease in perceived stress scores, a significant decrease of blood pressure response to cold pressor test and a significant increase in heart rate variability in the test group (p< 0.05, significant) which indicates that mindfulness meditation is a powerful modulator of the sympathetic nervous system and can thereby reduce the day-to-day perceived stress in pregnant women. Conclusion The results of this study suggest that mindfulness meditation improves parasympathetic functions in pregnant women and is a powerful modulator of the sympathetic nervous system during pregnancy. PMID:27190795

  19. mBEEF: An accurate semi-local Bayesian error estimation density functional

    NASA Astrophysics Data System (ADS)

    Wellendorff, Jess; Lundgaard, Keld T.; Jacobsen, Karsten W.; Bligaard, Thomas

    2014-04-01

    We present a general-purpose meta-generalized gradient approximation (MGGA) exchange-correlation functional generated within the Bayesian error estimation functional framework [J. Wellendorff, K. T. Lundgaard, A. Møgelhøj, V. Petzold, D. D. Landis, J. K. Nørskov, T. Bligaard, and K. W. Jacobsen, Phys. Rev. B 85, 235149 (2012)]. The functional is designed to give reasonably accurate density functional theory (DFT) predictions of a broad range of properties in materials physics and chemistry, while exhibiting a high degree of transferability. Particularly, it improves upon solid cohesive energies and lattice constants over the BEEF-vdW functional without compromising high performance on adsorption and reaction energies. We thus expect it to be particularly well-suited for studies in surface science and catalysis. An ensemble of functionals for error estimation in DFT is an intrinsic feature of exchange-correlation models designed this way, and we show how the Bayesian ensemble may provide a systematic analysis of the reliability of DFT based simulations.

  20. Application of independent component analysis for speech-music separation using an efficient score function estimation

    NASA Astrophysics Data System (ADS)

    Pishravian, Arash; Aghabozorgi Sahaf, Masoud Reza

    2012-12-01

    In this paper speech-music separation using Blind Source Separation is discussed. The separating algorithm is based on the mutual information minimization where the natural gradient algorithm is used for minimization. In order to do that, score function estimation from observation signals (combination of speech and music) samples is needed. The accuracy and the speed of the mentioned estimation will affect on the quality of the separated signals and the processing time of the algorithm. The score function estimation in the presented algorithm is based on Gaussian mixture based kernel density estimation method. The experimental results of the presented algorithm on the speech-music separation and comparing to the separating algorithm which is based on the Minimum Mean Square Error estimator, indicate that it can cause better performance and less processing time

  1. Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Schwenke, David W.; Chaban, Galina M.

    2005-01-01

    Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

  2. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749

  3. Gait and Glasgow Coma Scale scores can predict functional recovery in patients with traumatic brain injury.

    PubMed

    Bilgin, Sevil; Guclu-Gunduz, Arzu; Oruckaptan, Hakan; Kose, Nezire; Celik, Bülent

    2012-09-01

    Fifty-one patients with mild (n = 14), moderate (n = 10) and severe traumatic brain injury (n = 27) received early rehabilitation. Level of consciousness was evaluated using the Glasgow Coma Score. Functional level was determined using the Glasgow Outcome Score, whilst mobility was evaluated using the Mobility Scale for Acute Stroke. Activities of daily living were assessed using the Barthel Index. Following Bobath neurodevelopmental therapy, the level of consciousness was significantly improved in patients with moderate and severe traumatic brain injury, but was not greatly influenced in patients with mild traumatic brain injury. Mobility and functional level were significantly improved in patients with mild, moderate and severe traumatic brain injury. Gait recovery was more obvious in patients with mild traumatic brain injury than in patients with moderate and severe traumatic brain injury. Activities of daily living showed an improvement but this was insignificant except for patients with severe traumatic brain injury. Nevertheless, complete recovery was not acquired at discharge. Multiple regression analysis showed that gait and Glasgow Coma Scale scores can be considered predictors of functional outcomes following traumatic brain injury. PMID:25624828

  4. Accurate determination of renal function in patients with intestinal urinary diversions

    SciTech Connect

    McDougal, W.S.; Koch, M.O.

    1986-06-01

    The regular determination of renal function is a critical part of the management of patients who have had the urinary tract reconstructed with intestinal segments. These intestinal segments reabsorb urinary solutes and, thereby, complicate the determination of renal function by conventional methods. Urinary clearances of urea, creatinine and inulin were performed in patients with intestinal segments in the urinary tract and controls under varying diuretic conditions. Patients with intestinal diversions also underwent radioisotopic determination of renal function. The urinary clearances of urea, creatinine and inulin are highly dependent on the rate of urine flow in patients with intestinal segments in the urinary tract. Diuresis maximizes the urinary clearances of these solutes by minimizing intestinal reabsorption. Creatinine clearance prediction from the serum creatinine underestimates true glomerular filtration rate. Radioisotopic determination of renal function correlates poorly with true glomerular filtration rate. Only creatinine clearance measured under diuretic conditions correlates well with true renal function. Urine concentrating ability cannot be assessed accurately in patients with intestinal segments in the urinary tract, since osmolality rapidly equilibrates across the segments.

  5. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    DOE PAGES

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

  6. SIFTER search: a web server for accurate phylogeny-based protein function prediction.

    PubMed

    Sahraeian, Sayed M; Luo, Kevin R; Brenner, Steven E

    2015-07-01

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded. PMID:25979264

  7. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    SciTech Connect

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

  8. POEM: Parameter Optimization using Ensemble Methods: application to target specific scoring functions.

    PubMed

    Antes, Iris; Merkwirth, Christian; Lengauer, Thomas

    2005-01-01

    In computational biology processes such as docking, binding, and folding are often described by simplified, empirical models. These models are fitted to physical properties of the process by adjustable parameters. An appropriate choice of these parameters is crucial for the quality of the models. Locating the best choices for the parameters is often is a difficult task, depending on the complexity of the model. We describe a new method and program, POEM (Parameter Optimization using Ensemble Methods), for this task. In POEM we combine the DOE (Design Of Experiment) procedure with ensembles of different regression methods. We apply the method to the optimization of target specific scoring functions in molecular docking. The method consists of an iterative procedure that uses alternate evaluation and prediction steps. During each cycle of optimization we fit an approximate function to a defined loss function landscape and improve the quality of this fit from cycle to cycle by constantly augmenting our data set. As test applications we fitted the FlexX and Screenscore scoring functions to the kinase and ATPase protein classes. The results are promising: Starting from random parameters we are able to locate parameter sets which show superior performance compared to the original values. The POEM approach converges quickly and the approximated loss function landscapes are smooth, thus making the approach a suitable method for optimizations on rugged landscapes.

  9. Modelling the Constraints of Spatial Environment in Fauna Movement Simulations: Comparison of a Boundaries Accurate Function and a Cost Function

    NASA Astrophysics Data System (ADS)

    Jolivet, L.; Cohen, M.; Ruas, A.

    2015-08-01

    Landscape influences fauna movement at different levels, from habitat selection to choices of movements' direction. Our goal is to provide a development frame in order to test simulation functions for animal's movement. We describe our approach for such simulations and we compare two types of functions to calculate trajectories. To do so, we first modelled the role of landscape elements to differentiate between elements that facilitate movements and the ones being hindrances. Different influences are identified depending on landscape elements and on animal species. Knowledge were gathered from ecologists, literature and observation datasets. Second, we analysed the description of animal movement recorded with GPS at fine scale, corresponding to high temporal frequency and good location accuracy. Analysing this type of data provides information on the relation between landscape features and movements. We implemented an agent-based simulation approach to calculate potential trajectories constrained by the spatial environment and individual's behaviour. We tested two functions that consider space differently: one function takes into account the geometry and the types of landscape elements and one cost function sums up the spatial surroundings of an individual. Results highlight the fact that the cost function exaggerates the distances travelled by an individual and simplifies movement patterns. The geometry accurate function represents a good bottom-up approach for discovering interesting areas or obstacles for movements.

  10. Prediction of individual clinical scores in patients with Parkinson's disease using resting-state functional magnetic resonance imaging.

    PubMed

    Hou, YanBing; Luo, ChunYan; Yang, Jing; Ou, RuWei; Song, Wei; Wei, QianQian; Cao, Bei; Zhao, Bi; Wu, Ying; Shang, Hui-Fang; Gong, QiYong

    2016-07-15

    Neuroimaging holds the promise that it may one day aid the clinical assessment. However, the vast majority of studies using resting-state functional magnetic resonance imaging (fMRI) have reported average differences between Parkinson's disease (PD) patients and healthy controls, which do not permit inferences at the level of individuals. This study was to develop a model for the prediction of PD illness severity ratings from individual fMRI brain scan. The resting-state fMRI scans were obtained from 84 patients with PD and the Unified Parkinson's Disease Rating Scale-III (UPDRS-III) scores were obtained before scanning. The RVR method was used to predict clinical scores (UPDRS-III) from fMRI scans. The application of RVR to whole-brain resting-state fMRI data allowed prediction of UPDRS-III scores with statistically significant accuracy (correlation=0.35, P-value=0.001; mean sum of squares=222.17, P-value=0.002). This prediction was informed strongly by negative weight areas including prefrontal lobe and medial occipital lobe, and positive weight areas including medial parietal lobe. It was suggested that fMRI scans contained sufficient information about neurobiological change in patients with PD to permit accurate prediction about illness severity, on an individual subject basis. Our results provided preliminary evidence, as proof-of-concept, to support that fMRI might be possible to be a clinically useful quantitative assessment aid in PD at individual level. This may enable clinicians to target those uncooperative patients and machines to replace human for a more efficient use of health care resources. PMID:27288771

  11. Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function.

    PubMed

    Timmers, Luis Fernando Saraiva Macedo; Caceres, Rafael Andrade; Vivan, Ana Luiza; Gava, Lisandra Marques; Dias, Raquel; Ducati, Rodrigo Gay; Basso, Luiz Augusto; Santos, Diogenes Santiago; de Azevedo, Walter Filgueira

    2008-11-01

    Human purine nucleoside phosphorylase (HsPNP) is a target for inhibitor development aiming at T-cell immune response modulation. In this work, we report the development of a new set of empirical scoring functions and its application to evaluate binding affinities and docking results. To test these new functions, we solved the structure of HsPNP and 2-mercapto-4(3H)-quinazolinone (HsPNP:MQU) binary complex at 2.7A resolution using synchrotron radiation, and used these functions to predict ligand position obtained in docking simulations. We also employed molecular dynamics simulations to analyze HsPNP in two conditions, as apoenzyme and in the binary complex form, in order to assess the structural features responsible for stability. Analysis of the structural differences between systems provides explanation for inhibitor binding. The use of these scoring functions to evaluate binding affinities and molecular docking results may be used to guide future efforts on virtual screening focused on HsPNP.

  12. Association between Global Assessment of Functioning scores and indicators of functioning, severity, and prognosis in first-time schizophrenia

    PubMed Central

    Köhler, Ole; Horsdal, Henriette Thisted; Baandrup, Lone; Mors, Ole; Gasse, Christiane

    2016-01-01

    Background Assessment of psychosocial functioning in people with schizophrenia is important. The Global Assessment of Functioning (GAF-F) scale represents a widely applied, easy, and quick tool, but its validity and reliability have been debated. The aim was to investigate whether GAF-F scores are associated with other indicators of functioning, severity, and hospitalization. Methods A Danish population-based cohort study of adults (≥18 years) with a recorded GAF-F score at first-time schizophrenia diagnosis during 2004–2011 was performed. The internal validity of GAF-F was evaluated by assessing its association with other baseline measures of functioning and illness severity. Risk of schizophrenia hospitalization within 2 years was evaluated using Cox regression stratified by sex and adjusted for age, year of diagnosis, and inpatient/outpatient status at diagnosis. Results We identified 2,837 cases of schizophrenia with a GAF-F score at first-time diagnosis (73.0% inpatients; 62.6% males). GAF-F was associated with several baseline measures of functioning and illness severity, such as female sex, being in work, and a longer baseline hospitalization. Lower GAF-F scores were associated with higher hospitalization risk among males (reference GAF-F 61–100): GAF-F 51–60: hazard rate ratio (HRR) =1.24 (95% confidence interval [CI] =0.89–1.75); GAF-F 41–50: HRR =1.31 (95% CI =0.97–1.77); GAF-F 31–40: HRR =1.36 (95% CI =1.01–1.82); GAF-F 21–30: HRR =1.50 (95% CI =1.09–2.06); and GAF-F 1–20: HRR =2.30 (95% CI =1.36–3.90), fitting a dose–response relationship (P=0.031). This association was not found in females. Conclusion GAF-F at first-time schizophrenia diagnosis showed good internal validity against other measures of functionality in a Danish hospital setting. Severe impairment (as measured by the GAF-F score) at first-time schizophrenia diagnosis was associated with a higher risk of 2-year hospitalization among males, which may indicate sex

  13. Association between Global Assessment of Functioning scores and indicators of functioning, severity, and prognosis in first-time schizophrenia

    PubMed Central

    Köhler, Ole; Horsdal, Henriette Thisted; Baandrup, Lone; Mors, Ole; Gasse, Christiane

    2016-01-01

    Background Assessment of psychosocial functioning in people with schizophrenia is important. The Global Assessment of Functioning (GAF-F) scale represents a widely applied, easy, and quick tool, but its validity and reliability have been debated. The aim was to investigate whether GAF-F scores are associated with other indicators of functioning, severity, and hospitalization. Methods A Danish population-based cohort study of adults (≥18 years) with a recorded GAF-F score at first-time schizophrenia diagnosis during 2004–2011 was performed. The internal validity of GAF-F was evaluated by assessing its association with other baseline measures of functioning and illness severity. Risk of schizophrenia hospitalization within 2 years was evaluated using Cox regression stratified by sex and adjusted for age, year of diagnosis, and inpatient/outpatient status at diagnosis. Results We identified 2,837 cases of schizophrenia with a GAF-F score at first-time diagnosis (73.0% inpatients; 62.6% males). GAF-F was associated with several baseline measures of functioning and illness severity, such as female sex, being in work, and a longer baseline hospitalization. Lower GAF-F scores were associated with higher hospitalization risk among males (reference GAF-F 61–100): GAF-F 51–60: hazard rate ratio (HRR) =1.24 (95% confidence interval [CI] =0.89–1.75); GAF-F 41–50: HRR =1.31 (95% CI =0.97–1.77); GAF-F 31–40: HRR =1.36 (95% CI =1.01–1.82); GAF-F 21–30: HRR =1.50 (95% CI =1.09–2.06); and GAF-F 1–20: HRR =2.30 (95% CI =1.36–3.90), fitting a dose–response relationship (P=0.031). This association was not found in females. Conclusion GAF-F at first-time schizophrenia diagnosis showed good internal validity against other measures of functionality in a Danish hospital setting. Severe impairment (as measured by the GAF-F score) at first-time schizophrenia diagnosis was associated with a higher risk of 2-year hospitalization among males, which may indicate sex

  14. Macleaya cordata Extract Decreased Diarrhea Score and Enhanced Intestinal Barrier Function in Growing Piglets.

    PubMed

    Liu, Gang; Guan, Guiping; Fang, Jun; Martínez, Yordan; Chen, Shuai; Bin, Peng; Duraipandiyan, Veeramuthu; Gong, Ting; Tossou, Myrlene Carine B; Al-Dhabi, Naif Abdullah; Yin, Yulong

    2016-01-01

    Macleaya cordata extract is of great scientific and practical interest to researchers, due to its antimicrobial and anti-inflammatory responses within experimental animals. This study was designed to determine the diarrhea score and innate immunity of growing piglets after they had received Macleaya cordata extract supplements. A total of 240 growing pigs were randomly assigned to one of three dietary treatments, with 8 replicates per treatment and 10 piglets per replicate. All pigs received a basal diet containing similar amounts of nutrients. The three treatments were a control (no additive), an antibiotic (200 mg/kg colistin), and the Macleaya cordata extract supplement group (40 mg/kg Macleaya cordata extract). The diarrhea score was calculated after D 28. The jejunal samples were obtained from five piglets selected randomly from each treatment on D 28. In comparison with the control group, the dietary Macleaya cordata extract and colistin group demonstrated a substantially decreased diarrhea score. The introduction of Macleaya cordata extract supplements to the diet significantly increased volumes of ZO-1 and claudin-1, particularly in comparison with the pigs in the control group (P < 0.05). The findings indicate that Macleaya cordata extract does enhance intestinal barrier function in growing piglets and that it could be used as a viable substitute for antibiotics. PMID:27525260

  15. Predicting Functional Independence Measure Scores During Rehabilitation with Wearable Inertial Sensors

    PubMed Central

    Sprint, Gina; Cook, Diane J.; Weeks, Douglas L.; Borisov, Vladimir

    2016-01-01

    Evaluating patient progress and making discharge decisions regarding inpatient medical rehabilitation rely upon standard clinical assessments administered by trained clinicians. Wearable inertial sensors can offer more objective measures of patient movement and progress. We undertook a study to investigate the contribution of wearable sensor data to predict discharge functional independence measure (FIM) scores for 20 patients at an inpatient rehabilitation facility. The FIM utilizes a 7-point ordinal scale to measure patient independence while performing several activities of daily living, such as walking, grooming, and bathing. Wearable inertial sensor data were collected from ecological ambulatory tasks at two time points mid-stay during inpatient rehabilitation. Machine learning algorithms were trained with sensor-derived features and clinical information obtained from medical records at admission to the inpatient facility. While models trained only with clinical features predicted discharge scores well, we were able to achieve an even higher level of prediction accuracy when also including the wearable sensor-derived features. Correlations as high as 0.97 for leave-one-out cross validation predicting discharge FIM motor scores are reported. PMID:27054054

  16. Macleaya cordata Extract Decreased Diarrhea Score and Enhanced Intestinal Barrier Function in Growing Piglets

    PubMed Central

    Fang, Jun; Martínez, Yordan; Bin, Peng; Duraipandiyan, Veeramuthu; Yin, Yulong

    2016-01-01

    Macleaya cordata extract is of great scientific and practical interest to researchers, due to its antimicrobial and anti-inflammatory responses within experimental animals. This study was designed to determine the diarrhea score and innate immunity of growing piglets after they had received Macleaya cordata extract supplements. A total of 240 growing pigs were randomly assigned to one of three dietary treatments, with 8 replicates per treatment and 10 piglets per replicate. All pigs received a basal diet containing similar amounts of nutrients. The three treatments were a control (no additive), an antibiotic (200 mg/kg colistin), and the Macleaya cordata extract supplement group (40 mg/kg Macleaya cordata extract). The diarrhea score was calculated after D 28. The jejunal samples were obtained from five piglets selected randomly from each treatment on D 28. In comparison with the control group, the dietary Macleaya cordata extract and colistin group demonstrated a substantially decreased diarrhea score. The introduction of Macleaya cordata extract supplements to the diet significantly increased volumes of ZO-1 and claudin-1, particularly in comparison with the pigs in the control group (P < 0.05). The findings indicate that Macleaya cordata extract does enhance intestinal barrier function in growing piglets and that it could be used as a viable substitute for antibiotics. PMID:27525260

  17. Kyphoplasty Increases Vertebral Height, Decreases Both Pain Score and Opiate Requirements While Improving Functional Status

    PubMed Central

    Tolba, Reda; Bolash, Robert B.; Shroll, Joshua; Costandi, Shrif; Dalton, Jarrod E.; Sanghvi, Chirag; Mekhail, Nagy

    2014-01-01

    Vertebral compression fractures can result from advanced osteoporosis, or less commonly from metastatic or traumatic insults to the vertebral column, and result in disabling pain and decreased functional capacity. Various vertebral augmentation options including kyphoplasty aim at preventing the sequelae of pain and immobility that can develop as the result of the vertebral fractures. The mechanism for pain relief following kyphoplasty is not entirely understood, and the restoration of a portion of the lost vertebral height is a subject of debate. We retrospectively reviewed radiographic imaging, pain relief, analgesic intake and functional outcomes in 67 consecutive patients who underwent single- or multilevel kyphoplasty with the primary goal of quantifying the restoration of lost vertebral height. We observed a mean of 45% of the lost vertebral height restored postprocedurally. Secondarily, kyphoplasty was associated with significant decreases in pain scores, daily morphine consumption and improvement in patient-reported functional measures. PMID:24165285

  18. Kyphoplasty increases vertebral height, decreases both pain score and opiate requirements while improving functional status.

    PubMed

    Tolba, Reda; Bolash, Robert B; Shroll, Joshua; Costandi, Shrif; Dalton, Jarrod E; Sanghvi, Chirag; Mekhail, Nagy

    2014-03-01

    Vertebral compression fractures can result from advanced osteoporosis, or less commonly from metastatic or traumatic insults to the vertebral column, and result in disabling pain and decreased functional capacity. Various vertebral augmentation options including kyphoplasty aim at preventing the sequelae of pain and immobility that can develop as the result of the vertebral fractures. The mechanism for pain relief following kyphoplasty is not entirely understood, and the restoration of a portion of the lost vertebral height is a subject of debate. We retrospectively reviewed radiographic imaging, pain relief, analgesic intake and functional outcomes in 67 consecutive patients who underwent single- or multilevel kyphoplasty with the primary goal of quantifying the restoration of lost vertebral height. We observed a mean of 45% of the lost vertebral height restored postprocedurally. Secondarily, kyphoplasty was associated with significant decreases in pain scores, daily morphine consumption and improvement in patient-reported functional measures.

  19. Kyphoplasty increases vertebral height, decreases both pain score and opiate requirements while improving functional status.

    PubMed

    Tolba, Reda; Bolash, Robert B; Shroll, Joshua; Costandi, Shrif; Dalton, Jarrod E; Sanghvi, Chirag; Mekhail, Nagy

    2014-03-01

    Vertebral compression fractures can result from advanced osteoporosis, or less commonly from metastatic or traumatic insults to the vertebral column, and result in disabling pain and decreased functional capacity. Various vertebral augmentation options including kyphoplasty aim at preventing the sequelae of pain and immobility that can develop as the result of the vertebral fractures. The mechanism for pain relief following kyphoplasty is not entirely understood, and the restoration of a portion of the lost vertebral height is a subject of debate. We retrospectively reviewed radiographic imaging, pain relief, analgesic intake and functional outcomes in 67 consecutive patients who underwent single- or multilevel kyphoplasty with the primary goal of quantifying the restoration of lost vertebral height. We observed a mean of 45% of the lost vertebral height restored postprocedurally. Secondarily, kyphoplasty was associated with significant decreases in pain scores, daily morphine consumption and improvement in patient-reported functional measures. PMID:24165285

  20. Empirical scoring functions for advanced protein-ligand docking with PLANTS.

    PubMed

    Korb, Oliver; Stützle, Thomas; Exner, Thomas E

    2009-01-01

    In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.

  1. Empirical scoring functions for advanced protein-ligand docking with PLANTS.

    PubMed

    Korb, Oliver; Stützle, Thomas; Exner, Thomas E

    2009-01-01

    In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed. PMID:19125657

  2. A Bayesian Statistical Approach for Improving Scoring Functions for Protein-Ligand Interactions

    NASA Astrophysics Data System (ADS)

    Grinter, Sam Z.; Zou, Xiaoqin

    2013-03-01

    Even with large training sets, knowledge-based scoring functions face the inevitable problem of sparse data. In this work, we present a novel approach for handing the sparse data problem, which is based on estimating the inaccuracy caused by sparse count data in a potential of mean force (PMF). Our new scoring function, STScore, uses a consensus approach to combine a PMF with a simple force-field-based potential (FFP), where the relative weight given to the PMF and FFP is a function of their estimated inaccuracies. This weighting scheme implies that less weight will be given to the PMF for any pairs or distances that occur rarely in the training data, thus providing a natural way to deal with the sparse data problem. Simultaneously, by providing the FFP as a substitute, the method provides an improved approximation of the interactions between rare chemical groups, which tend to be excluded or reduced in influence by purely PMF-based approaches. Using several common test sets for protein-ligand interaction studies, we demonstrate that this sparse data method effectively combines the PMF and FFP, exceeding the performance of either potential alone, and is competitive with other commonly-used sparse data methods.

  3. Muscle function during brief maximal exercise: accurate measurements on a friction-loaded cycle ergometer.

    PubMed

    Arsac, L M; Belli, A; Lacour, J R

    1996-01-01

    A friction loaded cycle ergometer was instrumented with a strain gauge and an incremental encoder to obtain accurate measurement of human mechanical work output during the acceleration phase of a cycling sprint. This device was used to characterise muscle function in a group of 15 well-trained male subjects, asked to perform six short maximal sprints on the cycle against a constant friction load. Friction loads were successively set at 0.25, 0.35, 0.45, 0.55, 0.65 and 0.75 N.kg-1 body mass. Since the sprints were performed from a standing start, and since the acceleration was not restricted, the greatest attention was paid to the measurement of the acceleration balancing load due to flywheel inertia. Instantaneous pedalling velocity (v) and power output (P) were calculated each 5 ms and then averaged over each downstroke period so that each pedal downstroke provided a combination of v, force and P. Since an 8-s acceleration phase was composed of about 21 to 34 pedal downstrokes, this many v-P combinations were obtained amounting to 137-180 v-P combinations for all six friction loads in one individual, over the widest functional range of pedalling velocities (17-214 rpm). Thus, the individual's muscle function was characterised by the v-P relationships obtained during the six acceleration phases of the six sprints. An important finding of the present study was a strong linear relationship between individual optimal velocity (vopt) and individual maximal power output (Pmax) (n = 15, r = 0.95, P < 0.001) which has never been observed before. Since vopt has been demonstrated to be related to human fibre type composition both vopt, Pmax and their inter-relationship could represent a major feature in characterising muscle function in maximal unrestricted exercise. It is suggested that the present method is well suited to such analyses.

  4. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.

    PubMed

    Borbulevych, Oleg; Martin, Roger I; Tickle, Ian J; Westerhoff, Lance M

    2016-04-01

    Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  5. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

    PubMed Central

    Borbulevych, Oleg; Martin, Roger I.; Tickle, Ian J.; Westerhoff, Lance M.

    2016-01-01

    Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  6. Accurate and systematically improvable density functional theory embedding for correlated wavefunctions

    SciTech Connect

    Goodpaster, Jason D.; Barnes, Taylor A.; Miller, Thomas F.; Manby, Frederick R.

    2014-05-14

    We analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using wavefunction methods, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We test an MP2 correction for this term and demonstrate that the corrected embedding scheme accurately reproduces wavefunction calculations for a series of chemical reactions. Our projector-based embedding method uses localized occupied orbitals to partition the system; as with other local correlation methods, abrupt changes in the character of the localized orbitals along a reaction coordinate can lead to discontinuities in the embedded energy, but we show that these discontinuities are small and can be systematically reduced by increasing the size of the active region. Convergence of reaction energies with respect to the size of the active subsystem is shown to be rapid for all cases where the density functional treatment is able to capture the polarization of the environment, even in conjugated systems, and even when the partition cuts across a double bond.

  7. SCAN: An Efficient Density Functional Yielding Accurate Structures and Energies of Diversely-Bonded Materials

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei

    The accuracy and computational efficiency of the widely used Kohn-Sham density functional theory (DFT) are limited by the approximation to its exchange-correlation energy Exc. The earliest local density approximation (LDA) overestimates the strengths of all bonds near equilibrium (even the vdW bonds). By adding the electron density gradient to model Exc, generalized gradient approximations (GGAs) generally soften the bonds to give robust and overall more accurate descriptions, except for the vdW interaction which is largely lost. Further improvement for covalent, ionic, and hydrogen bonds can be obtained by the computationally more expensive hybrid GGAs, which mix GGAs with the nonlocal exact exchange. Meta-GGAs are still semilocal in computation and thus efficient. Compared to GGAs, they add the kinetic energy density that enables them to recognize and accordingly treat different bonds, which no LDA or GGA can. We show here that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-GGA improves significantly over LDA and the standard Perdew-Burke-Ernzerhof GGA for geometries and energies of diversely-bonded materials (including covalent, metallic, ionic, hydrogen, and vdW bonds) at comparable efficiency. Often SCAN matches or improves upon the accuracy of a hybrid functional, at almost-GGA cost. This work has been supported by NSF under DMR-1305135 and CNS-09-58854, and by DOE BES EFRC CCDM under DE-SC0012575.

  8. The Utility of CBM Written Language Indices: An Investigation of Production-Dependent, Production-Independent, and Accurate-Production Scores

    ERIC Educational Resources Information Center

    Jewell, Jennifer; Malecki, Christine Kerres

    2005-01-01

    This study examined the utility of three categories of CBM written language indices including production-dependent indices (Total Words Written, Words Spelled Correctly, and Correct Writing Sequences), production-independent indices (Percentage of Words Spelled Correctly and Percentage of Correct Writing Sequences), and an accurate-production…

  9. Accurate Automatic Delineation of Heterogeneous Functional Volumes in Positron Emission Tomography for Oncology Applications

    SciTech Connect

    Hatt, Mathieu; Cheze le Rest, Catherine; Descourt, Patrice; Dekker, Andre; De Ruysscher, Dirk; Oellers, Michel; Lambin, Philippe; Pradier, Olivier; Visvikis, Dimitris

    2010-05-01

    Purpose: Accurate contouring of positron emission tomography (PET) functional volumes is now considered crucial in image-guided radiotherapy and other oncology applications because the use of functional imaging allows for biological target definition. In addition, the definition of variable uptake regions within the tumor itself may facilitate dose painting for dosimetry optimization. Methods and Materials: Current state-of-the-art algorithms for functional volume segmentation use adaptive thresholding. We developed an approach called fuzzy locally adaptive Bayesian (FLAB), validated on homogeneous objects, and then improved it by allowing the use of up to three tumor classes for the delineation of inhomogeneous tumors (3-FLAB). Simulated and real tumors with histology data containing homogeneous and heterogeneous activity distributions were used to assess the algorithm's accuracy. Results: The new 3-FLAB algorithm is able to extract the overall tumor from the background tissues and delineate variable uptake regions within the tumors, with higher accuracy and robustness compared with adaptive threshold (T{sub bckg}) and fuzzy C-means (FCM). 3-FLAB performed with a mean classification error of less than 9% +- 8% on the simulated tumors, whereas binary-only implementation led to errors of 15% +- 11%. T{sub bckg} and FCM led to mean errors of 20% +- 12% and 17% +- 14%, respectively. 3-FLAB also led to more robust estimation of the maximum diameters of tumors with histology measurements, with <6% standard deviation, whereas binary FLAB, T{sub bckg} and FCM lead to 10%, 12%, and 13%, respectively. Conclusion: These encouraging results warrant further investigation in future studies that will investigate the impact of 3-FLAB in radiotherapy treatment planning, diagnosis, and therapy response evaluation.

  10. CT densitovolumetry in children with obliterative bronchiolitis: correlation with clinical scores and pulmonary function test results*,**

    PubMed Central

    Mocelin, Helena; Bueno, Gilberto; Irion, Klaus; Marchiori, Edson; Sarria, Edgar; Watte, Guilherme; Hochhegger, Bruno

    2013-01-01

    OBJECTIVE: To determine whether air trapping (expressed as the percentage of air trapping relative to total lung volume [AT%]) correlates with clinical and functional parameters in children with obliterative bronchiolitis (OB). METHODS: CT scans of 19 children with OB were post-processed for AT% quantification with the use of a fixed threshold of −950 HU (AT%950) and of thresholds selected with the aid of density masks (AT%DM). Patients were divided into three groups by AT% severity. We examined AT% correlations with oxygen saturation (SO2) at rest, six-minute walk distance (6MWD), minimum SO2 during the six-minute walk test (6MWT_SO2), FVC, FEV1, FEV1/FVC, and clinical parameters. RESULTS: The 6MWD was longer in the patients with larger normal lung volumes (r = 0.53). We found that AT%950 showed significant correlations (before and after the exclusion of outliers, respectively) with the clinical score (r = 0.72; 0.80), FVC (r = 0.24; 0.59), FEV1 (r = −0.58; −0.67), and FEV1/FVC (r = −0.53; r = −0.62), as did AT%DM with the clinical score (r = 0.58; r = 0.63), SO2 at rest (r = −0.40; r = −0.61), 6MWT_SO2 (r = −0.24; r = −0.55), FVC (r = −0.44; r = −0.80), FEV1 (r = −0.65; r = −0.71), and FEV1/FVC (r = −0.41; r = −0.52). CONCLUSIONS: Our results show that AT% correlates significantly with clinical scores and pulmonary function test results in children with OB. PMID:24473764

  11. The Kernel Levine Equipercentile Observed-Score Equating Function. Research Report. ETS RR-13-38

    ERIC Educational Resources Information Center

    von Davier, Alina A.; Chen, Haiwen

    2013-01-01

    In the framework of the observed-score equating methods for the nonequivalent groups with anchor test design, there are 3 fundamentally different ways of using the information provided by the anchor scores to equate the scores of a new form to those of an old form. One method uses the anchor scores as a conditioning variable, such as the Tucker…

  12. Model for end-stage liver disease-Na score or Maddrey discrimination function index, which score is best?

    PubMed Central

    Amieva-Balmori, Mercedes; Mejia-Loza, Scherezada María Isabel; Ramos-González, Roberto; Zamarripa-Dorsey, Felipe; García-Ruiz, Eli; Pérez y López, Nuria; Juárez-Valdés, Eumir I; López-Luria, Adriana; Remes-Troche, José María

    2015-01-01

    AIM: To compare the ability of model for end-stage liver disease (MELD)-Na and Maddrey discrimination function index (DFI) to predict mortality at 30 and 90 d in patients with alcoholic hepatitis (AH). METHODS: We prospectively assessed 52 patients with AH. Demographic, clinical and laboratory parameters were obtained. MELD-Na and Maddrey DFI were calculated on admission. Short-term mortality was assessed at 30 and 90 d. Receiver operating characteristic curve analysis was performed. RESULTS: Thirty-day and 90-d mortality was 44% and 58%, respectively. In the univariate analysis, sodium levels was associated with mortality at 30 and 90 d (P = 0.001 and P = 0.03). Child stage, encephalopathy, ascites, or types of treatment were not associated with mortality. MELD-Na was the only predictive factor for mortality at 90 d. For 30-d mortality area under the curve (AUC) was 0.763 (95%CI: 0.63-0.89) for Maddrey DFI and 0.784 for MELD-Na (95%CI: 0.65-0.91, P = 0.82). For 90-d mortality AUC was 0.685 (95%CI: 0.54-0.83) for Maddrey DFI and 0.8710 for MELD-Na (95%CI: 0.76-0.97, P = 0.041). CONCLUSION: AH is associated with high short-term mortality. Our results show that MELD-Na is a more valuable model than DFI to predict short-term mortality. PMID:26301054

  13. Upper Extremity Functional Evaluation by Fugl-Meyer Assessment Scoring Using Depth-Sensing Camera in Hemiplegic Stroke Patients

    PubMed Central

    Baek, Dongyoub; Bang, Hyunwoo; Paik, Nam-Jong

    2016-01-01

    Virtual home-based rehabilitation is an emerging area in stroke rehabilitation. Functional assessment tools are essential to monitor recovery and provide current function-based rehabilitation. We developed the Fugl-Meyer Assessment (FMA) tool using Kinect (Microsoft, USA) and validated it for hemiplegic stroke patients. Forty-one patients with hemiplegic stroke were enrolled. Thirteen of 33 items were selected for upper extremity motor FMA. One occupational therapist assessed the motor FMA while recording upper extremity motion with Kinect. FMA score was calculated using principal component analysis and artificial neural network learning from the saved motion data. The degree of jerky motion was also transformed to jerky scores. Prediction accuracy for each of the 13 items and correlations between real FMA scores and scores using Kinect were analyzed. Prediction accuracies ranged from 65% to 87% in each item and exceeded 70% for 9 items. Correlations were high for the summed score for the 13 items between real FMA scores and scores obtained using Kinect (Pearson’s correlation coefficient = 0.873, P<0.0001) and those between total upper extremity scores (66 in full score) and scores using Kinect (26 in full score) (Pearson’s correlation coefficient = 0.799, P<0.0001). Log transformed jerky scores were significantly higher in the hemiplegic side (1.81 ± 0.76) compared to non-hemiplegic side (1.21 ± 0.43) and showed significant negative correlations with Brunnstrom stage (3 to 6; Spearman correlation coefficient = -0.387, P = 0.046). FMA using Kinect is a valid way to assess upper extremity function and can provide additional results for movement quality in stroke patients. This may be useful in the setting of unsupervised home-based rehabilitation. PMID:27367518

  14. Upper Extremity Functional Evaluation by Fugl-Meyer Assessment Scoring Using Depth-Sensing Camera in Hemiplegic Stroke Patients.

    PubMed

    Kim, Won-Seok; Cho, Sungmin; Baek, Dongyoub; Bang, Hyunwoo; Paik, Nam-Jong

    2016-01-01

    Virtual home-based rehabilitation is an emerging area in stroke rehabilitation. Functional assessment tools are essential to monitor recovery and provide current function-based rehabilitation. We developed the Fugl-Meyer Assessment (FMA) tool using Kinect (Microsoft, USA) and validated it for hemiplegic stroke patients. Forty-one patients with hemiplegic stroke were enrolled. Thirteen of 33 items were selected for upper extremity motor FMA. One occupational therapist assessed the motor FMA while recording upper extremity motion with Kinect. FMA score was calculated using principal component analysis and artificial neural network learning from the saved motion data. The degree of jerky motion was also transformed to jerky scores. Prediction accuracy for each of the 13 items and correlations between real FMA scores and scores using Kinect were analyzed. Prediction accuracies ranged from 65% to 87% in each item and exceeded 70% for 9 items. Correlations were high for the summed score for the 13 items between real FMA scores and scores obtained using Kinect (Pearson's correlation coefficient = 0.873, P<0.0001) and those between total upper extremity scores (66 in full score) and scores using Kinect (26 in full score) (Pearson's correlation coefficient = 0.799, P<0.0001). Log transformed jerky scores were significantly higher in the hemiplegic side (1.81 ± 0.76) compared to non-hemiplegic side (1.21 ± 0.43) and showed significant negative correlations with Brunnstrom stage (3 to 6; Spearman correlation coefficient = -0.387, P = 0.046). FMA using Kinect is a valid way to assess upper extremity function and can provide additional results for movement quality in stroke patients. This may be useful in the setting of unsupervised home-based rehabilitation.

  15. Accurate Astrometry and Photometry of Saturated and Coronagraphic Point Spread Functions

    SciTech Connect

    Marois, C; Lafreniere, D; Macintosh, B; Doyon, R

    2006-02-07

    For ground-based adaptive optics point source imaging, differential atmospheric refraction and flexure introduce a small drift of the point spread function (PSF) with time, and seeing and sky transmission variations modify the PSF flux. These effects need to be corrected to properly combine the images and obtain optimal signal-to-noise ratios, accurate relative astrometry and photometry of detected companions as well as precise detection limits. Usually, one can easily correct for these effects by using the PSF core, but this is impossible when high dynamic range observing techniques are used, like coronagraphy with a non-transmissive occulting mask, or if the stellar PSF core is saturated. We present a new technique that can solve these issues by using off-axis satellite PSFs produced by a periodic amplitude or phase mask conjugated to a pupil plane. It will be shown that these satellite PSFs track precisely the PSF position, its Strehl ratio and its intensity and can thus be used to register and to flux normalize the PSF. This approach can be easily implemented in existing adaptive optics instruments and should be considered for future extreme adaptive optics coronagraph instruments and in high-contrast imaging space observatories.

  16. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    NASA Astrophysics Data System (ADS)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  17. Accurate description of van der Waals complexes by density functional theory including empirical corrections.

    PubMed

    Grimme, Stefan

    2004-09-01

    An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R(-6). The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The "double counting" of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene. H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies.

  18. Patellar resurfacing in total knee arthroplasty: functional outcome differs with different outcome scores

    PubMed Central

    Aunan, Eirik; Næss, Grethe; Clarke-Jenssen, John; Sandvik, Leiv; Kibsgård, Thomas Johan

    2016-01-01

    Background and purpose — Recent research on outcomes after total knee arthroplasty (TKA) has raised the question of the ability of traditional outcome measures to distinguish between treatments. We compared functional outcomes in patients undergoing TKA with and without patellar resurfacing, using the knee injury and osteoarthritis outcome score (KOOS) as the primary outcome and 3 traditional outcome measures as secondary outcomes. Patients and methods — 129 knees in 115 patients (mean age 70 (42–82) years; 67 female) were evaluated in this single-center, randomized, double-blind study. Data were recorded preoperatively, at 1 year, and at 3 years, and were assessed using repeated-measures mixed models. Results — The mean subscores for the KOOS after surgery were statistically significantly in favor of patellar resurfacing: sport/recreation, knee-related quality of life, pain, and symptoms. No statistically significant differences between the groups were observed with the Knee Society clinical rating system, with the Oxford knee score, and with visual analog scale (VAS) for patient satisfaction. Interpretation — In the present study, the KOOS—but no other outcome measure used—indicated that patellar resurfacing may be beneficial in TKA. PMID:26540368

  19. Accurate bond energies of biodiesel methyl esters from multireference averaged coupled-pair functional calculations.

    PubMed

    Oyeyemi, Victor B; Keith, John A; Carter, Emily A

    2014-09-01

    Accurate bond dissociation energies (BDEs) are important for characterizing combustion chemistry, particularly the initial stages of pyrolysis. Here we contribute to evaluating the thermochemistry of biodiesel methyl ester molecules using ab initio BDEs derived from a multireference averaged coupled-pair functional (MRACPF2)-based scheme. Having previously validated this approach for hydrocarbons and a variety of oxygenates, herein we provide further validation for bonds within carboxylic acids and methyl esters, finding our scheme predicts BDEs within chemical accuracy (i.e., within 1 kcal/mol) for these molecules. Insights into BDE trends with ester size are then analyzed for methyl formate through methyl crotonate. We find that the carbonyl group in the ester moiety has only a local effect on BDEs. C═C double bonds in ester alkyl chains are found to increase the strengths of bonds adjacent to the double bond. An important exception are bonds beta to C═C or C═O bonds, which produce allylic-like radicals upon dissociation. The observed trends arise from different degrees of geometric relaxation and resonance stabilization in the radicals produced. We also compute BDEs in various small alkanes and alkenes as models for the long hydrocarbon chain of actual biodiesel methyl esters. We again show that allylic bonds in the alkenes are much weaker than those in the small methyl esters, indicating that hydrogen abstractions are more likely at the allylic site and even more likely at bis-allylic sites of alkyl chains due to more electrons involved in π-resonance in the latter. Lastly, we use the BDEs in small surrogates to estimate heretofore unknown BDEs in large methyl esters of biodiesel fuels.

  20. Accurate bond energies of biodiesel methyl esters from multireference averaged coupled-pair functional calculations.

    PubMed

    Oyeyemi, Victor B; Keith, John A; Carter, Emily A

    2014-09-01

    Accurate bond dissociation energies (BDEs) are important for characterizing combustion chemistry, particularly the initial stages of pyrolysis. Here we contribute to evaluating the thermochemistry of biodiesel methyl ester molecules using ab initio BDEs derived from a multireference averaged coupled-pair functional (MRACPF2)-based scheme. Having previously validated this approach for hydrocarbons and a variety of oxygenates, herein we provide further validation for bonds within carboxylic acids and methyl esters, finding our scheme predicts BDEs within chemical accuracy (i.e., within 1 kcal/mol) for these molecules. Insights into BDE trends with ester size are then analyzed for methyl formate through methyl crotonate. We find that the carbonyl group in the ester moiety has only a local effect on BDEs. C═C double bonds in ester alkyl chains are found to increase the strengths of bonds adjacent to the double bond. An important exception are bonds beta to C═C or C═O bonds, which produce allylic-like radicals upon dissociation. The observed trends arise from different degrees of geometric relaxation and resonance stabilization in the radicals produced. We also compute BDEs in various small alkanes and alkenes as models for the long hydrocarbon chain of actual biodiesel methyl esters. We again show that allylic bonds in the alkenes are much weaker than those in the small methyl esters, indicating that hydrogen abstractions are more likely at the allylic site and even more likely at bis-allylic sites of alkyl chains due to more electrons involved in π-resonance in the latter. Lastly, we use the BDEs in small surrogates to estimate heretofore unknown BDEs in large methyl esters of biodiesel fuels. PMID:24621192

  1. On a more accurate half-discrete Hardy-Hilbert-type inequality related to the kernel of arc tangent function.

    PubMed

    Chen, Qiang; Yang, Bicheng

    2016-01-01

    By means of weight functions and Hermite-Hadamard's inequality, and introducing a discrete interval variable, a more accurate half-discrete Hardy-Hilbert-type inequality related to the kernel of arc tangent function and a best possible constant factor is given, which is an extension of a published result. The equivalent forms and the operator expressions are also considered. PMID:27563512

  2. On a more accurate half-discrete Hardy-Hilbert-type inequality related to the kernel of arc tangent function.

    PubMed

    Chen, Qiang; Yang, Bicheng

    2016-01-01

    By means of weight functions and Hermite-Hadamard's inequality, and introducing a discrete interval variable, a more accurate half-discrete Hardy-Hilbert-type inequality related to the kernel of arc tangent function and a best possible constant factor is given, which is an extension of a published result. The equivalent forms and the operator expressions are also considered.

  3. Obesity Has Minimal Impact on Short-Term Functional Scores After Reverse Shoulder Arthroplasty for Rotator Cuff Tear Arthropathy.

    PubMed

    Morris, Brent J; Haigler, Richard E; Cochran, John M; Laughlin, Mitzi S; Elkousy, Hussein A; Gartsman, Gary M; Edwards, T Bradley

    2016-01-01

    The potential adverse effect of body mass index (BMI) on shoulder function scores after reverse shoulder arthroplasty (RSA) has not been investigated. We conducted a study to examine outcomes of RSA performed for rotator cuff tear arthropathy (RCTA) across BMI categories (normal weight, overweight, obese). We hypothesized that, compared with normal-weight patients, obese patients would have worse shoulder function scores, worse mobility, and more complications. Using a prospective shoulder arthroplasty registry, we identified 77 primary RSAs performed for RCTA with minimum 2-year follow-up. Thirty-four patients had normal weight (BMI <25 kg/m2), 21 were overweight (BMI 25-30 kg/m2), and 22 were obese (BMI >30 kg/m2). Shoulder function scores, mobility, and satisfaction were evaluated before surgery and at final follow-up. The 3 BMI groups were not significantly different on demographic factors, preoperative shoulder function scores, or preoperative mobility (P > .05). For each group, shoulder function scores and mobility significantly improved between the preoperative and final follow-up assessments (P < .001). Patient satisfaction was similar between groups (P = .967). Improved shoulder function scores, mobility, and patient satisfaction can be expected after RSA for RCTA in patients regardless of BMI. PMID:27327923

  4. Clinical Correlates of Hachinski Ischemic Score and Vascular Factors in Cognitive Function of Elderly

    PubMed Central

    Kim, Youn Ho

    2014-01-01

    The aim of this study is to investigate the relationship between Hachinski ischemic score (HIS) and vascular factors as well as between HIS and the cognitive function in elderly community. Demographic characteristics, such as sex, age, education, history of drinking and smoking, family history of dementia and stroke, diabetes mellitus, hypertension, hyperlipidemia, cardiovascular disease, stroke, and dementia, were surveyed. Neurological examination was administered to every subject and HIS was checked by a neurologist. From a total of 392 participants aged 65 and over in a rural community, 348 completed the survey and were finally enrolled. Among the vascular factors, history of hypertension (P = 0.008), history of stroke (P < 0.001), family history of dementia (P = 0.01), and history of cardiac diseases (P = 0.012) showed a significant relationship with HIS. In the cognitive function tests, both Korean version of the Mini-Mental State Examination and the Clinical Dementia Rating (Global and Sum of Boxes) had a significant relationship with HIS. Our study suggested HIS may have an association with some vascular factors and cognitive scales in community dwelling elderly. In this study, the HIS seemed to contribute to the evaluation of the quantity of vascular factors and to the prediction of status of cognitive function. PMID:25247189

  5. Early indications that low mental quality of life scores in recently unwell older people predict downstream functional decline

    PubMed Central

    Atlas, Alvin; Grimmer, Karen; Kennedy, Kate

    2015-01-01

    Background Accurately detecting markers of early functional decline (FD) are essential to support older people to successfully age in place; however, these markers are poorly understood. We tested the hypothesis that compromised mental quality of life after a minor health crisis could be an early predictor of FD. Methods This longitudinal observational cohort study was conducted in the emergency department (ED) of a large Australian hospital and in the community. Data were collected from 148 community-dwelling people aged 65+ years, who provided data at recruitment (baseline), and at 1 month and 3 months post discharge from the ED. Short Form-12 mental quality of life component scores (MCS) were regressed with patient descriptors taken at baseline (age, sex, socioeconomic status, education, Mini-Mental State Examination, and primary language), and over-time estimates of FD taken at baseline, and at 1 and 3 months post discharge (instrumental activities of daily living, frequency of falls and hospitalizations, use of gait aids, receipt of community services, living status, and requiring a carer). Results MCS at 1 month (MCS1) post ED discharge was significantly associated with instrumental activities of daily living at 1 (r=0.45, P<0.001) and 3 months (r=0.401, P=0.001) post ED discharge, but not at baseline (r=0.010, P>0.05). Subjects with lower than the population median MCS showed a significant linear decline in total instrumental activities of daily living scores over 3 months (P=0.025). There was no linear trend over time in the relationship between MCS1 with frequency of falls (P=0.20) or hospitalizations (P=0.42); however, there was a significant difference at 3 months post ED discharge for falls (P=0.036) and hospitalizations (P=0.039) between low and high MCS1 groups. There were no significant confounders. Conclusion Low MCS scores 1 month after a minor health crisis appear to significantly predict downstream FD. This finding needs to be tested in a larger

  6. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  7. Is scoring system of computed tomography based metric parameters can accurately predicts shock wave lithotripsy stone-free rates and aid in the development of treatment strategies?

    PubMed Central

    Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim

    2016-01-01

    Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192

  8. Arterial Input Function Placement for Accurate CT Perfusion Map Construction in Acute Stroke

    PubMed Central

    Ferreira, Rafael M.; Lev, Michael H.; Goldmakher, Gregory V.; Kamalian, Shahmir; Schaefer, Pamela W.; Furie, Karen L.; Gonzalez, R. Gilberto; Sanelli, Pina C.

    2013-01-01

    OBJECTIVE The objective of our study was to evaluate the effect of varying arterial input function (AIF) placement on the qualitative and quantitative CT perfusion parameters. MATERIALS AND METHODS Retrospective analysis of CT perfusion data was performed on 14 acute stroke patients with a proximal middle cerebral artery (MCA) clot. Cerebral blood flow (CBF), cerebral blood volume (CBV), and mean transit time (MTT) maps were constructed using a systematic method by varying only the AIF placement in four positions relative to the MCA clot including proximal and distal to the clot in the ipsilateral and contralateral hemispheres. Two postprocessing software programs were used to evaluate the effect of AIF placement on perfusion parameters using a delay-insensitive deconvolution method compared with a standard deconvolution method. RESULTS One hundred sixty-eight CT perfusion maps were constructed for each software package. Both software programs generated a mean CBF at the infarct core of < 12 mL/100 g/min and a mean CBV of < 2 mL/100 g for AIF placement proximal to the clot in the ipsilateral hemisphere and proximal and distal to the clot in the contralateral hemisphere. For AIF placement distal to the clot in the ipsilateral hemisphere, the mean CBF significantly increased to 17.3 mL/100 g/min with delay-insensitive software and to 19.4 mL/100 g/min with standard software (p < 0.05). The mean MTT was significantly decreased for this AIF position. Furthermore, this AIF position yielded qualitatively different parametric maps, being most pronounced with MTT and CBF. Overall, CBV was least affected by AIF location. CONCLUSION For postprocessing of accurate quantitative CT perfusion maps, laterality of the AIF location is less important than avoiding AIF placement distal to the clot as detected on CT angiography. This pitfall is less severe with deconvolution-based software programs using a delay-insensitive technique than with those using a standard deconvolution

  9. A non-empirical, parameter-free, hybrid functional for accurate calculations of optoelectronic properties of finite systems

    NASA Astrophysics Data System (ADS)

    Brawand, Nicholas; Vörös, Márton; Govoni, Marco; Galli, Giulia

    The accurate prediction of optoelectronic properties of molecules and solids is a persisting challenge for current density functional theory (DFT) based methods. We propose a hybrid functional where the mixing fraction of exact and local exchange is determined by a non-empirical, system dependent function. This functional yields ionization potentials, fundamental and optical gaps of many, diverse systems in excellent agreement with experiments, including organic and inorganic molecules and nanocrystals. We further demonstrate that the newly defined hybrid functional gives the correct alignment between the energy level of the exemplary TTF-TCNQ donor-acceptor system. DOE-BES: DE-FG02-06ER46262.

  10. Accurate localization of supernumerary mediastinal parathyroid adenomas by a combination of structural and functional imaging.

    PubMed

    Mackie, G C; Schlicht, S M

    2004-09-01

    Reoperation for refractory or recurrent hyperparathyroidism following parathyroidectomy carries the potential for increased morbidity and the possibility of failure to localize and remove the lesion intraoperatively. Reported herein are three cases demonstrating the combined use of sestamibi scintigraphy, CT and MR for accurate localization of mediastinal parathyroid adenomas.

  11. Reliability and Construct Validity of Scores on the Behavioral Competence Inventory: A Measure of Adaptive Functioning.

    ERIC Educational Resources Information Center

    Jarjoura, David; Hartman-Stein, Paula; Speight, Joan; Reuter, Jeanette

    1999-01-01

    Examined the reliability and construct validity in an older adult population (n=149 older adults and their informants) of scores on the Behavioral Competence Inventory (BCI) (P. Hartman-Stein). Results indicate that scores on the BCI's seven scales show adequate internal consistencies and represent seven overlapping but distinct constructs in this…

  12. Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.

    PubMed

    Durrant, Jacob D; Carlson, Kathryn E; Martin, Teresa A; Offutt, Tavina L; Mayne, Christopher G; Katzenellenbogen, John A; Amaro, Rommie E

    2015-09-28

    The magnitude of the investment required to bring a drug to the market hinders medical progress, requiring hundreds of millions of dollars and years of research and development. Any innovation that improves the efficiency of the drug-discovery process has the potential to accelerate the delivery of new treatments to countless patients in need. "Virtual screening," wherein molecules are first tested in silico in order to prioritize compounds for subsequent experimental testing, is one such innovation. Although the traditional scoring functions used in virtual screens have proven useful, improved accuracy requires novel approaches. In the current work, we use the estrogen receptor to demonstrate that neural networks are adept at identifying structurally novel small molecules that bind to a selected drug target, ultimately allowing experimentalists to test fewer compounds in the earliest stages of lead identification while obtaining higher hit rates. We describe 39 novel estrogen-receptor ligands identified in silico with experimentally determined Ki values ranging from 460 nM to 20 μM, presented here for the first time. PMID:26286148

  13. Evaluation of the neural function of nonhuman primates with spinal cord injury using an evoked potential-based scoring system.

    PubMed

    Ye, Jichao; Ma, Mengjun; Xie, Zhongyu; Wang, Peng; Tang, Yong; Huang, Lin; Chen, Keng; Gao, Liangbin; Wu, Yanfeng; Shen, Huiyong; Zeng, Yuanshan

    2016-01-01

    Nonhuman primate models of spinal cord injury (SCI) have been widely used in evaluation of the efficacy and safety of experimental restorative interventions before clinical trials. However, no objective methods are currently available for the evaluation of neural function in nonhuman primates. In our long-term clinical practice, we have used evoked potential (EP) for neural function surveillance during operation and accumulated extensive experience. In the present study, a nonhuman primate model of SCI was established in 6 adult cynomologus monkeys through spinal cord contusion injury at T8-T9. The neural function before SCI and within 6 months after SCI was evaluated based on EP recording. A scoring system including somatosensory evoked potentials (SSEPs) and transcranial electrical stimulation-motor evoked potentials (TES-MEPs) was established for the evaluation of neural function of nonhuman primates with SCI. We compared the motor function scores of nonhuman primates before and after SCI. Our results showed that the EP below the injury level significantly changed during the 6 months after SCI. In addition, a positive correlation was identified between the EP scores and motor function. The EP-based scoring system is a reliable approach for evaluating the motor function changes in nonhuman primates with SCI. PMID:27629352

  14. Evaluation of the neural function of nonhuman primates with spinal cord injury using an evoked potential-based scoring system

    PubMed Central

    Ye, Jichao; Ma, Mengjun; Xie, Zhongyu; Wang, Peng; Tang, Yong; Huang, Lin; Chen, Keng; Gao, Liangbin; Wu, Yanfeng; Shen, Huiyong; Zeng, Yuanshan

    2016-01-01

    Nonhuman primate models of spinal cord injury (SCI) have been widely used in evaluation of the efficacy and safety of experimental restorative interventions before clinical trials. However, no objective methods are currently available for the evaluation of neural function in nonhuman primates. In our long-term clinical practice, we have used evoked potential (EP) for neural function surveillance during operation and accumulated extensive experience. In the present study, a nonhuman primate model of SCI was established in 6 adult cynomologus monkeys through spinal cord contusion injury at T8–T9. The neural function before SCI and within 6 months after SCI was evaluated based on EP recording. A scoring system including somatosensory evoked potentials (SSEPs) and transcranial electrical stimulation-motor evoked potentials (TES-MEPs) was established for the evaluation of neural function of nonhuman primates with SCI. We compared the motor function scores of nonhuman primates before and after SCI. Our results showed that the EP below the injury level significantly changed during the 6 months after SCI. In addition, a positive correlation was identified between the EP scores and motor function. The EP-based scoring system is a reliable approach for evaluating the motor function changes in nonhuman primates with SCI. PMID:27629352

  15. Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity.

    PubMed

    Kulharia, Mahesh; Goody, Roger S; Jackson, Richard M

    2008-10-01

    The development and validation of a new knowledge based scoring function (SIScoreJE) to predict binding energy between proteins and ligands is presented. SIScoreJE efficiently predicts the binding energy between a small molecule and its protein receptor. Protein-ligand atomic contact information was derived from a Non-Redundant Data set (NRD) of over 3000 X-ray crystal structures of protein-ligand complexes. This information was classified for individual "atom contact pairs" (ACP) which is used to calculate the atomic contact preferences. In addition to the two schemes generated in this study we have assessed a number of other common atom-type classification schemes. The preferences were calculated using an information theoretic relationship of joint entropy. Among 18 different atom-type classification schemes "ScoreJE Atom Type set2" (SATs2) was found to be the most suitable for our approach. To test the sensitivity of the method to the inclusion of solvent, Single-body Solvation Potentials (SSP) were also derived from the atomic contacts between the protein atom types and water molecules modeled using AQUARIUS2. Validation was carried out using an evaluation data set of 100 protein-ligand complexes with known binding energies to test the ability of the scoring functions to reproduce known binding affinities. In summary, it was found that a combined SSP/ScoreJE (SIScoreJE) performed significantly better than ScoreJE alone, and SIScoreJE and ScoreJE performed better than GOLD::GoldScore, GOLD::ChemScore, and XScore.

  16. Multiconfiguration Pair-Density Functional Theory Is as Accurate as CASPT2 for Electronic Excitation.

    PubMed

    Hoyer, Chad E; Ghosh, Soumen; Truhlar, Donald G; Gagliardi, Laura

    2016-02-01

    A correct description of electronically excited states is critical to the interpretation of visible-ultraviolet spectra, photochemical reactions, and excited-state charge-transfer processes in chemical systems. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory and a new kind of density functional called an on-top density functional. Here, we show that MC-PDFT with a first-generation on-top density functional performs as well as CASPT2 for an organic chemistry database including valence, Rydberg, and charge-transfer excitations. The results are very encouraging for practical applications. PMID:26794241

  17. Applicability of density functional theory in reproducing accurate vibrational spectra of surface bound species.

    PubMed

    Matanović, Ivana; Atanassov, Plamen; Kiefer, Boris; Garzon, Fernando H; Henson, Neil J

    2014-10-01

    The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energy for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of -2.62 and -1.1% for the N-N stretching and Rh-H stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the Rh-H and N-N stretching modes from the bulk phonons and by solving one- and two-dimensional Schrödinger equation associated with the Rh-H, Rh-N, and N-N potential energy we calculated the anharmonic correction for N-N and Rh-H stretching modes as -31 cm(-1) and -77 cm(-1) at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments. PMID:25164265

  18. Applicability of Density Functional Theory in Reproducing Accurate Vibrational Spectra of Surface Bound Species

    SciTech Connect

    Matanovic, Ivana; Atanassov, Plamen; Kiefer, Boris; Garzon, Fernando; Henson, Neil J.

    2014-10-05

    The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energy for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of 22.62 and 21.1% for the NAN stretching and RhAH stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the RhAH and NAN stretching modes from the bulk phonons and by solving one- and two-dimensional Schr€odinger equation associated with the RhAH, RhAN, and NAN potential energy we calculated the anharmonic correction for NAN and RhAH stretching modes as 231 cm21 and 277 cm21 at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments.

  19. APACHE II score, rather than cardiac function, may predict poor prognosis in patients with stress-induced cardiomyopathy.

    PubMed

    Joe, Byung-Hyun; Jo, Uk; Kim, Hyun-Soo; Park, Chang-Bum; Hwang, Hui-Jeong; Sohn, Il-Suk; Jin, Eun-Sun; Cho, Jin-Man; Park, Jeong-Hwan; Kim, Chong-Jin

    2012-01-01

    While the disease course of stress-induced cardiomyopathy (SIC) is usually benign, it can be fatal. The prognostic factors to predict poorer outcome are not well established, however. We analyzed the Acute Physiology And Chronic Health Evaluation (APACHE) II score to assess its value for predicting poor prognosis in patients with SIC. Thirty-seven consecutive patients with SIC were followed prospectively during their hospitalization. Clinical factors, including APACHE II score, coronary angiogram, echocardiography and cardiac enzymes at presentation were analyzed. Of the 37 patients, 27 patients (73%) were women. The mean age was 66.1 ± 15.6 yr, and the most common presentation was chest pain (38%). Initial echocardiographic left ventricular ejection fraction (EF) was 42.5% ± 9.3%, and the wall motion score index (WMSI) was 1.9 ± 0.3. Six patients (16%) expired during the follow-up period of hospitalization. Based on the analysis of characteristics and clinical factors, the only predictable variable in prognosis was APACHE II score. The patients with APACHE II score greater than 20 had tendency to expire than the others (P = 0.001). Based on present study, APACHE II score more than 20, rather than cardiac function, is associated with mortality in patients with SIC.

  20. Relationship between functional movement screen scores, core strength, posture, and body mass index in school children in Moldova.

    PubMed

    Mitchell, Ulrike H; Johnson, A Wayne; Adamson, Brynn

    2015-05-01

    The assessment of functionality should include parameters that consider postural control, limb asymmetries, range of motion limitations, proprioceptive deficits, and pain. An increasingly popular battery of tests, the Functional Movement Screen (FMS), is purported to assess the above named parameters. The purpose of our study was twofold: (a) to report differences in total FMS scores in children, provide preliminary normative reference values of each of the 7 individual FMS scores for both genders and report on asymmetries and (b) to evaluate the relationship between total FMS scores, age, body mass index (BMI), core strength/stability, and postural angles to explore the possibility of using the FMS in the assessment of children's functional fitness. Descriptive data on 77 children aged 8-11 years were collected. The children performed core strength/stability exercises. Photographs were taken from a lateral view for later calculation of postural angles. The children performed the FMS while being videotaped for later review. The average total FMS score (of 21) was 14.9 (+1.9), and BMI was 16.4 (+2.2). Static posture is not related to results of the FMS. Core strength was positively correlated to the total FMS score (r = 0.31; p = 0.006). Over 60% demonstrated at least 1 asymmetry. The individual test scores indicate that none of the test items is too difficult for the children. Based on the screen's correlation to core strength, and the fact that it identifies areas of asymmetry, we suggest to further investigate its possible use in the assessment of children's functional fitness.

  1. New density functional parameterizations to accurate calculations of electric field gradient variations among compounds.

    PubMed

    Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade

    2015-10-30

    This research provides a performance investigation of density functional theory and also proposes new functional parameterizations to deal with electric field gradient (EFG) calculations at nuclear positions. The entire procedure is conducted within the four-component formalism. First, we noticed that traditional hybrid and long-range corrected functionals are more efficient in the description of EFG variations for a set of elements (indium, antimony, iodine, lutetium, and hafnium) among linear molecules. Thus, we selected the PBE0, B3LYP, and CAM-B3LYP functionals and promoted a reoptimization of their parameters for a better description of these EFG changes. The PBE0q variant developed here showed an overall promising performance in a validation test conducted with potassium, iodine, copper, and gold. In general, the correlation coefficients found in linear regressions between experimental nuclear quadrupole coupling constants and calculated EFGs are improved while the systematic EFG errors also decrease as a result of this reparameterization. PMID:26284820

  2. Improving DOE-2's RESYS routine: User defined functions to provide more accurate part load energy use and humidity predictions

    SciTech Connect

    Henderson, Hugh I.; Parker, Danny; Huang, Yu J.

    2000-08-04

    In hourly energy simulations, it is important to properly predict the performance of air conditioning systems over a range of full and part load operating conditions. An important component of these calculations is to properly consider the performance of the cycling air conditioner and how it interacts with the building. This paper presents improved approaches to properly account for the part load performance of residential and light commercial air conditioning systems in DOE-2. First, more accurate correlations are given to predict the degradation of system efficiency at part load conditions. In addition, a user-defined function for RESYS is developed that provides improved predictions of air conditioner sensible and latent capacity at part load conditions. The user function also provides more accurate predictions of space humidity by adding ''lumped'' moisture capacitance into the calculations. The improved cooling coil model and the addition of moisture capacitance predicts humidity swings that are more representative of the performance observed in real buildings.

  3. The Mantel-Haenszel Method for Detecting Differential Item Functioning in Dichotomously Scored Items: A Multilevel Approach

    ERIC Educational Resources Information Center

    MacInnes, Jann Marie Wise

    2009-01-01

    Multilevel data often exist in educational studies. The focus of this study is to consider differential item functioning (DIF) for dichotomous items from a multilevel perspective. One of the most often used methods for detecting DIF in dichotomously scored items is the Mantel-Haenszel log odds-ratio. However, the Mantel-Haenszel reduces the…

  4. Accurate and efficient calculation of discrete correlation functions and power spectra

    NASA Astrophysics Data System (ADS)

    Xu, Y. F.; Liu, J. M.; Zhu, W. D.

    2015-07-01

    Operational modal analysis (OMA), or output-only modal analysis, has been widely conducted especially when excitation applied on a structure is unknown or difficult to measure. Discrete cross-correlation functions and cross-power spectra between a reference data series and measured response data series are bases for OMA to identify modal properties of a structure. Such functions and spectra can be efficiently transformed from each other using the discrete Fourier transform (DFT) and inverse DFT (IDFT) based on the cross-correlation theorem. However, a direct application of the theorem and transforms, including the DFT and IDFT, can yield physically erroneous results due to periodic extension of the DFT on a function of a finite length to be transformed, which is false most of the time. Padding zero series to ends of data series before applying the theorem and transforms can reduce the errors, but the results are still physically erroneous. A new methodology is developed in this work to calculate discrete cross-correlation functions of non-negative time delays and associated cross-power spectra, referred to as half spectra, for OMA. The methodology can be extended to cross-correlation functions of any time delays and associated cross-power spectra, referred to as full spectra. The new methodology is computationally efficient due to use of the transforms. Data series are properly processed to avoid the errors caused by the periodic extension, and the resulting cross-correlation functions and associated cross-power spectra perfectly comply with their definitions. A coherence function, a convergence function, and a convergence index are introduced to evaluate qualities of measured cross-correlation functions and associated cross-power spectra. The new methodology was numerically and experimentally applied to an ideal two-degree-of-freedom (2-DOF) mass-spring-damper system and a damaged aluminum beam, respectively, and OMA was conducted using half spectra to estimate

  5. Acrophobia Factor Scores As A Function Of Pole Height And Habituation.

    PubMed

    Royce, J R; Poley, W

    1976-04-01

    Thirty C57BL/ALB mice, fifteen male and fifteen female, were tested for "acrophobia" via the pole test. The animals were randomly distributed into three groups of 6, 12, or 24 inch (15.24, 30.48, or 60.96 cm) high poles:. Both factor scores and individual pole measures were analyzed by 2 x 3 x 5 ANOVA, with main effects for sex, pole height, and days of testing. The results provide experimental support for the interpretation of this factor as acrophobia-that is, the greater the pole height, the higher the factor score. The reduction of factor scores over days (habituation) is interpreted as an arousal-based response.

  6. A simple and accurate grading system for orthoiodohippurate renal scans in the assessment of post-transplant renal function

    SciTech Connect

    Zaki, S.K.; Bretan, P.N.; Go, R.T.; Rehm, P.K.; Streem, S.B.; Novick, A.C. )

    1990-06-01

    Orthoiodohippurate renal scanning has proved to be a reliable, noninvasive method for the evaluation and followup of renal allograft function. However, a standardized system for grading renal function with this test is not available. We propose a simple grading system to distinguish the different functional phases of hippurate scanning in renal transplant recipients. This grading system was studied in 138 patients who were evaluated 1 week after renal transplantation. There was a significant correlation between the isotope renographic functional grade and clinical correlates of allograft function such as the serum creatinine level (p = 0.0001), blood urea nitrogen level (p = 0.0001), urine output (p = 0.005) and need for hemodialysis (p = 0.007). We recommend this grading system as a simple and accurate method to interpret orthoiodohippurate renal scans in the evaluation and followup of renal allograft recipients.

  7. An extended set of yeast-based functional assays accurately identifies human disease mutations

    PubMed Central

    Sun, Song; Yang, Fan; Tan, Guihong; Costanzo, Michael; Oughtred, Rose; Hirschman, Jodi; Theesfeld, Chandra L.; Bansal, Pritpal; Sahni, Nidhi; Yi, Song; Yu, Analyn; Tyagi, Tanya; Tie, Cathy; Hill, David E.; Vidal, Marc; Andrews, Brenda J.; Boone, Charles; Dolinski, Kara; Roth, Frederick P.

    2016-01-01

    We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogenicity of human genetic variation. However, a systematic performance comparison between them has been lacking. Therefore, we developed and exploited a panel of 26 yeast-based functional complementation assays to measure the impact of 179 variants (101 disease- and 78 non-disease-associated variants) from 22 human disease genes. Using the resulting reference standard, we show that experimental functional assays in a 1-billion-year diverged model organism can identify pathogenic alleles with significantly higher precision and specificity than current computational methods. PMID:26975778

  8. An extended set of yeast-based functional assays accurately identifies human disease mutations.

    PubMed

    Sun, Song; Yang, Fan; Tan, Guihong; Costanzo, Michael; Oughtred, Rose; Hirschman, Jodi; Theesfeld, Chandra L; Bansal, Pritpal; Sahni, Nidhi; Yi, Song; Yu, Analyn; Tyagi, Tanya; Tie, Cathy; Hill, David E; Vidal, Marc; Andrews, Brenda J; Boone, Charles; Dolinski, Kara; Roth, Frederick P

    2016-05-01

    We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogenicity of human genetic variation. However, a systematic performance comparison between them has been lacking. Therefore, we developed and exploited a panel of 26 yeast-based functional complementation assays to measure the impact of 179 variants (101 disease- and 78 non-disease-associated variants) from 22 human disease genes. Using the resulting reference standard, we show that experimental functional assays in a 1-billion-year diverged model organism can identify pathogenic alleles with significantly higher precision and specificity than current computational methods. PMID:26975778

  9. An extended set of yeast-based functional assays accurately identifies human disease mutations.

    PubMed

    Sun, Song; Yang, Fan; Tan, Guihong; Costanzo, Michael; Oughtred, Rose; Hirschman, Jodi; Theesfeld, Chandra L; Bansal, Pritpal; Sahni, Nidhi; Yi, Song; Yu, Analyn; Tyagi, Tanya; Tie, Cathy; Hill, David E; Vidal, Marc; Andrews, Brenda J; Boone, Charles; Dolinski, Kara; Roth, Frederick P

    2016-05-01

    We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogenicity of human genetic variation. However, a systematic performance comparison between them has been lacking. Therefore, we developed and exploited a panel of 26 yeast-based functional complementation assays to measure the impact of 179 variants (101 disease- and 78 non-disease-associated variants) from 22 human disease genes. Using the resulting reference standard, we show that experimental functional assays in a 1-billion-year diverged model organism can identify pathogenic alleles with significantly higher precision and specificity than current computational methods.

  10. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

    PubMed

    Brylinski, Michal

    2013-11-25

    A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely

  11. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

    PubMed

    Brylinski, Michal

    2013-11-25

    A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely

  12. Communication: a density functional with accurate fractional-charge and fractional-spin behaviour for s-electrons.

    PubMed

    Johnson, Erin R; Contreras-García, Julia

    2011-08-28

    We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)] and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems.

  13. Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom.

    PubMed

    Mishra, Avdesh; Iqbal, Sumaiya; Hoque, Md Tamjidul

    2016-06-01

    The success of solving the protein folding and structure prediction problems in molecular and structural biology relies on an accurate energy function. With the rapid advancement in the computational biology and bioinformatics fields, there is a growing need of solving unknown fold and structure faster and thus an accurate energy function is indispensable. To address this need, we develop a new potential function, namely 3DIGARS3.0, which is a linearly weighted combination of 3DIGARS, mined accessible surface area (ASA) and ubiquitously computed Phi (uPhi) and Psi (uPsi) energies - optimized by a Genetic Algorithm (GA). We use a dataset of 4332 protein-structures to generate uPhi and uPsi based score libraries to be used within the core 3DIGARS method. The optimized weight of each component is obtained by applying Genetic Algorithm based optimization on three challenging decoy sets. The improved 3DIGARS3.0 outperformed state-of-the-art methods significantly based on a set of independent test datasets.

  14. A method for the accurate and smooth approximation of standard thermodynamic functions

    NASA Astrophysics Data System (ADS)

    Coufal, O.

    2013-01-01

    A method is proposed for the calculation of approximations of standard thermodynamic functions. The method is consistent with the physical properties of standard thermodynamic functions. This means that the approximation functions are, in contrast to the hitherto used approximations, continuous and smooth in every temperature interval in which no phase transformations take place. The calculation algorithm was implemented by the SmoothSTF program in the C++ language which is part of this paper. Program summaryProgram title:SmoothSTF Catalogue identifier: AENH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3807 No. of bytes in distributed program, including test data, etc.: 131965 Distribution format: tar.gz Programming language: C++. Computer: Any computer with gcc version 4.3.2 compiler. Operating system: Debian GNU Linux 6.0. The program can be run in operating systems in which the gcc compiler can be installed, see http://gcc.gnu.org/install/specific.html. RAM: 256 MB are sufficient for the table of standard thermodynamic functions with 500 lines Classification: 4.9. Nature of problem: Standard thermodynamic functions (STF) of individual substances are given by thermal capacity at constant pressure, entropy and enthalpy. STF are continuous and smooth in every temperature interval in which no phase transformations take place. The temperature dependence of STF as expressed by the table of its values is for further application approximated by temperature functions. In the paper, a method is proposed for calculating approximation functions which, in contrast to the hitherto used approximations, are continuous and smooth in every temperature interval. Solution method: The approximation functions are

  15. Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.; Lomakina, Ekaterina I.

    2009-08-01

    Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

  16. Accurate Zero Parameter Correlation Energy Functional Obtained from the Homogeneous Electron Gas with an Energy Gap

    NASA Astrophysics Data System (ADS)

    Krieger, J. B.; Chen, Jiqiang; Iafrate, G. J.; Savin, A.

    1998-03-01

    We have obtained an analytic approximation to E_c(r_g, ζ,G) where G is an energy gap separating the occupied and unoccupied states of a homogeneous electron gas for ζ=3D0 and ξ=3D1. When G=3D0, E_c(r_g, ζ) reduces to the usual LSD result. This functional is employed in calculating correlation energies for unpolarized atoms and ions for Z <= 18 by taking G[n]=3D1/8|nabla ln n|^2, which reduces to the ionization energy in the large r limit in an exact Kohn-Sham (KS) theory. The resulting functional is self-interaction-corrected employing a method which is invariant under a unitary transformation. We find that the application of this approach to the calculation of the Ec functional reduces the error in the LSD result by more than 95%. When the value of G is approximately corrected to include the effect of higher lying unoccupied localized states, the resulting values of Ec are within a few percent of the exact results.

  17. Accurate Diels-Alder reaction energies from efficient density functional calculations.

    PubMed

    Mezei, Pál D; Csonka, Gábor I; Kállay, Mihály

    2015-06-01

    We assess the performance of the semilocal PBE functional; its global hybrid variants; the highly parametrized empirical M06-2X and M08-SO; the range separated rCAM-B3LYP and MCY3; the atom-pairwise or nonlocal dispersion corrected semilocal PBE and TPSS; the dispersion corrected range-separated ωB97X-D; the dispersion corrected double hybrids such as PWPB95-D3; the direct random phase approximation, dRPA, with Hartree-Fock, Perdew-Burke-Ernzerhof, and Perdew-Burke-Ernzerhof hybrid reference orbitals and the RPAX2 method based on a Perdew-Burke-Ernzerhof exchange reference orbitals for the Diels-Alder, DARC; and self-interaction error sensitive, SIE11, reaction energy test sets with large, augmented correlation consistent valence basis sets. The dRPA energies for the DARC test set are extrapolated to the complete basis set limit. CCSD(T)/CBS energies were used as a reference. The standard global hybrid functionals show general improvements over the typical endothermic energy error of semilocal functionals, but despite the increased accuracy the precision of the methods increases only slightly, and thus all reaction energies are simply shifted into the exothermic direction. Dispersion corrections give mixed results for the DARC test set. Vydrov-Van Voorhis 10 correction to the reaction energies gives superior quality results compared to the too-small D3 correction. Functionals parametrized for energies of noncovalent interactions like M08-SO give reasonable results without any dispersion correction. The dRPA method that seamlessly and theoretically correctly includes noncovalent interaction energies gives excellent results with properly chosen reference orbitals. As the results for the SIE11 test set and H2(+) dissociation show that the dRPA methods suffer from delocalization error, good reaction energies for the DARC test set from a given method do not prove that the method is free from delocalization error. The RPAX2 method shows good performance for the DARC

  18. Accurate vibrational frequencies using the self-consistent-charge density-functional tight-binding method

    NASA Astrophysics Data System (ADS)

    Małolepsza, Edyta; Witek, Henryk A.; Morokuma, Keiji

    2005-09-01

    An optimization technique for enhancing the quality of repulsive two-body potentials of the self-consistent-charge density-functional tight-binding (SCC-DFTB) method is presented and tested. The new, optimized potentials allow for significant improvement of calculated harmonic vibrational frequencies. Mean absolute deviation from experiment computed for a group of 14 hydrocarbons is reduced from 59.0 to 33.2 cm -1 and maximal absolute deviation, from 436.2 to 140.4 cm -1. A drawback of the new family of potentials is a lower quality of reproduced geometrical and energetic parameters.

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

    PubMed

    Venner, Eric; Lisewski, Andreas Martin; Erdin, Serkan; Ward, R Matthew; Amin, Shivas R; Lichtarge, Olivier

    2010-01-01

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

  20. Two functionally distinct kinetochore pools of BubR1 ensure accurate chromosome segregation

    PubMed Central

    Zhang, Gang; Mendez, Blanca Lopez; Sedgwick, Garry G.; Nilsson, Jakob

    2016-01-01

    The BubR1/Bub3 complex is an important regulator of chromosome segregation as it facilitates proper kinetochore–microtubule interactions and is also an essential component of the spindle assembly checkpoint (SAC). Whether BubR1/Bub3 localization to kinetochores in human cells stimulates SAC signalling or only contributes to kinetochore–microtubule interactions is debated. Here we show that two distinct pools of BubR1/Bub3 exist at kinetochores and we uncouple these with defined BubR1/Bub3 mutants to address their function. The major kinetochore pool of BubR1/Bub3 is dependent on direct Bub1/Bub3 binding and is required for chromosome alignment but not for the SAC. A distinct pool of BubR1/Bub3 localizes by directly binding to phosphorylated MELT repeats on the outer kinetochore protein KNL1. When we prevent the direct binding of BubR1/Bub3 to KNL1 the checkpoint is weakened because BubR1/Bub3 is not incorporated into checkpoint complexes efficiently. In conclusion, kinetochore localization supports both known functions of BubR1/Bub3. PMID:27457023

  1. Compact and accurate linear and nonlinear autoregressive moving average model parameter estimation using laguerre functions.

    PubMed

    Chon, K H; Cohen, R J; Holstein-Rathlou, N H

    1997-01-01

    A linear and nonlinear autoregressive moving average (ARMA) identification algorithm is developed for modeling time series data. The algorithm uses Laguerre expansion of kernals (LEK) to estimate Volterra-Wiener kernals. However, instead of estimating linear and nonlinear system dynamics via moving average models, as is the case for the Volterra-Wiener analysis, we propose an ARMA model-based approach. The proposed algorithm is essentially the same as LEK, but this algorithm is extended to include past values of the output as well. Thus, all of the advantages associated with using the Laguerre function remain with our algorithm; but, by extending the algorithm to the linear and nonlinear ARMA model, a significant reduction in the number of Laguerre functions can be made, compared with the Volterra-Wiener approach. This translates into a more compact system representation and makes the physiological interpretation of higher order kernels easier. Furthermore, simulation results show better performance of the proposed approach in estimating the system dynamics than LEK in certain cases, and it remains effective in the presence of significant additive measurement noise. PMID:9236985

  2. Estimation method of point spread function based on Kalman filter for accurately evaluating real optical properties of photonic crystal fibers.

    PubMed

    Shen, Yan; Lou, Shuqin; Wang, Xin

    2014-03-20

    The evaluation accuracy of real optical properties of photonic crystal fibers (PCFs) is determined by the accurate extraction of air hole edges from microscope images of cross sections of practical PCFs. A novel estimation method of point spread function (PSF) based on Kalman filter is presented to rebuild the micrograph image of the PCF cross-section and thus evaluate real optical properties for practical PCFs. Through tests on both artificially degraded images and microscope images of cross sections of practical PCFs, we prove that the proposed method can achieve more accurate PSF estimation and lower PSF variance than the traditional Bayesian estimation method, and thus also reduce the defocus effect. With this method, we rebuild the microscope images of two kinds of commercial PCFs produced by Crystal Fiber and analyze the real optical properties of these PCFs. Numerical results are in accord with the product parameters.

  3. Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds.

    PubMed

    Moreira, Ney H; Dolgonos, Grygoriy; Aradi, Bálint; da Rosa, Andreia L; Frauenheim, Thomas

    2009-03-10

    An extended self-consistent charge density-functional tight-binding (SCC-DFTB) parametrization for Zn-X (X = H, C, N, O, S, and Zn) interactions has been derived. The performance of this new parametrization has been validated by calculating the structural and energetic properties of zinc solid phases such as bulk Zn, ZnO, and ZnS; ZnO surfaces and nanostructures; adsorption of small species (H, CO2, and NH3) on ZnO surfaces; and zinc-containing complexes mimicking the biological environment. Our results show that the derived parameters are universal and fully transferable, describing all the above-mentioned systems with accuracies comparable to those of first-principles DFT results. PMID:26610226

  4. The Balthazar Scales of Adaptive Behavior. Measures of Program Development for the Severely and Profoundly Mentally Retarded. Section 1. Skills of Functional Independence. Part Three: Program Scoring Form.

    ERIC Educational Resources Information Center

    Balthazar, Earl E.

    The scoring form for functional independence skills for the mentally retarded includes a section for recording subjects' demographic characteristics as well as tests used, date administered, and raw score. Other sections provide for a brief description of the program being used, an item scoring sheet for the Eating Scales (dependent feeding,…

  5. Relationship between functional movement screening score and history of injury and identifying the predictive value of the FMS for injury.

    PubMed

    Shojaedin, Seyyed Sadredin; Letafatkar, Amir; Hadadnezhad, Malihe; Dehkhoda, Mohamad Reza

    2014-01-01

    This study aimed to reveal the functional ability of functional movement screening (FMS) scores in determining an athlete's predisposition to injury. One hundred (50 females and 50 males) university level athletes, weight of 69.44 ± 5.84 kg, height of 172.69 ± 7.26 cm, age of 22.56 ± 2.99 years and Baecke score 21.66 ± 1.73, practised in football, handball and basketball sports (at least for 5 years), with no recent (<6 weeks) history of musculoskeletal injury were recruited. Of the 100 subjects, 35 of them suffered an acute, lower extremity (ankle = 20 and knee = 15 subjects) injury. An odds ratio was calculated at 4.70, meaning that an athlete has an approximately 4.7 times greater chance of suffering a lower extremity injury during a regular competitive season if they score less than 17 on the FMS. This study provides FMS reference values for university level athletes that will assist in the interpretation of individual scores when screening athletes for musculoskeletal injury and performance factors. More research is still necessary before implementing the FMS into a pre-participation physical examination for athletics, but due to the low cost and its simplicity to implement, it should be considered by clinicians and researchers in the future.

  6. Characterization of Thin Film Materials using SCAN MetaGGA, an Accurate Nonempirical Density Functional

    NASA Astrophysics Data System (ADS)

    Buda, Ioana-Gianina; Lane, Christopher; Barbiellini, Bernardo; Ruzsinszky, Adrienn; Sun, Jianwei; Perdew, John P.; Bansil, Arun

    The exact ground-state properties of a material can be derived from the single-particle Kohn-Sham equations within the framework of the Density Functional Theory (DFT), provided the exact exchange-correlation potential is known. The simplest approximation is the local density approximation (LDA), but it usually leads to overbinding in molecules and solids. On the other hand, the generalized gradient approximation (GGA) introduces corrections that expand and soften bonds. The newly developed nonempirical SCAN (strongly-constrained and appropriately-normed) MetaGGA [Phys. Rev. Lett. 115, 036402] has been shown to be comparable in efficiency to LDA and GGA, and to significantly improve LDA and the Perdew-Burke-Ernzerhof version of the GGA for ground-state properties such as equilibrium geometry and lattice constants for a number of standard datasets for molecules and solids. Here we discuss the performance of SCAN MetaGGA for thin films and monolayers and demonstrate improvements of predicted ground-state properties. Examples include graphene, phosphorene and MoS2.

  7. Efficient Approximation of Head-Related Transfer Functions in Subbands for Accurate Sound Localization

    PubMed Central

    Marelli, Damián; Baumgartner, Robert; Majdak, Piotr

    2015-01-01

    Head-related transfer functions (HRTFs) describe the acoustic filtering of incoming sounds by the human morphology and are essential for listeners to localize sound sources in virtual auditory displays. Since rendering complex virtual scenes is computationally demanding, we propose four algorithms for efficiently representing HRTFs in subbands, i.e., as an analysis filterbank (FB) followed by a transfer matrix and a synthesis FB. All four algorithms use sparse approximation procedures to minimize the computational complexity while maintaining perceptually relevant HRTF properties. The first two algorithms separately optimize the complexity of the transfer matrix associated to each HRTF for fixed FBs. The other two algorithms jointly optimize the FBs and transfer matrices for complete HRTF sets by two variants. The first variant aims at minimizing the complexity of the transfer matrices, while the second one does it for the FBs. Numerical experiments investigate the latency-complexity trade-off and show that the proposed methods offer significant computational savings when compared with other available approaches. Psychoacoustic localization experiments were modeled and conducted to find a reasonable approximation tolerance so that no significant localization performance degradation was introduced by the subband representation. PMID:26681930

  8. Accurate alignment of functional EPI data to anatomical MRI using a physics-based distortion model.

    PubMed

    Studholme, C; Constable, R T; Duncan, J S

    2000-11-01

    Mapping of functional magnetic resonance imaging (fMRI) to conventional anatomical MRI is a valuable step in the interpretation of fMRI activations. One of the main limits on the accuracy of this alignment arises from differences in the geometric distortion induced by magnetic field inhomogeneity. This paper describes an approach to the registration of echo planar image (EPI) data to conventional anatomical images which takes into account this difference in geometric distortion. We make use of an additional spin echo EPI image and use the known signal conservation in spin echo distortion to derive a specialized multimodality nonrigid registration algorithm. We also examine a plausible modification using log-intensity evaluation of the criterion to provide increased sensitivity in areas of low EPI signal. A phantom-based imaging experiment is used to evaluate the behavior of the different criteria, comparing nonrigid displacement estimates to those provided by a imagnetic field mapping acquisition. The algorithm is then applied to a range of nine brain imaging studies illustrating global and local improvement in the anatomical alignment and localization of fMRI activations.

  9. Accurate predictions of C-SO2R bond dissociation enthalpies using density functional theory methods.

    PubMed

    Yu, Hai-Zhu; Fu, Fang; Zhang, Liang; Fu, Yao; Dang, Zhi-Min; Shi, Jing

    2014-10-14

    The dissociation of the C-SO2R bond is frequently involved in organic and bio-organic reactions, and the C-SO2R bond dissociation enthalpies (BDEs) are potentially important for understanding the related mechanisms. The primary goal of the present study is to provide a reliable calculation method to predict the different C-SO2R bond dissociation enthalpies (BDEs). Comparing the accuracies of 13 different density functional theory (DFT) methods (such as B3LYP, TPSS, and M05 etc.), and different basis sets (such as 6-31G(d) and 6-311++G(2df,2p)), we found that M06-2X/6-31G(d) gives the best performance in reproducing the various C-S BDEs (and especially the C-SO2R BDEs). As an example for understanding the mechanisms with the aid of C-SO2R BDEs, some primary mechanistic studies were carried out on the chemoselective coupling (in the presence of a Cu-catalyst) or desulfinative coupling reactions (in the presence of a Pd-catalyst) between sulfinic acid salts and boryl/sulfinic acid salts.

  10. An Accurate Method for Prediction of Protein-Ligand Binding Site on Protein Surface Using SVM and Statistical Depth Function

    PubMed Central

    Wang, Kui; Gao, Jianzhao; Shen, Shiyi; Tuszynski, Jack A.; Ruan, Jishou

    2013-01-01

    Since proteins carry out their functions through interactions with other molecules, accurately identifying the protein-ligand binding site plays an important role in protein functional annotation and rational drug discovery. In the past two decades, a lot of algorithms were present to predict the protein-ligand binding site. In this paper, we introduce statistical depth function to define negative samples and propose an SVM-based method which integrates sequence and structural information to predict binding site. The results show that the present method performs better than the existent ones. The accuracy, sensitivity, and specificity on training set are 77.55%, 56.15%, and 87.96%, respectively; on the independent test set, the accuracy, sensitivity, and specificity are 80.36%, 53.53%, and 92.38%, respectively. PMID:24195070

  11. Towards an accurate specific reaction parameter density functional for water dissociation on Ni(111): RPBE versus PW91.

    PubMed

    Jiang, Bin; Guo, Hua

    2016-08-01

    In search for an accurate description of the dissociative chemisorption of water on the Ni(111) surface, we report a new nine-dimensional potential energy surface (PES) based on a large number of density functional theory points using the RPBE functional. Seven-dimensional quantum dynamical calculations have been carried out on the RPBE PES, followed by site averaging and lattice effect corrections, yielding sticking probabilities that are compared with both the previous theoretical results based on a PW91 PES and experiment. It is shown that the RPBE functional increases the reaction barrier, but has otherwise a minor impact on the PES topography. Better agreement with experimental results is obtained with the new PES, but the agreement is still not quantitative. Possible sources of the remaining discrepancies are discussed.

  12. Training compliance control yields improvements in drawing as a function of Beery scores.

    PubMed

    Snapp-Childs, Winona; Flatters, Ian; Fath, Aaron; Mon-Williams, Mark; Bingham, Geoffrey P

    2014-01-01

    Many children have difficulty producing movements well enough to improve in sensori-motor learning. Previously, we developed a training method that supports active movement generation to allow improvement at a 3D tracing task requiring good compliance control. Here, we tested 7-8 year old children from several 2nd grade classrooms to determine whether 3D tracing performance could be predicted using the Beery VMI. We also examined whether 3D tracing training lead to improvements in drawing. Baseline testing included Beery, a drawing task on a tablet computer, and 3D tracing. We found that baseline performance in 3D tracing and drawing co-varied with the visual perception (VP) component of the Beery. Differences in 3D tracing between children scoring low versus high on the Beery VP replicated differences previously found between children with and without motor impairments, as did post-training performance that eliminated these differences. Drawing improved as a result of training in the 3D tracing task. The training method improved drawing and reduced differences predicted by Beery scores. PMID:24651280

  13. Functional cerebral distance and the effect of emotional music on spatial rotation scores in undergraduate women and men.

    PubMed

    Bertsch, Sharon; Knee, H Donald; Webb, Jeffrey L

    2011-02-01

    The influence of listening to music on subsequent spatial rotation scores has a controversial history. The effect is unreliable, seeming to depend on several as yet unexplored factors. Using a large sample (167 women, 160 men; M age = 18.9 yr.), two related variables were investigated: participants' sex and the emotion conveyed by the music. Participants listened to 90 sec. of music that portrayed emotions of approach (happiness), or withdrawal (anger), or heard no music at all. They then performed a two-dimensional spatial rotation task. No significant difference was found in spatial rotation scores between groups exposed to music and those who were not. However, a significant interaction was found based on the sex of the participants and the emotion portrayed in the music they heard. Women's scores increased (relative to a no-music condition) only after hearing withdrawal-based music, while men's scores increased only after listening to the approach-based music. These changes were explained using the theory of functional cerebral distance.

  14. Predicting stroke through genetic risk functions: The CHARGE risk score project

    PubMed Central

    Ibrahim-Verbaas, Carla A; Fornage, Myriam; Bis, Joshua C; Choi, Seung Hoan; Psaty, Bruce M; Meigs, James B; Rao, Madhu; Nalls, Mike; Fontes, Joao D; O’Donnell, Christopher J.; Kathiresan, Sekar; Ehret, Georg B.; Fox, Caroline S; Malik, Rainer; Dichgans, Martin; Schmidt, Helena; Lahti, Jari; Heckbert, Susan R; Lumley, Thomas; Rice, Kenneth; Rotter, Jerome I; Taylor, Kent D; Folsom, Aaron R; Boerwinkle, Eric; Rosamond, Wayne D; Shahar, Eyal; Gottesman, Rebecca F.; Koudstaal, Peter J; Amin, Najaf; Wieberdink, Renske G.; Dehghan, Abbas; Hofman, Albert; Uitterlinden, André G; DeStefano, Anita L.; Debette, Stephanie; Xue, Luting; Beiser, Alexa; Wolf, Philip A.; DeCarli, Charles; Ikram, M. Arfan; Seshadri, Sudha; Mosley, Thomas H; Longstreth, WT; van Duijn, Cornelia M; Launer, Lenore J

    2014-01-01

    Background and Purpose Beyond the Framingham Stroke Risk Score (FSRS), prediction of future stroke may improve with a genetic risk score (GRS) based on Single nucleotide polymorphisms (SNPs) associated with stroke and its risk factors. Methods The study includes four population-based cohorts with 2,047 first incident strokes from 22,720 initially stroke-free European origin participants aged 55 years and older, who were followed for up to 20 years. GRS were constructed with 324 SNPs implicated in stroke and 9 risk factors. The association of the GRS to first incident stroke was tested using Cox regression; the GRS predictive properties were assessed with Area under the curve (AUC) statistics comparing the GRS to age sex, and FSRS models, and with reclassification statistics. These analyses were performed per cohort and in a meta-analysis of pooled data. Replication was sought in a case-control study of ischemic stroke (IS). Results In the meta-analysis, adding the GRS to the FSRS, age and sex model resulted in a significant improvement in discrimination (All stroke: Δjoint AUC =0.016, p-value=2.3*10-6; IS: Δ joint AUC =0.021, p-value=3.7*10−7), although the overall AUC remained low. In all studies there was a highly significantly improved net reclassification index (p-values <10−4). Conclusions The SNPs associated with stroke and its risk factors result only in a small improvement in prediction of future stroke compared to the classical epidemiological risk factors for stroke. PMID:24436238

  15. [A comparative study of clinical score and lung function tests in the classification of asthma by severity of disease].

    PubMed

    Nakaie, C M; Rozov, T; Manissadjian, A

    1998-01-01

    Fifty nine asthmatic children and adolescents, clinically stable, aged 6 to 15 years, 37 boys and 22 girls, from Instituto da Criança do Hospital das Clínicas da FMUSP, were studied from September to November, 1994. The patients were classified by the clinical score of the International Consensus for Asthma Diagnosis and Management. They performed baseline spirometry and peak expiratory flow rates (PEFR), before and after bronchodilator, and measured PEFR three times a day (6 pm, at bedtime and on waking), for one day, at home. Five PEF measurements were made serially and the best readings were considered. Variability of PFE was calculated for 24 hours, as assessed by maximal amplitude. The results were summited to statistical analysis of the Laboratorio de Informática Médica da Faculdade de Medicina da USP. The results of PEFR and it's variability were compared to spirometry, (functional score, FEV1-forced expiratory volume in the first second) and to the clinical score of the International Consensus for Asthma Diagnosis and Management. In case of disagreement between the clinical parameters, the more severe one was chosen. The clinical score classified 20.3% of our patients as mild obstruction, 49.2% as moderate and 30.5% as severely compromised. According to FEV1, 58% of patients were classified as normal while the PEFR and its variability classified as normal 76% and 71%. The PEFR and it's variability in 24 hours, correlated with the VEF1, as gold standard, showed good specificity, 91% and 76% respectively and low sensibility, 44% and 32%. It was detected a low level of agreement between FEV1, PEFR and it's variability in 24 hours, in the clinical severity classification of asthma. The results of this study showed that FEV1 and PEFR had a low level of agreement in the clinical severity classification of asthma and when they were correlated to the clinical score of the International Consensus, they both presented low sensitivity.

  16. The effect of floor surface on dairy cow immune function and locomotion score.

    PubMed

    O'Driscoll, K K M; Schutz, M M; Lossie, A C; Eicher, S D

    2009-09-01

    This study evaluated the effect of 2 dairy cow housing systems on cow locomotion, immune status, and expression of genes associated with lameness during the dry and periparturient periods. Cows were assigned to freestall housing with either rubber (RUB; n = 13) or concrete (CON; n = 14) at the feed-bunk and alley immediately after their first calving, and managed on this system during all subsequent lactations. At dry off, cows were moved to a straw bedded-pack dry cow pen, and remained there until about 2 d before subsequent calving. To investigate whether greater exposure to RUB or CON increased the differences between cows on each treatment, cows at the end of either their first (n = 16) or second (n = 11) lactations were included in the experiment. Locomotion scores and blood samples were obtained at -60 (beginning of the dry period), -30, 0 (after calving), +10 and +18 d relative to calving. Leukocyte counts were obtained by using an automated cell counter. Phagocytic activity, and cells positive for CD14 and CD18 expression were measured by flow cytometry using labeled microbeads and antibodies. Expression of tachikinin 1(TAC1), histamine receptor 1 (H1), and metalloproteinase (MMP)13 in blood leukocytes was estimated using quantitative real-time PCR. Treatment effects were determined using a repeated measures model. Provision of rubber flooring did not improve dairy cow locomotion during the subsequent study period. However, time relative to calving had an effect on locomotion score and speed, which were worst on d 0, probably because of the discomfort associated with calving. An interaction occurred between treatment and time for neutrophil and lymphocyte counts. The RUB cows had greater neutrophil and lesser lymphocyte numbers postpartum than CON. These cows also had more cells positive for CD14 postpartum compared with prepartum. Moreover, RUB cows showed upregulation of MMP13 and TAC1 compared with CON. These genes are associated with lameness and pain

  17. Improved image quality in pinhole SPECT by accurate modeling of the point spread function in low magnification systems

    SciTech Connect

    Pino, Francisco; Roé, Nuria; Aguiar, Pablo; Falcon, Carles; Ros, Domènec; Pavía, Javier

    2015-02-15

    Purpose: Single photon emission computed tomography (SPECT) has become an important noninvasive imaging technique in small-animal research. Due to the high resolution required in small-animal SPECT systems, the spatially variant system response needs to be included in the reconstruction algorithm. Accurate modeling of the system response should result in a major improvement in the quality of reconstructed images. The aim of this study was to quantitatively assess the impact that an accurate modeling of spatially variant collimator/detector response has on image-quality parameters, using a low magnification SPECT system equipped with a pinhole collimator and a small gamma camera. Methods: Three methods were used to model the point spread function (PSF). For the first, only the geometrical pinhole aperture was included in the PSF. For the second, the septal penetration through the pinhole collimator was added. In the third method, the measured intrinsic detector response was incorporated. Tomographic spatial resolution was evaluated and contrast, recovery coefficients, contrast-to-noise ratio, and noise were quantified using a custom-built NEMA NU 4–2008 image-quality phantom. Results: A high correlation was found between the experimental data corresponding to intrinsic detector response and the fitted values obtained by means of an asymmetric Gaussian distribution. For all PSF models, resolution improved as the distance from the point source to the center of the field of view increased and when the acquisition radius diminished. An improvement of resolution was observed after a minimum of five iterations when the PSF modeling included more corrections. Contrast, recovery coefficients, and contrast-to-noise ratio were better for the same level of noise in the image when more accurate models were included. Ring-type artifacts were observed when the number of iterations exceeded 12. Conclusions: Accurate modeling of the PSF improves resolution, contrast, and recovery

  18. Accurate potential energy curve of the LiH{sup +} molecule calculated with explicitly correlated Gaussian functions

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  19. Application of the 4D fingerprint method with a robust scoring function for scaffold-hopping and drug repurposing strategies.

    PubMed

    Hamza, Adel; Wagner, Jonathan M; Wei, Ning-Ning; Kwiatkowski, Stefan; Zhan, Chang-Guo; Watt, David S; Korotkov, Konstantin V

    2014-10-27

    Two factors contribute to the inefficiency associated with screening pharmaceutical library collections as a means of identifying new drugs: [1] the limited success of virtual screening (VS) methods in identifying new scaffolds; [2] the limited accuracy of computational methods in predicting off-target effects. We recently introduced a 3D shape-based similarity algorithm of the SABRE program, which encodes a consensus molecular shape pattern of a set of active ligands into a 4D fingerprint descriptor. Here, we report a mathematical model for shape similarity comparisons and ligand database filtering using this 4D fingerprint method and benchmarked the scoring function HWK (Hamza-Wei-Korotkov), using the 81 targets of the DEKOIS database. Subsequently, we applied our combined 4D fingerprint and HWK scoring function VS approach in scaffold-hopping and drug repurposing using the National Cancer Institute (NCI) and Food and Drug Administration (FDA) databases, and we identified new inhibitors with different scaffolds of MycP1 protease from the mycobacterial ESX-1 secretion system. Experimental evaluation of nine compounds from the NCI database and three from the FDA database displayed IC50 values ranging from 70 to 100 μM against MycP1 and possessed high structural diversity, which provides departure points for further structure-activity relationship (SAR) optimization. In addition, this study demonstrates that the combination of our 4D fingerprint algorithm and the HWK scoring function may provide a means for identifying repurposed drugs for the treatment of infectious diseases and may be used in the drug-target profile strategy. PMID:25229183

  20. Application of the 4D Fingerprint Method with a Robust Scoring Function for Scaffold-Hopping and Drug Repurposing Strategies

    PubMed Central

    2015-01-01

    Two factors contribute to the inefficiency associated with screening pharmaceutical library collections as a means of identifying new drugs: [1] the limited success of virtual screening (VS) methods in identifying new scaffolds; [2] the limited accuracy of computational methods in predicting off-target effects. We recently introduced a 3D shape-based similarity algorithm of the SABRE program, which encodes a consensus molecular shape pattern of a set of active ligands into a 4D fingerprint descriptor. Here, we report a mathematical model for shape similarity comparisons and ligand database filtering using this 4D fingerprint method and benchmarked the scoring function HWK (Hamza–Wei–Korotkov), using the 81 targets of the DEKOIS database. Subsequently, we applied our combined 4D fingerprint and HWK scoring function VS approach in scaffold-hopping and drug repurposing using the National Cancer Institute (NCI) and Food and Drug Administration (FDA) databases, and we identified new inhibitors with different scaffolds of MycP1 protease from the mycobacterial ESX-1 secretion system. Experimental evaluation of nine compounds from the NCI database and three from the FDA database displayed IC50 values ranging from 70 to 100 μM against MycP1 and possessed high structural diversity, which provides departure points for further structure–activity relationship (SAR) optimization. In addition, this study demonstrates that the combination of our 4D fingerprint algorithm and the HWK scoring function may provide a means for identifying repurposed drugs for the treatment of infectious diseases and may be used in the drug-target profile strategy. PMID:25229183

  1. Application of the 4D fingerprint method with a robust scoring function for scaffold-hopping and drug repurposing strategies.

    PubMed

    Hamza, Adel; Wagner, Jonathan M; Wei, Ning-Ning; Kwiatkowski, Stefan; Zhan, Chang-Guo; Watt, David S; Korotkov, Konstantin V

    2014-10-27

    Two factors contribute to the inefficiency associated with screening pharmaceutical library collections as a means of identifying new drugs: [1] the limited success of virtual screening (VS) methods in identifying new scaffolds; [2] the limited accuracy of computational methods in predicting off-target effects. We recently introduced a 3D shape-based similarity algorithm of the SABRE program, which encodes a consensus molecular shape pattern of a set of active ligands into a 4D fingerprint descriptor. Here, we report a mathematical model for shape similarity comparisons and ligand database filtering using this 4D fingerprint method and benchmarked the scoring function HWK (Hamza-Wei-Korotkov), using the 81 targets of the DEKOIS database. Subsequently, we applied our combined 4D fingerprint and HWK scoring function VS approach in scaffold-hopping and drug repurposing using the National Cancer Institute (NCI) and Food and Drug Administration (FDA) databases, and we identified new inhibitors with different scaffolds of MycP1 protease from the mycobacterial ESX-1 secretion system. Experimental evaluation of nine compounds from the NCI database and three from the FDA database displayed IC50 values ranging from 70 to 100 μM against MycP1 and possessed high structural diversity, which provides departure points for further structure-activity relationship (SAR) optimization. In addition, this study demonstrates that the combination of our 4D fingerprint algorithm and the HWK scoring function may provide a means for identifying repurposed drugs for the treatment of infectious diseases and may be used in the drug-target profile strategy.

  2. Comparison of molecular mechanics, semi-empirical quantum mechanical, and density functional theory methods for scoring protein-ligand interactions.

    PubMed

    Yilmazer, Nusret Duygu; Korth, Martin

    2013-07-11

    Correctly ranking protein-ligand interactions with respect to overall free energy of binding is a grand challenge for virtual drug design. Here we compare the performance of various quantum chemical approaches for tackling this so-called "scoring" problem. Relying on systematically generated benchmark sets of large protein/ligand model complexes based on the PDBbind database, we show that the performance depends first of all on the general level of theory. Comparing classical molecular mechanics (MM), semiempirical quantum mechanical (SQM), and density functional theory (DFT) based methods, we find that enhanced SQM approaches perform very similar to DFT methods and substantially different from MM potentials.

  3. Comparison of molecular mechanics, semi-empirical quantum mechanical, and density functional theory methods for scoring protein-ligand interactions.

    PubMed

    Yilmazer, Nusret Duygu; Korth, Martin

    2013-07-11

    Correctly ranking protein-ligand interactions with respect to overall free energy of binding is a grand challenge for virtual drug design. Here we compare the performance of various quantum chemical approaches for tackling this so-called "scoring" problem. Relying on systematically generated benchmark sets of large protein/ligand model complexes based on the PDBbind database, we show that the performance depends first of all on the general level of theory. Comparing classical molecular mechanics (MM), semiempirical quantum mechanical (SQM), and density functional theory (DFT) based methods, we find that enhanced SQM approaches perform very similar to DFT methods and substantially different from MM potentials. PMID:23758433

  4. The relationship between subjective knee scores, isokinetic testing, and functional testing in the ACL-reconstructed knee.

    PubMed

    Wilk, K E; Romaniello, W T; Soscia, S M; Arrigo, C A; Andrews, J R

    1994-08-01

    It is important to examine the functional relationships between commonly performed clinical tests and to resolve inconsistencies in previous investigative results. The purpose of this study was to determine if a correlation exists between three commonly performed clinical tests: isokinetic isolated knee concentric muscular testing, the single-leg hop test, and the subjective knee score in anterior cruciate ligament reconstructed knees. To determine if a relationship exists would be beneficial to clinicians in determining patient progression, treatment modification, and return-to-sport objective parameters. Several investigators have analyzed two of these parameters, but no one has investigated three parameters to date. Additionally, this study explored the concept of limb acceleration and deceleration during high-speed isokinetics and its relationship to function. Fifty patients were randomly selected (29 males) with a mean age of 23.7 years (range 15-52). The subjects completed a subjective knee score questionnaire that rated symptoms (pain, swelling, giving way) and specific sport function and completed an overall knee score assessment. The patients were then evaluated performing three one-legged functional tests: 1) hop for distance, 2) timed hop, and 3) cross-over triple hop. Isokinetic testing was performed on a Biodex dynamometer at 180, 300, and 450 degrees/sec for knee extension/flexion. The patients' mean value of the self-assessed knee rating was 86 points. Sixty-four percent of the patients exhibited normal limb symmetry (within 85%) on all three single-leg hop tests. Sixteen percent exhibited quadriceps strength at least 90% of the contralateral limb isokinetically. A positive correlation was noted between isokinetic knee extension peak torque (180, 300 degrees/sec) and subjective knee scores, and the three hop tests (p < 0.001). A statistical trend was noted between knee extension acceleration and deceleration range at 180 and 300 degrees/sec for the

  5. Contrast Sensitivity Function Scores, Choices of Illuminated Stand Magnifiers, and Reading

    ERIC Educational Resources Information Center

    Gerritsen, Bryan

    2010-01-01

    Far too often, professionals focus almost solely on individuals' needs for magnification level for reading. Visual acuities are measured and decisions are made for low vision devices largely on the basis of acuity levels. Contrast sensitivity function is often overlooked as a critical need for and predictor of the selection and preference for low…

  6. Effect of Incorporating Adaptive Functioning Scores on the Prevalence of Intellectual Disability

    ERIC Educational Resources Information Center

    Obi, Obianuju; Braun, Kim Van Naarden; Baio, Jon; Drews-Botsch, Carolyn; Devine, Owen; Yeargin-Allsopp, Marshalyn

    2011-01-01

    Surveillance and epidemiologic research on intellectual disability often do not incorporate adaptive functioning (AF) data. Exclusion of AF data leads to overestimation of the prevalence of intellectual disability, the extent of which is not known. In this study, the authors evaluated the effect of incorporating AF data on overall intellectual…

  7. Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins

    PubMed Central

    2009-01-01

    Background Setting the rules for the identification of a stable conformation of a protein is of utmost importance for the efficient generation of structures in computer simulation. For structure prediction, a considerable number of possible models are generated from which the best model has to be selected. Results Two scoring functions, Rs and Rp, based on the consideration of packing of residues, which indicate if the conformation of an amino acid sequence is native-like, are presented. These are defined using the solvent accessible surface area (ASA) and the partner number (PN) (other residues that are within 4.5 Å) of a particular residue. The two functions evaluate the deviation from the average packing properties (ASA or PN) of all residues in a polypeptide chain corresponding to a model of its three-dimensional structure. While simple in concept and computationally less intensive, both the functions are at least as efficient as any other energy functions in discriminating the native structure from decoys in a large number of standard decoy sets, as well as on models submitted for the targets of CASP7. Rs appears to be slightly more effective than Rp, as determined by the number of times the native structure possesses the minimum value for the function and its separation from the average value for the decoys. Conclusion Two parameters, Rs and Rp, are discussed that can very efficiently recognize the native fold for a sequence from an ensemble of decoy structures. Unlike many other algorithms that rely on the use of composite scoring function, these are based on a single parameter, viz., the accessible surface area (or the number of residues in contact), but still able to capture the essential attribute of the native fold. PMID:20038291

  8. The effect of an intervention program on functional movement screen test scores in mixed martial arts athletes.

    PubMed

    Bodden, Jamie G; Needham, Robert A; Chockalingam, Nachiappan

    2015-01-01

    This study assessed the basic fundamental movements of mixed martial arts (MMA) athletes using the functional movement screen (FMS) assessment and determined if an intervention program was successful at improving results. Participants were placed into 1 of the 2 groups: intervention and control groups. The intervention group was required to complete a corrective exercise program 4 times per week, and all participants were asked to continue their usual MMA training routine. A mid-intervention FMS test was included to examine if successful results were noticed sooner than the 8-week period. Results highlighted differences in FMS test scores between the control group and intervention group (p = 0.006). Post hoc testing revealed a significant increase in the FMS score of the intervention group between weeks 0 and 8 (p = 0.00) and weeks 0 and 4 (p = 0.00) and no significant increase between weeks 4 and 8 (p = 1.00). A χ analysis revealed that the intervention group participants were more likely to have an FMS score >14 than participants in the control group at week 4 (χ = 7.29, p < 0.01) and week 8 (χ = 5.2, p ≤ 0.05). Finally, a greater number of participants in the intervention group were free from asymmetry at week 4 and week 8 compared with the initial test period. The results of the study suggested that a 4-week intervention program was sufficient at improving FMS scores. Most if not all, the movements covered on the FMS relate to many aspects of MMA training. The knowledge that the FMS can identify movement dysfunctions and, furthermore, the fact that the issues can be improved through a standardized intervention program could be advantageous to MMA coaches, thus, providing the opportunity to adapt and implement new additions to training programs. PMID:23860293

  9. The effect of an intervention program on functional movement screen test scores in mixed martial arts athletes.

    PubMed

    Bodden, Jamie G; Needham, Robert A; Chockalingam, Nachiappan

    2015-01-01

    This study assessed the basic fundamental movements of mixed martial arts (MMA) athletes using the functional movement screen (FMS) assessment and determined if an intervention program was successful at improving results. Participants were placed into 1 of the 2 groups: intervention and control groups. The intervention group was required to complete a corrective exercise program 4 times per week, and all participants were asked to continue their usual MMA training routine. A mid-intervention FMS test was included to examine if successful results were noticed sooner than the 8-week period. Results highlighted differences in FMS test scores between the control group and intervention group (p = 0.006). Post hoc testing revealed a significant increase in the FMS score of the intervention group between weeks 0 and 8 (p = 0.00) and weeks 0 and 4 (p = 0.00) and no significant increase between weeks 4 and 8 (p = 1.00). A χ analysis revealed that the intervention group participants were more likely to have an FMS score >14 than participants in the control group at week 4 (χ = 7.29, p < 0.01) and week 8 (χ = 5.2, p ≤ 0.05). Finally, a greater number of participants in the intervention group were free from asymmetry at week 4 and week 8 compared with the initial test period. The results of the study suggested that a 4-week intervention program was sufficient at improving FMS scores. Most if not all, the movements covered on the FMS relate to many aspects of MMA training. The knowledge that the FMS can identify movement dysfunctions and, furthermore, the fact that the issues can be improved through a standardized intervention program could be advantageous to MMA coaches, thus, providing the opportunity to adapt and implement new additions to training programs.

  10. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

    PubMed

    Thomas, Paul D; Kejariwal, Anish; Guo, Nan; Mi, Huaiyu; Campbell, Michael J; Muruganujan, Anushya; Lazareva-Ulitsky, Betty

    2006-07-01

    The vast amount of protein sequence data now available, together with accumulating experimental knowledge of protein function, enables modeling of protein sequence and function evolution. The PANTHER database was designed to model evolutionary sequence-function relationships on a large scale. There are a number of applications for these data, and we have implemented web services that address three of them. The first is a protein classification service. Proteins can be classified, using only their amino acid sequences, to evolutionary groups at both the family and subfamily levels. Specific subfamilies, and often families, are further classified when possible according to their functions, including molecular function and the biological processes and pathways they participate in. The second application, then, is an expression data analysis service, where functional classification information can help find biological patterns in the data obtained from genome-wide experiments. The third application is a coding single-nucleotide polymorphism scoring service. In this case, information about evolutionarily related proteins is used to assess the likelihood of a deleterious effect on protein function arising from a single substitution at a specific amino acid position in the protein. All three web services are available at http://www.pantherdb.org/tools.

  11. Net and Global Differential Item Functioning in PISA Polytomously Scored Science Items: Application of the Differential Step Functioning Framework

    ERIC Educational Resources Information Center

    Akour, Mutasem; Sabah, Saed; Hammouri, Hind

    2015-01-01

    The purpose of this study was to apply two types of Differential Item Functioning (DIF), net and global DIF, as well as the framework of Differential Step Functioning (DSF) to real testing data to investigate measurement invariance related to test language. Data from the Program for International Student Assessment (PISA)-2006 polytomously scored…

  12. The index of orthognathic functional treatment need accurately prioritises those patients already selected for orthognathic surgery within the NHS.

    PubMed

    Shah, Rupal; Breeze, John; Chand, Mohit; Stockton, Peter

    2016-06-01

    The index of orthognathic functional treatment need (IOFTN) is a newly-proposed system to help to prioritise patients for orthognathic treatment. The five categories are similar to those used in orthodontics, but include additional parameters such as sleep apnoea and facial asymmetry. The aim of this audit was to validate the index and find out the potential future implications, should such a system ever be adopted by commissioners. We calculated the IOFTN category of 100 consecutive patients who had orthognathic surgery between 2010-14 using clinical notes, photographs, study models, and radiographs, and determined the number in categories 4 or 5, analogous to the current indications for orthodontic treatment within the NHS. Sufficient clinical information was available to categorise 59/100 patients, and 56 of the 59 (95%) were in either category 4 or 5. All three of the remaining patients (in categories 1-3) who were operated on were treated because of the anticipated favourable impact on their quality of life. The IOFTN has been proposed for use in future commissioning of orthognathic services within the NHS, and this study has confirmed its efficacy in prioritising treatment accurately, with 95% of patients being in categories 4 or 5. We recommend that the orthognathic treatment index be adapted to include additional psychosocial assessment so that patients who fall into the lower functional categories are not automatically excluded from this potentially life-changing treatment.

  13. Accurate PSF-matched photometry and photometric redshifts for the extreme deep field with the Chebyshev-Fourier functions

    NASA Astrophysics Data System (ADS)

    Jiménez-Teja, Y.; Benítez, N.; Molino, A.; Fernandes, C. A. C.

    2015-10-01

    Photometric redshifts, which have become the cornerstone of several of the largest astronomical surveys like PanStarrs, DES, J-PAS and LSST, require precise measurements of galaxy photometry in different bands using a consistent physical aperture. This is not trivial, due to the variation in the shape and width of the point spread function (PSF) introduced by wavelength differences, instrument positions and atmospheric conditions. Current methods to correct for this effect rely on a detailed knowledge of PSF characteristics as a function of the survey coordinates, which can be difficult due to the relative paucity of stars tracking the PSF behaviour. Here we show that it is possible to measure accurate, consistent multicolour photometry without knowing the shape of the PSF. The Chebyshev-Fourier functions (CHEFs) can fit the observed profile of each object and produce high signal-to-noise integrated flux measurements unaffected by the PSF. These total fluxes, which encompass all the galaxy populations, are much more useful for galaxy evolution studies than aperture photometry. We compare the total magnitudes and colours obtained using our software to traditional photometry with SEXTRACTOR, using real data from the COSMOS survey and the Hubble Ultra-Deep Field (HUDF). We also apply the CHEF technique to the recently published eXtreme Deep Field (XDF) and compare the results to those from COLORPRO on the HUDF. We produce a photometric catalogue with 35 732 sources (10 823 with signal-to-noise ratio ≥5), reaching a photometric redshift precision of 2 per cent due to the extraordinary depth and wavelength coverage of the eXtreme Deep Field images.

  14. FRESCO: flexible alignment with rectangle scoring schemes.

    PubMed

    Dalca, A V; Brudno, M

    2008-01-01

    While the popular DNA sequence alignment tools incorporate powerful heuristics to allow for fast and accurate alignment of DNA, most of them still optimize the classical Needleman Wunsch scoring scheme. The development of novel scoring schemes is often hampered by the difficulty of finding an optimizing algorithm for each non-trivial scheme. In this paper we define the broad class of rectangle scoring schemes, and describe an algorithm and tool that can align two sequences with an arbitrary rectangle scoring scheme in polynomial time. Rectangle scoring schemes encompass some of the popular alignment scoring metrics currently in use, as well as many other functions. We investigate a novel scoring function based on minimizing the expected number of random diagonals observed with the given scores and show that it rivals the LAGAN and Clustal-W aligners, without using any biological or evolutionary parameters. The FRESCO program, freely available at http://compbio.cs.toronto.edu/fresco, gives bioinformatics researchers the ability to quickly compare the performance of other complex scoring formulas without having to implement new algorithms to optimize them.

  15. A preliminary investigation into the relationship between functional movement screen scores and athletic physical performance in female team sport athletes

    PubMed Central

    Schultz, AB; Callaghan, SJ; Jordan, CA; Luczo, TM; Jeffriess, MD

    2014-01-01

    There is little research investigating relationships between the Functional Movement Screen (FMS) and athletic performance in female athletes. This study analyzed the relationships between FMS (deep squat; hurdle step [HS]; in-line lunge [ILL]; shoulder mobility; active straight-leg raise [ASLR]; trunk stability push-up; rotary stability) scores, and performance tests (bilateral and unilateral sit-and-reach [flexibility]; 20-m sprint [linear speed]; 505 with turns from each leg; modified T-test with movement to left and right [change-of-direction speed]; bilateral and unilateral vertical and standing broad jumps; lateral jumps [leg power]). Nine healthy female recreational team sport athletes (age = 22.67 ± 5.12 years; height = 1.66 ± 0.05 m; body mass = 64.22 ± 4.44 kilograms) were screened in the FMS and completed the afore-mentioned tests. Percentage between-leg differences in unilateral sit-and-reach, 505 turns and the jumps, and difference between the T-test conditions, were also calculated. Spearman's correlations (p ≤ 0.05) examined relationships between the FMS and performance tests. Stepwise multiple regressions (p ≤ 0.05) were conducted for the performance tests to determine FMS predictors. Unilateral sit-and-reach positive correlated with the left-leg ASLR (r = 0.704-0.725). However, higher-scoring HS, ILL, and ASLR related to poorer 505 and T-test performance (r = 0.722-0.829). A higher-scored left-leg ASLR related to a poorer unilateral vertical and standing broad jump, which were the only significant relationships for jump performance. Predictive data tended to confirm the correlations. The results suggest limitations in using the FMS to identify movement deficiencies that could negatively impact athletic performance in female team sport athletes. PMID:25729149

  16. A preliminary investigation into the relationship between functional movement screen scores and athletic physical performance in female team sport athletes.

    PubMed

    Lockie, Rg; Schultz, Ab; Callaghan, Sj; Jordan, Ca; Luczo, Tm; Jeffriess, Md

    2015-03-01

    There is little research investigating relationships between the Functional Movement Screen (FMS) and athletic performance in female athletes. This study analyzed the relationships between FMS (deep squat; hurdle step [HS]; in-line lunge [ILL]; shoulder mobility; active straight-leg raise [ASLR]; trunk stability push-up; rotary stability) scores, and performance tests (bilateral and unilateral sit-and-reach [flexibility]; 20-m sprint [linear speed]; 505 with turns from each leg; modified T-test with movement to left and right [change-of-direction speed]; bilateral and unilateral vertical and standing broad jumps; lateral jumps [leg power]). Nine healthy female recreational team sport athletes (age = 22.67 ± 5.12 years; height = 1.66 ± 0.05 m; body mass = 64.22 ± 4.44 kilograms) were screened in the FMS and completed the afore-mentioned tests. Percentage between-leg differences in unilateral sit-and-reach, 505 turns and the jumps, and difference between the T-test conditions, were also calculated. Spearman's correlations (p ≤ 0.05) examined relationships between the FMS and performance tests. Stepwise multiple regressions (p ≤ 0.05) were conducted for the performance tests to determine FMS predictors. Unilateral sit-and-reach positive correlated with the left-leg ASLR (r = 0.704-0.725). However, higher-scoring HS, ILL, and ASLR related to poorer 505 and T-test performance (r = 0.722-0.829). A higher-scored left-leg ASLR related to a poorer unilateral vertical and standing broad jump, which were the only significant relationships for jump performance. Predictive data tended to confirm the correlations. The results suggest limitations in using the FMS to identify movement deficiencies that could negatively impact athletic performance in female team sport athletes.

  17. Accurate and Efficient Calculation of van der Waals Interactions Within Density Functional Theory by Local Atomic Potential Approach

    SciTech Connect

    Sun, Y. Y.; Kim, Y. H.; Lee, K.; Zhang, S. B.

    2008-01-01

    Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.

  18. In silico structure-based screening of versatile P-glycoprotein inhibitors using polynomial empirical scoring functions.

    PubMed

    Shityakov, Sergey; Förster, Carola

    2014-01-01

    P-glycoprotein (P-gp) is an ATP (adenosine triphosphate)-binding cassette transporter that causes multidrug resistance of various chemotherapeutic substances by active efflux from mammalian cells. P-gp plays a pivotal role in limiting drug absorption and distribution in different organs, including the intestines and brain. Thus, the prediction of P-gp-drug interactions is of vital importance in assessing drug pharmacokinetic and pharmacodynamic properties. To find the strongest P-gp blockers, we performed an in silico structure-based screening of P-gp inhibitor library (1,300 molecules) by the gradient optimization method, using polynomial empirical scoring (POLSCORE) functions. We report a strong correlation (r (2)=0.80, F=16.27, n=6, P<0.0157) of inhibition constants (Kiexp or pKiexp; experimental Ki or negative decimal logarithm of Kiexp) converted from experimental IC50 (half maximal inhibitory concentration) values with POLSCORE-predicted constants (KiPOLSCORE or pKiPOLSCORE), using a linear regression fitting technique. The hydrophobic interactions between P-gp and selected drug substances were detected as the main forces responsible for the inhibition effect. The results showed that this scoring technique might be useful in the virtual screening and filtering of databases of drug-like compounds at the early stage of drug development processes. PMID:24711707

  19. In silico structure-based screening of versatile P-glycoprotein inhibitors using polynomial empirical scoring functions.

    PubMed

    Shityakov, Sergey; Förster, Carola

    2014-01-01

    P-glycoprotein (P-gp) is an ATP (adenosine triphosphate)-binding cassette transporter that causes multidrug resistance of various chemotherapeutic substances by active efflux from mammalian cells. P-gp plays a pivotal role in limiting drug absorption and distribution in different organs, including the intestines and brain. Thus, the prediction of P-gp-drug interactions is of vital importance in assessing drug pharmacokinetic and pharmacodynamic properties. To find the strongest P-gp blockers, we performed an in silico structure-based screening of P-gp inhibitor library (1,300 molecules) by the gradient optimization method, using polynomial empirical scoring (POLSCORE) functions. We report a strong correlation (r (2)=0.80, F=16.27, n=6, P<0.0157) of inhibition constants (Kiexp or pKiexp; experimental Ki or negative decimal logarithm of Kiexp) converted from experimental IC50 (half maximal inhibitory concentration) values with POLSCORE-predicted constants (KiPOLSCORE or pKiPOLSCORE), using a linear regression fitting technique. The hydrophobic interactions between P-gp and selected drug substances were detected as the main forces responsible for the inhibition effect. The results showed that this scoring technique might be useful in the virtual screening and filtering of databases of drug-like compounds at the early stage of drug development processes.

  20. Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules

    NASA Astrophysics Data System (ADS)

    Nassiri, Isar; Lombardo, Rosario; Lauria, Mario; Morine, Melissa J.; Moyseos, Petros; Varma, Vijayalakshmi; Nolen, Greg T.; Knox, Bridgett; Sloper, Daniel; Kaput, Jim; Priami, Corrado

    2016-07-01

    The investigation of the complex processes involved in cellular differentiation must be based on unbiased, high throughput data processing methods to identify relevant biological pathways. A number of bioinformatics tools are available that can generate lists of pathways ranked by statistical significance (i.e. by p-value), while ideally it would be desirable to functionally score the pathways relative to each other or to other interacting parts of the system or process. We describe a new computational method (Network Activity Score Finder - NASFinder) to identify tissue-specific, omics-determined sub-networks and the connections with their upstream regulator receptors to obtain a systems view of the differentiation of human adipocytes. Adipogenesis of human SBGS pre-adipocyte cells in vitro was monitored with a transcriptomic data set comprising six time points (0, 6, 48, 96, 192, 384 hours). To elucidate the mechanisms of adipogenesis, NASFinder was used to perform time-point analysis by comparing each time point against the control (0 h) and time-lapse analysis by comparing each time point with the previous one. NASFinder identified the coordinated activity of seemingly unrelated processes between each comparison, providing the first systems view of adipogenesis in culture. NASFinder has been implemented into a web-based, freely available resource associated with novel, easy to read visualization of omics data sets and network modules.

  1. Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules.

    PubMed

    Nassiri, Isar; Lombardo, Rosario; Lauria, Mario; Morine, Melissa J; Moyseos, Petros; Varma, Vijayalakshmi; Nolen, Greg T; Knox, Bridgett; Sloper, Daniel; Kaput, Jim; Priami, Corrado

    2016-01-01

    The investigation of the complex processes involved in cellular differentiation must be based on unbiased, high throughput data processing methods to identify relevant biological pathways. A number of bioinformatics tools are available that can generate lists of pathways ranked by statistical significance (i.e. by p-value), while ideally it would be desirable to functionally score the pathways relative to each other or to other interacting parts of the system or process. We describe a new computational method (Network Activity Score Finder - NASFinder) to identify tissue-specific, omics-determined sub-networks and the connections with their upstream regulator receptors to obtain a systems view of the differentiation of human adipocytes. Adipogenesis of human SBGS pre-adipocyte cells in vitro was monitored with a transcriptomic data set comprising six time points (0, 6, 48, 96, 192, 384 hours). To elucidate the mechanisms of adipogenesis, NASFinder was used to perform time-point analysis by comparing each time point against the control (0 h) and time-lapse analysis by comparing each time point with the previous one. NASFinder identified the coordinated activity of seemingly unrelated processes between each comparison, providing the first systems view of adipogenesis in culture. NASFinder has been implemented into a web-based, freely available resource associated with novel, easy to read visualization of omics data sets and network modules. PMID:27385551

  2. Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules

    PubMed Central

    Nassiri, Isar; Lombardo, Rosario; Lauria, Mario; Morine, Melissa J.; Moyseos, Petros; Varma, Vijayalakshmi; Nolen, Greg T.; Knox, Bridgett; Sloper, Daniel; Kaput, Jim; Priami, Corrado

    2016-01-01

    The investigation of the complex processes involved in cellular differentiation must be based on unbiased, high throughput data processing methods to identify relevant biological pathways. A number of bioinformatics tools are available that can generate lists of pathways ranked by statistical significance (i.e. by p-value), while ideally it would be desirable to functionally score the pathways relative to each other or to other interacting parts of the system or process. We describe a new computational method (Network Activity Score Finder - NASFinder) to identify tissue-specific, omics-determined sub-networks and the connections with their upstream regulator receptors to obtain a systems view of the differentiation of human adipocytes. Adipogenesis of human SBGS pre-adipocyte cells in vitro was monitored with a transcriptomic data set comprising six time points (0, 6, 48, 96, 192, 384 hours). To elucidate the mechanisms of adipogenesis, NASFinder was used to perform time-point analysis by comparing each time point against the control (0 h) and time-lapse analysis by comparing each time point with the previous one. NASFinder identified the coordinated activity of seemingly unrelated processes between each comparison, providing the first systems view of adipogenesis in culture. NASFinder has been implemented into a web-based, freely available resource associated with novel, easy to read visualization of omics data sets and network modules. PMID:27385551

  3. Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules.

    PubMed

    Nassiri, Isar; Lombardo, Rosario; Lauria, Mario; Morine, Melissa J; Moyseos, Petros; Varma, Vijayalakshmi; Nolen, Greg T; Knox, Bridgett; Sloper, Daniel; Kaput, Jim; Priami, Corrado

    2016-07-07

    The investigation of the complex processes involved in cellular differentiation must be based on unbiased, high throughput data processing methods to identify relevant biological pathways. A number of bioinformatics tools are available that can generate lists of pathways ranked by statistical significance (i.e. by p-value), while ideally it would be desirable to functionally score the pathways relative to each other or to other interacting parts of the system or process. We describe a new computational method (Network Activity Score Finder - NASFinder) to identify tissue-specific, omics-determined sub-networks and the connections with their upstream regulator receptors to obtain a systems view of the differentiation of human adipocytes. Adipogenesis of human SBGS pre-adipocyte cells in vitro was monitored with a transcriptomic data set comprising six time points (0, 6, 48, 96, 192, 384 hours). To elucidate the mechanisms of adipogenesis, NASFinder was used to perform time-point analysis by comparing each time point against the control (0 h) and time-lapse analysis by comparing each time point with the previous one. NASFinder identified the coordinated activity of seemingly unrelated processes between each comparison, providing the first systems view of adipogenesis in culture. NASFinder has been implemented into a web-based, freely available resource associated with novel, easy to read visualization of omics data sets and network modules.

  4. In silico structure-based screening of versatile P-glycoprotein inhibitors using polynomial empirical scoring functions

    PubMed Central

    Shityakov, Sergey; Förster, Carola

    2014-01-01

    P-glycoprotein (P-gp) is an ATP (adenosine triphosphate)-binding cassette transporter that causes multidrug resistance of various chemotherapeutic substances by active efflux from mammalian cells. P-gp plays a pivotal role in limiting drug absorption and distribution in different organs, including the intestines and brain. Thus, the prediction of P-gp–drug interactions is of vital importance in assessing drug pharmacokinetic and pharmacodynamic properties. To find the strongest P-gp blockers, we performed an in silico structure-based screening of P-gp inhibitor library (1,300 molecules) by the gradient optimization method, using polynomial empirical scoring (POLSCORE) functions. We report a strong correlation (r2=0.80, F=16.27, n=6, P<0.0157) of inhibition constants (Kiexp or pKiexp; experimental Ki or negative decimal logarithm of Kiexp) converted from experimental IC50 (half maximal inhibitory concentration) values with POLSCORE-predicted constants (KiPOLSCORE or pKiPOLSCORE), using a linear regression fitting technique. The hydrophobic interactions between P-gp and selected drug substances were detected as the main forces responsible for the inhibition effect. The results showed that this scoring technique might be useful in the virtual screening and filtering of databases of drug-like compounds at the early stage of drug development processes. PMID:24711707

  5. Apgar score

    MedlinePlus

    ... the baby's: Breathing effort Heart rate Muscle tone Reflexes Skin color Each category is scored with 0, ... scores 2 for muscle tone. Grimace response or reflex irritability is a term describing response to stimulation, ...

  6. A hidden Markov model for multimodal biometrics score fusion

    NASA Astrophysics Data System (ADS)

    Zheng, Yufeng

    2011-05-01

    There are strong evidences of that multimodal biometric score fusion can significantly improve human identification performance. Score level fusion usually involves score normalization, score fusion, and fusion decision. There are several types of score fusion methods, direct combination of fusion scores, classifier-based fusion, and density-based fusion. The real applications require achieving greater reliability in determining or verifying person's identity. The goal of this research is to improve the accuracy and robustness of human identification by using multimodal biometrics score fusion. The accuracy means high verification rate if tested on a closed dataset, or a high genuine accept rate under low false accept rate if tested on an open dataset. While the robustness means the fusion performance is stable with variant biometric scores. We propose a hidden Markov model (HMM) for multiple score fusion, where the biometric scores include multimodal scores and multi-matcher scores. The state probability density functions in a HHM model are estimated by Gaussian mixture model. The proposed HMM model for multiple score fusion is accurate for identification, flexible and reliable with biometrics. The proposed HMM method are tested on three NIST-BSSR1 multimodal databases and on three face-score databases. The results show the HMM method is an excellent and reliable score fusion method.

  7. Performance of the Framingham and SCORE cardiovascular risk prediction functions in a non-diabetic population of a Spanish health care centre: a validation study

    PubMed Central

    Barroso, Lourdes Cañón; Muro, Eloísa Cruces; Herrera, Natalio Díaz; Ochoa, Gerardo Fernández; Hueros, Juan Ignacio Calvo; Buitrago, Francisco

    2010-01-01

    Objective To analyse the 10-year performance of the original Framingham coronary risk function and of the SCORE cardiovascular death risk function in a non-diabetic population of 40–65 years of age served by a Spanish healthcare centre. Also, to estimate the percentage of patients who are candidates for antihypertensive and lipid-lowering therapy. Design Longitudinal, observational study of a retrospective cohort followed up for 10 years. Setting Primary care health centre. Patients A total of 608 non-diabetic patients of 40–65 years of age (mean 52.8 years, 56.7% women), without evidence of cardiovascular disease were studied. Main outcome measures Coronary risk at 10 years from the time of their recruitment, using the tables based on the original Framingham function, and of their 10-year risk of fatal cardiovascular disease using the SCORE tables. Results The actual incidence rates of coronary and fatal cardiovascular events were 7.9% and 1.5%, respectively. The original Framingham equation over-predicted risk by 64%, while SCORE function over-predicted risk by 40%, but the SCORE model performed better than the Framingham one for discrimination and calibration statistics. The original Framingham function classified 18.3% of the population as high risk and SCORE 9.2%. The proportions of patients who would be candidates for lipid-lowering therapy were 31.0% and 23.8% according to the original Framingham and SCORE functions, respectively, and 36.8% and 31.2% for antihypertensive therapy. Conclusion The SCORE function showed better values than the original Framingham function for each of the discrimination and calibration statistics. The original Framingham function selected a greater percentage of candidates for antihypertensive and lipid-lowering therapy. PMID:20873973

  8. Poorer clock draw test scores are associated with greater functional impairment in peripheral artery disease: The Walking and Leg Circulation Study II

    PubMed Central

    Zimmermann, Laura J; Ferrucci, Luigi; Liu, Kiang; Tian, Lu; Guralnik, Jack M; Criqui, Michael H; Liao, Yihua; McDermott, Mary M

    2016-01-01

    We hypothesized that, in the absence of clinically recognized dementia, cognitive dysfunction measured by the clock draw test (CDT) is associated with greater functional impairment in men and women with peripheral artery disease (PAD). Participants were men and women aged 60 years and older with Mini-Mental Status Examination scores ≥ 24 with PAD (n = 335) and without PAD (n = 234). We evaluated the 6-minute walk test, 4-meter walking velocity at usual and fastest pace, the Short Physical Performance Battery (SPPB), and accelerometer-measured physical activity. CDTs were scored using the Shulman system as follows: Category 1 (worst): CDT score 0–2; Category 2: CDT score 3; Category 3 (best): CDT score 4–5. Results were adjusted for age, sex, race, education, ankle–brachial index (ABI), and comorbidities. In individuals with PAD, lower CDT scores were associated with slower 4-meter usual-paced walking velocity (Category 1: 0.78 meters/second; Category 2: 0.83 meters/second; Category 3: 0.86 meters/second; p-trend = 0.025) and lower physical activity (Category 1: 420 activity units; Category 2: 677 activity units; Category 3: 701 activity units; p-trend = 0.045). Poorer CDT scores were also associated with worse functional performance in individuals without PAD (usual and fast-paced walking velocity and SPPB, p-trend = 0.022, 0.043, and 0.031, respectively). In conclusion, cognitive impairment identified with CDT is independently associated with greater functional impairment in older, dementia-free individuals with and without PAD. Longitudinal studies are necessary to explore whether baseline CDT scores and changes in CDT scores over time can predict long-term decline in functional performance in individuals with and without PAD. PMID:21636676

  9. Quadratic function between arterial partial oxygen pressure and mortality risk in sepsis patients: an interaction with simplified acute physiology score

    PubMed Central

    Zhang, Zhongheng; Ji, Xuqing

    2016-01-01

    Oxygen therapy is widely used in emergency and critical care settings, while there is little evidence on its real therapeutic effect. The study aimed to explore the impact of arterial oxygen partial pressure (PaO2) on clinical outcomes in patients with sepsis. A large clinical database was employed for the study. Subjects meeting the diagnostic criteria of sepsis were eligible for the study. All measurements of PaO2 were extracted. The primary endpoint was death from any causes during hospital stay. Survey data analysis was performed by using individual ICU admission as the primary sampling unit. Quadratic function was assumed for PaO2 and its interaction with other covariates were explored. A total of 199,125 PaO2 samples were identified for 11,002 ICU admissions. Each ICU stay comprised 18 PaO2 samples in average. The fitted multivariable model supported our hypothesis that the effect of PaO2 on mortality risk was in quadratic form. There was significant interaction between PaO2 and SAPS-I (p = 0.007). Furthermore, the main effect of PaO2 on SOFA score was nonlinear. The study shows that the effect of PaO2 on mortality risk is in quadratic function form, and there is significant interaction between PaO2 and severity of illness. PMID:27734905

  10. Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties.

    PubMed

    Ou, Yu-Yen; Chen, Shu-An; Gromiha, M Michael

    2010-05-15

    Transporters are proteins that are involved in the movement of ions or molecules across biological membranes. Transporters are generally classified into channels/pores, electrochemical transporters, and active transporters. Discriminating the specific class of transporters and their subfamilies are essential tasks in computational biology for the advancement of structural and functional genomics. We have systematically analyzed the amino acid composition, residue pair preference and amino acid properties in six different families of transporters. Utilizing the information, we have developed a radial basis function (RBF) network method based on profiles obtained with position specific scoring matrices for discriminating transporters belonging to three different classes and six families. Our method showed a fivefold cross validation accuracy of 76%, 73%, and 69% for discriminating transporters and nontransporters, three different classes and six different families of transporters, respectively. Further, the method was tested with independent datasets, which showed similar level of accuracy. A web server has been developed for discriminating transporters based on three classes and six families, and it is available at http://rbf.bioinfo.tw/ approximately sachen/tcrbf.html. We suggest that our method could be effectively used to identify transporters and discriminating them into different classes and families.

  11. Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties.

    PubMed

    Ou, Yu-Yen; Chen, Shu-An; Chang, Yun-Min; Velmurugan, Devadasan; Fukui, Kazuhiko; Michael Gromiha, M

    2013-09-01

    Efflux proteins are membrane proteins, which are involved in the transportation of multidrugs. The annotation of efflux proteins in genomic sequences would aid to understand the function. Although the percentage of membrane proteins in genomes is estimated to be 25-30%, there is no information about the content of efflux proteins. For annotating such class of proteins it is necessary to develop a reliable method to identify efflux proteins from amino acid sequence information. In this work, we have developed a method based on radial basis function networks using position specific scoring matrices (PSSM) and amino acid properties. We noticed that the C-terminal domain of efflux proteins contain vital information for discrimination. Our method showed an accuracy of 78 and 92% in discriminating efflux proteins from transporters and membrane proteins, respectively using fivefold cross-validation. We utilized our method for annotating the genomes E. coli and P. aeruginosa and it predicted 8.7 and 9.2% of proteins as efflux proteins in these genomes, respectively. The predicted efflux proteins have been compared with available experimental data and we observed a very good agreement between them. Further, we developed a web server for classifying efflux proteins and it is freely available at http://rbf.bioinfo.tw/∼sachen/EFFLUXpredict/Efflux-RBF.php. We suggest that our method could be an effective tool for annotating efflux proteins in genomic sequences.

  12. Accurate dipole polarizabilities for water clusters n=2-12 at the coupled-cluster level of theory and benchmarking of various density functionals.

    SciTech Connect

    Hammond, J.; Govind, N.; Kowalski, K.; Autschbach, J.; Xantheas, S.; PNNL; Univ. of Buffalo

    2009-12-07

    The static dipole polarizabilities of water clusters (2 {le} N {le} 12) are determined at the coupled-cluster level of theory (CCSD). For the dipole polarizability of the water monomer it was determined that the role of the basis set is more important than that of electron correlation and that the basis set augmentation converges with two sets of diffuse functions. The CCSD results are used to benchmark a variety of density functionals while the performance of several families of basis sets (Dunning, Pople, and Sadlej) in producing accurate values for the polarizabilities was also examined. The Sadlej family of basis sets was found to produce accurate results when compared to the ones obtained with the much larger Dunning basis sets. It was furthermore determined that the PBE0 density functional with the aug-cc-pVDZ basis set produces overall remarkably accurate polarizabilities at a moderate computational cost.

  13. A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.

    PubMed

    Amini, Ata; Shrimpton, Paul J; Muggleton, Stephen H; Sternberg, Michael J E

    2007-12-01

    Despite the increased recent use of protein-ligand and protein-protein docking in the drug discovery process due to the increases in computational power, the difficulty of accurately ranking the binding affinities of a series of ligands or a series of proteins docked to a protein receptor remains largely unsolved. This problem is of major concern in lead optimization procedures and has lead to the development of scoring functions tailored to rank the binding affinities of a series of ligands to a specific system. However, such methods can take a long time to develop and their transferability to other systems remains open to question. Here we demonstrate that given a suitable amount of background information a new approach using support vector inductive logic programming (SVILP) can be used to produce system-specific scoring functions. Inductive logic programming (ILP) learns logic-based rules for a given dataset that can be used to describe properties of each member of the set in a qualitative manner. By combining ILP with support vector machine regression, a quantitative set of rules can be obtained. SVILP has previously been used in a biological context to examine datasets containing a series of singular molecular structures and properties. Here we describe the use of SVILP to produce binding affinity predictions of a series of ligands to a particular protein. We also for the first time examine the applicability of SVILP techniques to datasets consisting of protein-ligand complexes. Our results show that SVILP performs comparably with other state-of-the-art methods on five protein-ligand systems as judged by similar cross-validated squares of their correlation coefficients. A McNemar test comparing SVILP to CoMFA and CoMSIA across the five systems indicates our method to be significantly better on one occasion. The ability to graphically display and understand the SVILP-produced rules is demonstrated and this feature of ILP can be used to derive hypothesis for

  14. Scoring Package

    National Institute of Standards and Technology Data Gateway

    NIST Scoring Package (PC database for purchase)   The NIST Scoring Package (Special Database 1) is a reference implementation of the draft Standard Method for Evaluating the Performance of Systems Intended to Recognize Hand-printed Characters from Image Data Scanned from Forms.

  15. Scored Discussions.

    ERIC Educational Resources Information Center

    Zola, John

    1992-01-01

    Suggests a classroom strategy to help students learn to analyze and discuss significant issues from history and current policy debates. Describes scored discussions in which small groups of students receive points for participation. Provides an example of a discussion on gold mining. Includes an agenda. Explores uses of scored discussions and…

  16. Graduate Student WAIS-III Scoring Accuracy Is a Function of Full Scale IQ and Complexity of Examiner Tasks

    ERIC Educational Resources Information Center

    Hopwood, Christopher J.; Richard, David C. S.

    2005-01-01

    Research on the Wechsler Adult Intelligence Scale-Revised and Wechsler Adult Intelligence Scale-Third Edition (WAIS-III) suggests that practicing clinical psychologists and graduate students make item-level scoring errors that affect IQ, index, and subtest scores. Studies have been limited in that Full-Scale IQ (FSIQ) and examiner administration,…

  17. A comparison between MRI, sonography and Functional Independence Score in Haemophilia methods in diagnosis, evaluation and classification of arthropathy in severe haemophilia A and B.

    PubMed

    Tasbihi, Mandana; Pishdad, Parisa; Haghpanah, Sezaneh; Ardeshiri, Rezvan; Tavoosi, Hakimeh; Karimi, Mehran

    2016-03-01

    Evaluation of joints in children with haemophilia is important in detecting abnormalities, staging their severity and following the effects of treatment. The aim of this study is to evaluate the correlation of FISH score (Functional Independence Score in Haemophilia) with the scores obtained by MRI and sonography for the diagnosis, evaluation and classification of arthropathy in severe haemophilia. In this cross-sectional study on 25 severe haemophilia patients, FISH, MRI and sonography procedures were performed in the elbow or knee joint. All patients' information, including age, type of haemophilia, affected joint, scores of MRI, sonography and FISH, dose of factor consumed, weight and prophylaxis protocol were collected and analysed. Among the 25 patients (age range of 11-70 years), 22 patients were haemophilia A and three patients were haemophilia B. Affected joints were right knee in 12 patients, left knee in nine and right elbow in four. There was only a statistically significant negative correlation between FISH and MRI Additive (A) scale (rs = -0.537, P = 0.006). Considering cartilage loss domain (related MRI A scale: 13-20), 20 patients (80%) were classified in this group with FISH scores ranged from 17 to 22. On the basis of our results, FISH scores in severe haemophilia patients were negatively correlated with MRI A scale. Also, it seems that a FISH score less than 22 could be considered as loss of cartilage; however, due to the small number of our patients, it needs further assessment in different populations.

  18. Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment

    PubMed Central

    Ranwez, Vincent

    2016-01-01

    Background Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Results Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement. PMID:27505054

  19. Application of new WAIS-III/WMS-III discrepancy scores for evaluating memory functioning: relationship between intellectual and memory ability.

    PubMed

    Lange, Rael T; Chelune, Gordon J

    2006-05-01

    Analysis of the discrepancy between memory and intellectual ability has received some support as a means for evaluating memory impairment. Recently, comprehensive base rate tables for General Ability Index (GAI) minus memory discrepancy scores (i.e., GAI-memory) were developed using the WAIS-III/WMS-III standardization sample (Lange, Chelune, & Tulsky, in press). The purpose of this study was to evaluate the clinical utility of GAI-memory discrepancy scores to identify memory impairment in 34 patients with Alzheimer's type dementia (DAT) versus a sample of 34 demographically matched healthy participants. On average, patients with DAT obtained significantly lower scores on all WAIS-III and WMS-III indexes and had larger GAI-memory discrepancy scores. Clinical outcome analyses revealed that GAI-memory scores were useful at identifying memory impairment in patients with DAT versus matched healthy participants. However, GAI-memory discrepancy scores failed to provide unique interpretive information beyond that which is gained from the memory indexes alone. Implications and future research directions are discussed.

  20. Application of new WAIS-III/WMS-III discrepancy scores for evaluating memory functioning: relationship between intellectual and memory ability.

    PubMed

    Lange, Rael T; Chelune, Gordon J

    2006-05-01

    Analysis of the discrepancy between memory and intellectual ability has received some support as a means for evaluating memory impairment. Recently, comprehensive base rate tables for General Ability Index (GAI) minus memory discrepancy scores (i.e., GAI-memory) were developed using the WAIS-III/WMS-III standardization sample (Lange, Chelune, & Tulsky, in press). The purpose of this study was to evaluate the clinical utility of GAI-memory discrepancy scores to identify memory impairment in 34 patients with Alzheimer's type dementia (DAT) versus a sample of 34 demographically matched healthy participants. On average, patients with DAT obtained significantly lower scores on all WAIS-III and WMS-III indexes and had larger GAI-memory discrepancy scores. Clinical outcome analyses revealed that GAI-memory scores were useful at identifying memory impairment in patients with DAT versus matched healthy participants. However, GAI-memory discrepancy scores failed to provide unique interpretive information beyond that which is gained from the memory indexes alone. Implications and future research directions are discussed. PMID:16624786

  1. Relationship of the sexual functions with the clinical parameters, radiological scores and the quality of life in male patients with ankylosing spondylitis.

    PubMed

    Sariyildiz, Mustafa Akif; Batmaz, Ibrahim; Dilek, Banu; Inanir, Ahmet; Bez, Yasin; Tahtasiz, Mehmet; Em, Serda; Cevik, Remzi

    2013-03-01

    The aim of this study was to explore the impact of ankylosing spondylitis (AS) and the disease-related variables on the patients' sexual function according to the International Index of Erectile Function (IIEF) scoring system. A total of 70 sexually active male AS patients and 60 healthy controls were enrolled in this study. Their demographic data were evaluated, and the pain was assessed according to the visual analogue scale (VAS). Laboratory tests were conducted in order to measure the C-reactive protein (CRP) and erythrocyte sedimentation rates (ESR) of the patients. The disease activity was evaluated using the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI). Functional statement was evaluated with the help of the Bath Ankylosing Spondylitis Functional Index (BASFI) and with the scores obtained from the spinal measurements with the Bath Ankylosing Spondylitis Metrology Index (BASMI). The Bath Ankylosing Spondylitis Radiology Index (BASRI) was used to evaluate the radiological damage. The disease-related quality of life was measured with the Ankylosing Spondylitis Quality of Life Questionnaire (ASQoL). The anxiety and depression level of the patients was revealed through the Hospital Anxiety and Depression Scale (HADS). In comparison with the healthy control group, patients with AS had significantly lower scores in each of the 5 domains of the IIEF (p < 0.0001). The BASDAI, BASFI, BASMI, BASRI, ASQoL, HADS scores and CRP levels were negatively correlated with IIEF (p < 0.05). Orgasmic function and sexual desire scores were significantly lower in patients with peripheral arthritis (p < 0.05). No significant correlation was observed with the disease duration, smoking status, pain (VAS), and ESR levels when the total scores and the scores from the domains of IIEF were compared. The multivariate regression analyses indicated that BASFI and BASMI were independently associated with the sexual function. The sexual function is impaired in male patients

  2. LETTER TO THE EDITOR: Accurate Hylleraas-like functions for the He atom with correct cusp conditions

    NASA Astrophysics Data System (ADS)

    Rodriguez, K. V.; Gasaneo, G.

    2005-08-01

    In this letter, a set of ground state wavefunctions for the He atom is given. The functions are constructed in terms of exponential and power series as similar as possible to the Hylleraas functions of Chandrasekhar and Herzberg (1955 Phys. Rev. 98 1050). The accuracy of the calculated energies is found to be about 10-4 au and all the cusp conditions at the Coulomb singularities are satisfied. The nine-parameter functions proposed here are found to have better local energy than those given by the 6 and 14 terms Hylleraas functions of Chandrasekhar. The mean value of various functions evaluated with the different proposals shows their good quality. These properties highly qualify the function to be used as an alternative to the Chandrasekhar functions in collisional problems. The whole set of functions given here can be considered as an alternative to the proposals of Chandrasekhar (1955 Phys. Rev. 98 1050), Bonham and Kohl (1966 J. Chem. Phys. 45 2471) and Le Sech (1997 J. Phys. B: At. Mol. Opt. Phys. 30 L47).

  3. A Comparison of Methods for Estimating Conditional Item Score Differences in Differential Item Functioning (DIF) Assessments. Research Report. ETS RR-10-15

    ERIC Educational Resources Information Center

    Moses, Tim; Miao, Jing; Dorans, Neil

    2010-01-01

    This study compared the accuracies of four differential item functioning (DIF) estimation methods, where each method makes use of only one of the following: raw data, logistic regression, loglinear models, or kernel smoothing. The major focus was on the estimation strategies' potential for estimating score-level, conditional DIF. A secondary focus…

  4. Number Right and Elimination Score as a Function of Item Arrangement, Knowledge of Arrangement, and Test Anxiety.

    ERIC Educational Resources Information Center

    Plake, Barbara S.; And Others

    Number right and elimination scores were analyzed on a 48-item college level mathematics test that was assembled from pretest data in three forms by varying the item orderings: easy-hard, uniform, or random. Half of the forms contained information explaining the item arrangement and suggesting strategies for taking the test. Several anxiety…

  5. Polytomous Differential Item Functioning and Violations of Ordering of the Expected Latent Trait by the Raw Score

    ERIC Educational Resources Information Center

    DeMars, Christine E.

    2008-01-01

    The graded response (GR) and generalized partial credit (GPC) models do not imply that examinees ordered by raw observed score will necessarily be ordered on the expected value of the latent trait (OEL). Factors were manipulated to assess whether increased violations of OEL also produced increased Type I error rates in differential item…

  6. Test Score Measurement Error, Short-Term Knowledge, and Lagged Dependent Variables in Models of the Education Production Function

    ERIC Educational Resources Information Center

    Stacy, Brian; Lockwood, J. R.; McCaffrey, Daniel

    2012-01-01

    Researchers and policymakers are interested in the causal effects of educational inputs on student achievement. Unfortunately, it is not possible to directly observe student learning, so test score data is often used as an approximate measure. To measure their achievement at a given point in time (e.g., in the spring of the school year) students…

  7. Toward Accurate Reaction Energetics for Molecular Line Growth at Surface: Quantum Monte Carlo and Density Functional Theory Calculations

    SciTech Connect

    Kanai, Y; Takeuchi, N

    2009-10-14

    We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

  8. On the use of spring baseflow recession for a more accurate parameterization of aquifer transit time distribution functions

    NASA Astrophysics Data System (ADS)

    Farlin, J.; Maloszewski, P.

    2013-05-01

    Baseflow recession analysis and groundwater dating have up to now developed as two distinct branches of hydrogeology and have been used to solve entirely different problems. We show that by combining two classical models, namely the Boussinesq equation describing spring baseflow recession, and the exponential piston-flow model used in groundwater dating studies, the parameters describing the transit time distribution of an aquifer can be in some cases estimated to a far more accurate degree than with the latter alone. Under the assumption that the aquifer basis is sub-horizontal, the mean transit time of water in the saturated zone can be estimated from spring baseflow recession. This provides an independent estimate of groundwater transit time that can refine those obtained from tritium measurements. The approach is illustrated in a case study predicting atrazine concentration trend in a series of springs draining the fractured-rock aquifer known as the Luxembourg Sandstone. A transport model calibrated on tritium measurements alone predicted different times to trend reversal following the nationwide ban on atrazine in 2005 with different rates of decrease. For some of the springs, the actual time of trend reversal and the rate of change agreed extremely well with the model calibrated using both tritium measurements and the recession of spring discharge during the dry season. The agreement between predicted and observed values was however poorer for the springs displaying the most gentle recessions, possibly indicating a stronger influence of continuous groundwater recharge during the summer months.

  9. On the use of spring baseflow recession for a more accurate parameterization of aquifer transit time distribution functions

    NASA Astrophysics Data System (ADS)

    Farlin, J.; Maloszewski, P.

    2012-12-01

    Baseflow recession analysis and groundwater dating have up to now developed as two distinct branches of hydrogeology and were used to solve entirely different problems. We show that by combining two classical models, namely Boussinesq's Equation describing spring baseflow recession and the exponential piston-flow model used in groundwater dating studies, the parameters describing the transit time distribution of an aquifer can be in some cases estimated to a far more accurate degree than with the latter alone. Under the assumption that the aquifer basis is sub-horizontal, the mean residence time of water in the saturated zone can be estimated from spring baseflow recession. This provides an independent estimate of groundwater residence time that can refine those obtained from tritium measurements. This approach is demonstrated in a case study predicting atrazine concentration trend in a series of springs draining the fractured-rock aquifer known as the Luxembourg Sandstone. A transport model calibrated on tritium measurements alone predicted different times to trend reversal following the nationwide ban on atrazine in 2005 with different rates of decrease. For some of the springs, the best agreement between observed and predicted time of trend reversal was reached for the model calibrated using both tritium measurements and the recession of spring discharge during the dry season. The agreement between predicted and observed values was however poorer for the springs displaying the most gentle recessions, possibly indicating the stronger influence of continuous groundwater recharge during the dry period.

  10. Functional connectivity and structural covariance between regions of interest can be measured more accurately using multivariate distance correlation.

    PubMed

    Geerligs, Linda; Cam-Can; Henson, Richard N

    2016-07-15

    Studies of brain-wide functional connectivity or structural covariance typically use measures like the Pearson correlation coefficient, applied to data that have been averaged across voxels within regions of interest (ROIs). However, averaging across voxels may result in biased connectivity estimates when there is inhomogeneity within those ROIs, e.g., sub-regions that exhibit different patterns of functional connectivity or structural covariance. Here, we propose a new measure based on "distance correlation"; a test of multivariate dependence of high dimensional vectors, which allows for both linear and non-linear dependencies. We used simulations to show how distance correlation out-performs Pearson correlation in the face of inhomogeneous ROIs. To evaluate this new measure on real data, we use resting-state fMRI scans and T1 structural scans from 2 sessions on each of 214 participants from the Cambridge Centre for Ageing & Neuroscience (Cam-CAN) project. Pearson correlation and distance correlation showed similar average connectivity patterns, for both functional connectivity and structural covariance. Nevertheless, distance correlation was shown to be 1) more reliable across sessions, 2) more similar across participants, and 3) more robust to different sets of ROIs. Moreover, we found that the similarity between functional connectivity and structural covariance estimates was higher for distance correlation compared to Pearson correlation. We also explored the relative effects of different preprocessing options and motion artefacts on functional connectivity. Because distance correlation is easy to implement and fast to compute, it is a promising alternative to Pearson correlations for investigating ROI-based brain-wide connectivity patterns, for functional as well as structural data.

  11. Surgical Release of the First Extensor Compartment for Refractory de Quervain's Tenosynovitis: Surgical Findings and Functional Evaluation Using DASH Scores

    PubMed Central

    Lee, Hyun-Joo; Kim, Poong-Taek; Aminata, Iman Widya; Hong, Han-Pyo; Yoon, Jong-Pil

    2014-01-01

    Background Few studies have evaluated surgical outcomes in patients with refractory de Quervain's disease using validated outcome measures. We assessed the clinical outcomes of dorsal release of the first extensor compartment for the treatment of de Quervain's disease using the disabilities of the arm, shoulder and hand (DASH) score. Methods From October 2003 to May 2009, we retrospectively evaluated 33 patients (3 men and 30 women) who underwent surgical treatment for de Quervain's disease. All patients had a positive Finkelstein test and localized tenderness over the first dorsal compartment. All operations were performed under local anesthesia. A 2-cm-long transverse skin incision was made over the first extensor compartment and the dorsal retinaculum covering the extensor pollicis brevis was incised longitudinally. Preoperative and postoperative clinical evaluation included the use of DASH score, Finkelstein test, and visual analogue scale (VAS) score. Results In 18 patients (55%), the extensor pollicis brevis tendon compartment was separated from the abductor pollicis longus compartment. Eight patients had intracompartmental ganglia in the extensor pollicis brevis subcompartment. All patients except one had negative sign on Finkelstein test at the last follow-up. The average VAS score decreased from 7.42 preoperatively to 1.33 postoperatively (p < 0.05), and DASH score was improved from 53.2 to 3.45 (p < 0.05). There were no postoperative complications such as subluxation of the tendon of the first dorsal compartment or injury to the sensory branch of the radial nerve. Conclusions Intracompartment ganglia and the separate septum of extensor pollicis brevis are often related to de Quervain's disease. The release of the first extensor compartment for refractory de Quervain's disease resulted in good clinical outcomes with minimal morbidity. PMID:25436064

  12. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system.

    PubMed

    Pearlman, D A; Charifson, P S

    2001-10-11

    Precise thermodynamic integration free energy simulations have been applied to a congeneric series of 16 inhibitors to the p38 MAP kinase protein for which the experimental binding data (IC(50)) is known. The relative free energy of binding for each compound has been determined. For comparison, the same series of compounds have also scored using the best rapid scoring functions used in database screening. From the results of these calculations, we find (1) that precise free energy simulations allow predictions that are reliable and in good agreement with experiment; (2) that predictions of lower reliability, but still in good qualitative agreement with experiment, can be obtained using the OWFEG free energy grid method, at a much lower computational cost; (3) and that other methods, not based on free energy simulations yield results in much poorer agreement with experiment. A new predictive index, which measures the reliability of a prediction method in the context of normal use, is defined and calculated for each scoring method. Predictive indices of 0.84, 0.56, 0.04, -0.05, and 0.25 are calculated for thermodynamic integration, OWFEG, ChemScore, PLPScore, and Dock Energy Score, respectively, where +1.0 is perfect correct prediction, -1.0 is perfect incorrect prediction, and 0.0 is random.

  13. Three dimensional neuronal cell cultures more accurately model voltage gated calcium channel functionality in freshly dissected nerve tissue.

    PubMed

    Lai, Yinzhi; Cheng, Ke; Kisaalita, William

    2012-01-01

    It has been demonstrated that neuronal cells cultured on traditional flat surfaces may exhibit exaggerated voltage gated calcium channel (VGCC) functionality. To gain a better understanding of this phenomenon, primary neuronal cells harvested from mice superior cervical ganglion (SCG) were cultured on two dimensional (2D) flat surfaces and in three dimensional (3D) synthetic poly-L-lactic acid (PLLA) and polystyrene (PS) polymer scaffolds. These 2D- and 3D-cultured cells were compared to cells in freshly dissected SCG tissues, with respect to intracellular calcium increase in response to high K(+) depolarization. The calcium increases were identical for 3D-cultured and freshly dissected, but significantly higher for 2D-cultured cells. This finding established the physiological relevance of 3D-cultured cells. To shed light on the mechanism behind the exaggerated 2D-cultured cells' functionality, transcriptase expression and related membrane protein distributions (caveolin-1) were obtained. Our results support the view that exaggerated VGCC functionality from 2D cultured SCG cells is possibly due to differences in membrane architecture, characterized by uniquely organized caveolar lipid rafts. The practical implication of use of 3D-cultured cells in preclinical drug discovery studies is that such platforms would be more effective in eliminating false positive hits and as such improve the overall yield from screening campaigns.

  14. Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

    PubMed

    Iwakiri, Junichi; Hamada, Michiaki; Asai, Kiyoshi; Kameda, Tomoshi

    2016-09-13

    RNA-protein interactions play fundamental roles in many biological processes. To understand these interactions, it is necessary to know the three-dimensional structures of RNA-protein complexes. However, determining the tertiary structure of these complexes is often difficult, suggesting that an accurate rigid body docking for RNA-protein complexes is needed. In general, the rigid body docking process is divided into two steps: generating candidate structures from the individual RNA and protein structures and then narrowing down the candidates. In this study, we focus on the former problem to improve the prediction accuracy in RNA-protein docking. Our method is based on the integration of physicochemical information about RNA into ZDOCK, which is known as one of the most successful computer programs for protein-protein docking. Because recent studies showed the current force field for molecular dynamics simulation of protein and nucleic acids is quite accurate, we modeled the physicochemical information about RNA by force fields such as AMBER and CHARMM. A comprehensive benchmark of RNA-protein docking, using three recently developed data sets, reveals the remarkable prediction accuracy of the proposed method compared with existing programs for docking: the highest success rate is 34.7% for the predicted structure of the RNA-protein complex with the best score and 79.2% for 3,600 predicted ones. Three full atomistic force fields for RNA (AMBER94, AMBER99, and CHARMM22) produced almost the same accurate result, which showed current force fields for nucleic acids are quite accurate. In addition, we found that the electrostatic interaction and the representation of shape complementary between protein and RNA plays the important roles for accurate prediction of the native structures of RNA-protein complexes.

  15. Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

    PubMed

    Iwakiri, Junichi; Hamada, Michiaki; Asai, Kiyoshi; Kameda, Tomoshi

    2016-09-13

    RNA-protein interactions play fundamental roles in many biological processes. To understand these interactions, it is necessary to know the three-dimensional structures of RNA-protein complexes. However, determining the tertiary structure of these complexes is often difficult, suggesting that an accurate rigid body docking for RNA-protein complexes is needed. In general, the rigid body docking process is divided into two steps: generating candidate structures from the individual RNA and protein structures and then narrowing down the candidates. In this study, we focus on the former problem to improve the prediction accuracy in RNA-protein docking. Our method is based on the integration of physicochemical information about RNA into ZDOCK, which is known as one of the most successful computer programs for protein-protein docking. Because recent studies showed the current force field for molecular dynamics simulation of protein and nucleic acids is quite accurate, we modeled the physicochemical information about RNA by force fields such as AMBER and CHARMM. A comprehensive benchmark of RNA-protein docking, using three recently developed data sets, reveals the remarkable prediction accuracy of the proposed method compared with existing programs for docking: the highest success rate is 34.7% for the predicted structure of the RNA-protein complex with the best score and 79.2% for 3,600 predicted ones. Three full atomistic force fields for RNA (AMBER94, AMBER99, and CHARMM22) produced almost the same accurate result, which showed current force fields for nucleic acids are quite accurate. In addition, we found that the electrostatic interaction and the representation of shape complementary between protein and RNA plays the important roles for accurate prediction of the native structures of RNA-protein complexes. PMID:27494732

  16. Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Wang, Mingjun; Wang, Huilin; Tan, Hao; Zhang, Ziding; Webb, Geoffrey I.; Song, Jiangning

    2014-07-01

    Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation, and apoptosis. To fully understand acetylation mechanisms, identification of substrates and specific acetylation sites is crucial. Experimental identification is often time-consuming and expensive. Alternative bioinformatics methods are cost-effective and can be used in a high-throughput manner to generate relatively precise predictions. Here we develop a method termed as SSPKA for species-specific lysine acetylation prediction, using random forest classifiers that combine sequence-derived and functional features with two-step feature selection. Feature importance analysis indicates functional features, applied for lysine acetylation site prediction for the first time, significantly improve the predictive performance. We apply the SSPKA model to screen the entire human proteome and identify many high-confidence putative substrates that are not previously identified. The results along with the implemented Java tool, serve as useful resources to elucidate the mechanism of lysine acetylation and facilitate hypothesis-driven experimental design and validation.

  17. Automated Essay Scoring

    ERIC Educational Resources Information Center

    Dikli, Semire

    2006-01-01

    The impacts of computers on writing have been widely studied for three decades. Even basic computers functions, i.e. word processing, have been of great assistance to writers in modifying their essays. The research on Automated Essay Scoring (AES) has revealed that computers have the capacity to function as a more effective cognitive tool (Attali,…

  18. An efficient and accurate approximation to time-dependent density functional theory for systems of weakly coupled monomers

    NASA Astrophysics Data System (ADS)

    Liu, Jie; Herbert, John M.

    2015-07-01

    A novel formulation of time-dependent density functional theory (TDDFT) is derived, based on non-orthogonal, absolutely-localized molecular orbitals (ALMOs). We call this approach TDDFT(MI), in reference to ALMO-based methods for describing molecular interactions (MI) that have been developed for ground-state applications. TDDFT(MI) is intended for efficient excited-state calculations in systems composed of multiple, weakly interacting chromophores. The efficiency is based upon (1) a local excitation approximation; (2) monomer-based, singly-excited basis states; (3) an efficient localization procedure; and (4) a one-step Davidson method to solve the TDDFT(MI) working equation. We apply this methodology to study molecular dimers, water clusters, solvated chromophores, and aggregates of naphthalene diimide that form the building blocks of self-assembling organic nanotubes. Absolute errors of 0.1-0.3 eV with respect to supersystem methods are achievable for these systems, especially for cases involving an excited chromophore that is weakly coupled to several explicit solvent molecules. Excited-state calculations in an aggregate of nine naphthalene diimide monomers are ˜40 times faster than traditional TDDFT calculations.

  19. Associations of Cognitive Function Scores with Carbon Dioxide, Ventilation, and Volatile Organic Compound Exposures in Office Workers: A Controlled Exposure Study of Green and Conventional Office Environments

    PubMed Central

    Allen, Joseph G.; MacNaughton, Piers; Satish, Usha; Santanam, Suresh; Vallarino, Jose; Spengler, John D.

    2015-01-01

    Background: The indoor built environment plays a critical role in our overall well-being because of both the amount of time we spend indoors (~90%) and the ability of buildings to positively or negatively influence our health. The advent of sustainable design or green building strategies reinvigorated questions regarding the specific factors in buildings that lead to optimized conditions for health and productivity. Objective: We simulated indoor environmental quality (IEQ) conditions in “Green” and “Conventional” buildings and evaluated the impacts on an objective measure of human performance: higher-order cognitive function. Methods: Twenty-four participants spent 6 full work days (0900–1700 hours) in an environmentally controlled office space, blinded to test conditions. On different days, they were exposed to IEQ conditions representative of Conventional [high concentrations of volatile organic compounds (VOCs)] and Green (low concentrations of VOCs) office buildings in the United States. Additional conditions simulated a Green building with a high outdoor air ventilation rate (labeled Green+) and artificially elevated carbon dioxide (CO2) levels independent of ventilation. Results: On average, cognitive scores were 61% higher on the Green building day and 101% higher on the two Green+ building days than on the Conventional building day (p < 0.0001). VOCs and CO2 were independently associated with cognitive scores. Conclusions: Cognitive function scores were significantly better under Green+ building conditions than in the Conventional building conditions for all nine functional domains. These findings have wide-ranging implications because this study was designed to reflect conditions that are commonly encountered every day in many indoor environments. Citation: Allen JG, MacNaughton P, Satish U, Santanam S, Vallarino J, Spengler JD. 2016. Associations of cognitive function scores with carbon dioxide, ventilation, and volatile organic compound

  20. An accurate cluster selection function for the J-PAS narrow-band wide-field survey

    NASA Astrophysics Data System (ADS)

    Ascaso, B.; Benítez, N.; Dupke, R.; Cypriano, E.; Lima-Neto, G.; López-Sanjuan, C.; Varela, J.; Alcaniz, J. S.; Broadhurst, T.; Cenarro, A. J.; Devi, N. Chandrachani; Díaz-García, L. A.; Fernandes, C. A. C.; Hernández-Monteagudo, C.; Mei, S.; Mendes de Oliveira, C.; Molino, A.; Oteo, I.; Schoenell, W.; Sodré, L.; Viironen, K.; Marín-Franch, A.

    2016-03-01

    The impending Javalambre Physics of the accelerating Universe Astrophysical Survey (J-PAS) will be the first wide-field survey of ≳ 8500 deg2 to reach the `stage IV' category. Because of the redshift resolution afforded by 54 narrow-band filters, J-PAS is particularly suitable for cluster detection in the range z<1. The photometric redshift dispersion is estimated to be only ˜0.003 with few outliers ≲4 per cent for galaxies brighter than i ˜ 23 AB, because of the sensitivity of narrow band imaging to absorption and emission lines. Here, we evaluate the cluster selection function for J-PAS using N-body+semi-analytical realistic mock catalogues. We optimally detect clusters from this simulation with the Bayesian Cluster Finder, and we assess the completeness and purity of cluster detection against the mock data. The minimum halo mass threshold we find for detections of galaxy clusters and groups with both >80 per cent completeness and purity is Mh ˜ 5 × 1013 M⊙ up to z ˜ 0.7. We also model the optical observable, M^{*}_CL-halo mass relation, finding a non-evolution with redshift and main scatter of σ _{M^{*}_CL | M_h}˜ 0.14 dex down to a factor 2 lower in mass than other planned broad-band stage IV surveys, at least. For the Mh ˜ 1 × 1014 M⊙ Planck mass limit, J-PAS will arrive up to z ˜ 0.85 with a σ _{M^{*}_CL | M_h}˜ 0.12 dex. Therefore, J-PAS will provide the largest sample of clusters and groups up to z ˜ 0.8 with a mass calibration accuracy comparable to X-ray data.

  1. The route to MBxNyCz molecular wheels: II. Results using accurate functionals and basis sets

    NASA Astrophysics Data System (ADS)

    Güthler, A.; Mukhopadhyay, S.; Pandey, R.; Boustani, I.

    2014-04-01

    Applying ab initio quantum chemical methods, molecular wheels composed of metal and light atoms were investigated. High quality basis sets 6-31G*, TZPV, and cc-pVTZ as well as exchange and non-local correlation functionals B3LYP, BP86 and B3P86 were used. The ground-state energy and structures of cyclic planar and pyramidal clusters TiBn (for n = 3-10) were computed. In addition, the relative stability and electronic structures of molecular wheels TiBxNyCz (for x, y, z = 0-10) and MBnC10-n (for n = 2 to 5 and M = Sc to Zn) were determined. This paper sustains a follow-up study to the previous one of Boustani and Pandey [Solid State Sci. 14 (2012) 1591], in which the calculations were carried out at the HF-SCF/STO3G/6-31G level of theory to determine the initial stability and properties. The results show that there is a competition between the 2D planar and the 3D pyramidal TiBn clusters (for n = 3-8). Different isomers of TiB10 clusters were also studied and a structural transition of 3D-isomer into 2D-wheel is presented. Substitution boron in TiB10 by carbon or/and nitrogen atoms enhances the stability and leads toward the most stable wheel TiB3C7. Furthermore, the computations show that Sc, Ti and V at the center of the molecular wheels are energetically favored over other transition metal atoms of the first row.

  2. Accurate Analytic Potential Functions for the a ^3Π_1 and X ^1Σ^+ States of {IBr}

    NASA Astrophysics Data System (ADS)

    Yukiya, Tokio; Nishimiya, Nobuo; Suzuki, Masao; Le Roy, Robert

    2014-06-01

    Spectra of IBr in various wavelength regions have been measured by a number of researchers using traditional diffraction grating and microwave methods, as well as using high-resolution laser techniques combined with a Fourier transform spectrometer. In a previous paper at this meeting, we reported a preliminary determination of analytic potential energy functions for the A ^3Π_1 and X ^1Σ^+ states of IBr from a direct-potential-fit (DPF) analysis of all of the data available at that time. That study also confirmed the presence of anomalous fluctuations in the v--dependence of the first differences of the inertial rotational constant, Δ Bv=Bv+1-Bv in the A ^3Π_1 state for vibrational levels with v'(A) in the mid 20's. However, our previous experience in a recent study of the analogous A ^3Π_1-X ^1Σ_g^+ system of Br_2 suggested that the effect of such fluctuations may be overcome if sufficient data are available. The present work therefore reports new measurements of transitions to levels in the v'(A)=23-26 region, together with a new global DPF analysis that uses ``robust" least-squares fits to average properly over the effect of such fluctuations in order to provide an optimum delineation of the underlying potential energy curve(s). L.E.Selin,Ark. Fys. 21,479(1962) E. Tiemann and Th. Moeller, Z. Naturforsch. A 30,986 (1975) E.M. Weinstock and A. Preston, J. Mol. Spectrosc. 70, 188 (1978) D.R.T. Appadoo, P.F. Bernath, and R.J. Le Roy, Can. J. Phys. 72, 1265 (1994) N. Nishimiya, T. Yukiya and M. Suzuki, J. Mol. Spectrosc. 173, 8 (1995). T. Yukiya, N. Nishimiya, and R.J. Le Roy, Paper MF12 at the 65th Ohio State University International Symposium on Molecular Spectroscopy, Columbus, Ohio, June 20-24, 2011. T. Yukiya, N. Nishimiya, Y. Samajima, K. Yamaguchi, M. Suzuki, C.D. Boone, I. Ozier and R.J. Le Roy, J. Mol. Spectrosc. 283, 32 (2013) J.K.G. Watson, J. Mol. Spectrosc. 219, 326 (2003).

  3. Relationship between the climbing up and climbing down stairs domain scores on the FES-DMD, the score on the Vignos Scale, age and timed performance of functional activities in boys with Duchenne muscular dystrophy

    PubMed Central

    Fernandes, Lilian A. Y.; Caromano, Fátima A.; Assis, Silvana M. B.; Hukuda, Michele E.; Voos, Mariana C.; Carvalho, Eduardo V.

    2014-01-01

    BACKGROUND: Knowing the potential for and limitations of information generated using different evaluation instruments favors the development of more accurate functional diagnoses and therapeutic decision-making. OBJECTIVE: To investigate the relationship between the number of compensatory movements when climbing up and going down stairs, age, functional classification and time taken to perform a tested activity (TA) of going up and down stairs in boys with Duchenne muscular dystrophy (DMD). METHOD: A bank of movies featuring 30 boys with DMD performing functional activities was evaluated. Compensatory movements were assessed using the climbing up and going down stairs domain of the Functional Evaluation Scale for Duchenne Muscular Dystrophy (FES-DMD); age in years; functional classification using the Vignos Scale (VS), and TA using a timer. Statistical analyses were performed using the Spearman correlation test. RESULTS: There is a moderate relationship between the climbing up stairs domain of the FES-DMD and age (r=0.53, p=0.004) and strong relationships with VS (r=0.72, p=0.001) and TA for this task (r=0.83, p<0.001). There were weak relationships between the going down stairs domain of the FES-DMD-going down stairs with age (r=0.40, p=0.032), VS (r=0.65, p=0.002) and TA for this task (r=0.40, p=0.034). CONCLUSION: These findings indicate that the evaluation of compensatory movements used when climbing up stairs can provide more relevant information about the evolution of the disease, although the activity of going down stairs should be investigated, with the aim of enriching guidance and strengthening accident prevention. Data from the FES-DMD, age, VS and TA can be used in a complementary way to formulate functional diagnoses. Longitudinal studies and with broader age groups may supplement this information. PMID:25590443

  4. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    PubMed

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  5. Differences between Mothers' and Fathers' Ratings of Family Functioning with the Family Assessment Device: The Validity of Combined Parent Scores

    ERIC Educational Resources Information Center

    Cooke, Dawson; Marais, Ida; Cavanagh, Robert; Kendall, Garth; Priddis, Lynn

    2015-01-01

    The psychometric properties of the General Functioning subscale of the McMaster Family Assessment Device were examined using the Rasch Model (N = 237 couples). Mothers' and fathers' ratings of the General Functioning subscale of the McMaster Family Assessment Device are recommended, provided these are analyzed separately. More than a quarter of…

  6. The near-equivalence of five species of spectrally-accurate radial basis functions (RBFs): Asymptotic approximations to the RBF cardinal functions on a uniform, unbounded grid

    NASA Astrophysics Data System (ADS)

    Boyd, John P.

    2011-02-01

    Radial basis function (RBF) interpolants have become popular in computer graphics, neural networks and for solving partial differential equations in many fields of science and engineering. In this article, we compare five different species of RBFs: Gaussians, hyperbolic secant (sech's), inverse quadratics, multiquadrics and inverse multiquadrics. We show that the corresponding cardinal functions for a uniform, unbounded grid are all approximated by the same function: C(X) ∼ (1/(ρ)) sin (πX)/sinh (πX/ρ) for some constant ρ(α) which depends on the inverse width parameter (“shape parameter”) α of the RBF and also on the RBF species. The error in this approximation is exponentially small in 1/α for sech's and inverse quadratics and exponentially small in 1/α2 for Gaussians; the error is proportional to α4 for multiquadrics and inverse multiquadrics. The error in all cases is small even for α ∼ O(1). These results generalize to higher dimensions. The Gaussian RBF cardinal functions in any number of dimensions d are, without approximation, the tensor product of one dimensional Gaussian cardinal functions: Cd(x1,x2…,xd)=∏j=1dC(xj). For other RBF species, we show that the two-dimensional cardinal functions are well approximated by the products of one-dimensional cardinal functions; again the error goes to zero as α → 0. The near-identity of the cardinal functions implies that all five species of RBF interpolants are (almost) the same, despite the great differences in the RBF ϕ's themselves.

  7. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  8. Scoring from Contests

    PubMed Central

    Penn, Elizabeth Maggie

    2014-01-01

    This article presents a new model for scoring alternatives from “contest” outcomes. The model is a generalization of the method of paired comparison to accommodate comparisons between arbitrarily sized sets of alternatives in which outcomes are any division of a fixed prize. Our approach is also applicable to contests between varying quantities of alternatives. We prove that under a reasonable condition on the comparability of alternatives, there exists a unique collection of scores that produces accurate estimates of the overall performance of each alternative and satisfies a well-known axiom regarding choice probabilities. We apply the method to several problems in which varying choice sets and continuous outcomes may create problems for standard scoring methods. These problems include measuring centrality in network data and the scoring of political candidates via a “feeling thermometer.” In the latter case, we also use the method to uncover and solve a potential difficulty with common methods of rescaling thermometer data to account for issues of interpersonal comparability. PMID:24748759

  9. The Youth Throwing Score

    PubMed Central

    Ahmad, Christopher S.; Padaki, Ajay S.; Noticewala, Manish Suresh; Makhni, Eric Chugh; Popkin, Charles Aaron

    2016-01-01

    Objectives: Epidemic levels of shoulder and elbow injuries have been reported in youth and adolescent baseball players. Despite the concerning frequency of these injuries, no instrument has been validated to assess upper extremity injury in this patient population. The purpose of this study was to validate an upper extremity assessment tool specifically designed for youth baseball players. We hypothesize this tool will be reliable, responsive and valid. Methods: The Youth Throwing Score (YTS) was constructed by a multidisciplinary healthcare provider team in addition to baseball coaches as a tool to assess upper extremity injury in 10 to 18 year old baseball players. The instrument was comprised of a demographics section and a 14 item assessment of pain, fatigue and psychosocial health. The 14 items were scored from 1 to 5 and weighted equally, with higher scores reflecting fewer symptoms and less functional disability. The psychometric properties, including the test-retest reliability, internal consistency, and responsiveness were calculated. Additionally, the Pearson correlation coefficient to 4 validated outcomes was determined. Results: A pilot form of the instrument was administered to 25 players to assess comprehension and mean item importance. Pilot analysis resulted in none of the 14 items receiving less than a 3 out of 5 mean athlete importance rating and the final instrument read at a Flesch-Kincaid level of 4.1, appropriate for patients age 9 and older. A total of 223 players completed the Youth Throwing Score, with an average player age of 14.3 ± 2.7 years old. The players self-assigned injury status, resulting in an average survey score of 59.7 ± 8.4 for the 148 players ‘playing without pain,’ 42.0 ± 11.5 for the 60 players ‘playing with pain,’ and 40.4 ± 10.5 for the 15 players ‘not playing due to pain.’ Players playing without pain scored significantly higher than those playing with pain (p < .001). The scoring tiers of the Youth

  10. Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

    2015-01-01

    The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

  11. Two-component density functional theory within the projector augmented-wave approach: Accurate and self-consistent computations of positron lifetimes and momentum distributions

    NASA Astrophysics Data System (ADS)

    Wiktor, Julia; Jomard, Gérald; Torrent, Marc

    2015-09-01

    Many techniques have been developed in the past in order to compute positron lifetimes in materials from first principles. However, there is still a lack of a fast and accurate self-consistent scheme that could handle accurately the forces acting on the ions induced by the presence of the positron. We will show in this paper that we have reached this goal by developing the two-component density functional theory within the projector augmented-wave (PAW) method in the open-source code abinit. This tool offers the accuracy of the all-electron methods with the computational efficiency of the plane-wave ones. We can thus deal with supercells that contain few hundreds to thousands of atoms to study point defects as well as more extended defects clusters. Moreover, using the PAW basis set allows us to use techniques able to, for instance, treat strongly correlated systems or spin-orbit coupling, which are necessary to study heavy elements, such as the actinides or their compounds.

  12. Parent-Youth Rating Concordance for Hair Pulling Variables, Functional Impairment, and Anxiety Scale Scores in Trichotillomania

    ERIC Educational Resources Information Center

    Keuthen, Nancy J.; Flessner, Christopher A.; Woods, Douglas W.; Franklin, Martin E.; Piacentini, John A.; Khanna, Muniya; Moore, Phoebe; Cashin, Susan

    2008-01-01

    Knowledge of cross-informant rating concordance is critical for the assessment of child and adolescent problems in clinical and research settings. We explored parent-youth rating concordance for hair pulling variables, functional impairment, and anxiety symptoms in a sample of child and adolescent hair pullers (n = 133) satisfying conservative…

  13. A DPF Analysis Yields Quantum Mechanically Accurate Analytic Potential Energy Functions for the a ^1Σ^+ and X ^1Σ^+ States of NaH

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Walji, Sadru; Sentjens, Katherine

    2013-06-01

    Alkali hydride diatomic molecules have long been the object of spectroscopic studies. However, their small reduced mass makes them species for which the conventional semiclassical-based methods of analysis tend to have the largest errors. To date, the only quantum-mechanically accurate direct-potential-fit (DPF) analysis for one of these molecules was the one for LiH reported by Coxon and Dickinson. The present paper extends this level of analysis to NaH, and reports a DPF analysis of all available spectroscopic data for the A ^1Σ^+-X ^1Σ^+ system of NaH which yields analytic potential energy functions for these two states that account for those data (on average) to within the experimental uncertainties. W.C. Stwalley, W.T. Zemke and S.C. Yang, J. Phys. Chem. Ref. Data {20}, 153-187 (1991). J.A. Coxon and C.S. Dickinson, J. Chem. Phys. {121}, 8378 (2004).

  14. Type 2 Diabetes, Diabetes Genetic Score and Risk of Decreased Renal Function and Albuminuria: A Mendelian Randomization Study

    PubMed Central

    Xu, Min; Bi, Yufang; Huang, Ya; Xie, Lan; Hao, Mingli; Zhao, Zhiyun; Xu, Yu; Lu, Jieli; Chen, Yuhong; Sun, Yimin; Qi, Lu; Wang, Weiqing; Ning, Guang

    2016-01-01

    Background Type 2 diabetes (T2D) is a risk factor for dysregulation of glomerular filtration rate (GFR) and albuminuria. However, whether the association is causal remains unestablished. Research Design and Methods We performed a Mendelian Randomization (MR) analysis in 11,502 participants aged 40 and above, from a well-defined community in Shanghai during 2011–2013, to explore the causal association between T2D and decreased estimated GFR (eGFR) and increased urinary albumin-to-creatinine ratio (uACR). We genotyped 34 established T2D common variants in East Asians, and created a T2D-genetic risk score (GRS). We defined decreased eGFR as eGFR < 90 ml/min/1.73 m2 and increased uACR as uACR ≥ 30 mg/g. We used the T2D_GRS as the instrumental variable (IV) to quantify the causal effect of T2D on decreased eGFR and increased uACR. Results Each 1-standard deviation (SD, 3.90 points) increment in T2D_GRS was associated with decreased eGFR: odds ratio (OR) = 1.18 (95% confidence interval [CI]: 1.01, 1.30). In the MR analysis, we demonstrated a causal relationship between genetically determined T2D and decreased eGFR (OR = 1.47, 95% CI: 1.15, 1.88, P = 0.0003). When grouping the genetic loci according to their relations with either insulin secretion (IS) or insulin resistance (IR), we found both IS_GRS and IR_GRS were significantly related to decreased eGFR (both P < 0.02). In addition, T2D_GRS and IS_GRS were significantly associated with Log-uACR (both P = 0.04). Conclusion Our results provide novel evidence for a causal association between T2D and decreased eGFR by using MR approach in a Chinese population. PMID:27211558

  15. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types

    SciTech Connect

    Doherty, Kimberly R. Talbert, Dominique R.; Trusk, Patricia B.; Moran, Diarmuid M.; Shell, Scott A.; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability. - Highlights: • 24 drugs were tested for cardiac liability using an in vitro multi-parameter screen. • Changes in beating activity were the most sensitive in predicting cardiac risk. • Structural effects add in

  16. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types.

    PubMed

    Doherty, Kimberly R; Talbert, Dominique R; Trusk, Patricia B; Moran, Diarmuid M; Shell, Scott A; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability.

  17. DUF1220 copy number is linearly associated with increased cognitive function as measured by total IQ and mathematical aptitude scores.

    PubMed

    Davis, Jonathon M; Searles, Veronica B; Anderson, Nathan; Keeney, Jonathon; Raznahan, Armin; Horwood, L John; Fergusson, David M; Kennedy, Martin A; Giedd, Jay; Sikela, James M

    2015-01-01

    DUF1220 protein domains exhibit the greatest human lineage-specific copy number expansion of any protein-coding sequence in the genome, and variation in DUF1220 copy number has been linked to both brain size in humans and brain evolution among primates. Given these findings, we examined associations between DUF1220 subtypes CON1 and CON2 and cognitive aptitude. We identified a linear association between CON2 copy number and cognitive function in two independent populations of European descent. In North American males, an increase in CON2 copy number corresponded with an increase in WISC IQ (R (2) = 0.13, p = 0.02), which may be driven by males aged 6-11 (R (2) = 0.42, p = 0.003). We utilized ddPCR in a subset as a confirmatory measurement. This group had 26-33 copies of CON2 with a mean of 29, and each copy increase of CON2 was associated with a 3.3-point increase in WISC IQ (R (2) = 0.22, p = 0.045). In individuals from New Zealand, an increase in CON2 copy number was associated with an increase in math aptitude ability (R (2) = 0.10 p = 0.018). These were not confounded by brain size. To our knowledge, this is the first study to report a replicated association between copy number of a gene coding sequence and cognitive aptitude. Remarkably, dosage variations involving DUF1220 sequences have now been linked to human brain expansion, autism severity and cognitive aptitude, suggesting that such processes may be genetically and mechanistically inter-related. The findings presented here warrant expanded investigations in larger, well-characterized cohorts.

  18. DUF1220 copy number is linearly associated with increased cognitive function as measured by total IQ and mathematical aptitude scores.

    PubMed

    Davis, Jonathon M; Searles, Veronica B; Anderson, Nathan; Keeney, Jonathon; Raznahan, Armin; Horwood, L John; Fergusson, David M; Kennedy, Martin A; Giedd, Jay; Sikela, James M

    2015-01-01

    DUF1220 protein domains exhibit the greatest human lineage-specific copy number expansion of any protein-coding sequence in the genome, and variation in DUF1220 copy number has been linked to both brain size in humans and brain evolution among primates. Given these findings, we examined associations between DUF1220 subtypes CON1 and CON2 and cognitive aptitude. We identified a linear association between CON2 copy number and cognitive function in two independent populations of European descent. In North American males, an increase in CON2 copy number corresponded with an increase in WISC IQ (R (2) = 0.13, p = 0.02), which may be driven by males aged 6-11 (R (2) = 0.42, p = 0.003). We utilized ddPCR in a subset as a confirmatory measurement. This group had 26-33 copies of CON2 with a mean of 29, and each copy increase of CON2 was associated with a 3.3-point increase in WISC IQ (R (2) = 0.22, p = 0.045). In individuals from New Zealand, an increase in CON2 copy number was associated with an increase in math aptitude ability (R (2) = 0.10 p = 0.018). These were not confounded by brain size. To our knowledge, this is the first study to report a replicated association between copy number of a gene coding sequence and cognitive aptitude. Remarkably, dosage variations involving DUF1220 sequences have now been linked to human brain expansion, autism severity and cognitive aptitude, suggesting that such processes may be genetically and mechanistically inter-related. The findings presented here warrant expanded investigations in larger, well-characterized cohorts. PMID:25287832

  19. Comparison of scores on the Checklist for Autism Spectrum Disorder, Childhood Autism Rating Scale, and Gilliam Asperger's Disorder Scale for children with low functioning autism, high functioning autism, Asperger's disorder, ADHD, and typical development.

    PubMed

    Mayes, Susan Dickerson; Calhoun, Susan L; Murray, Michael J; Morrow, Jill D; Yurich, Kirsten K L; Mahr, Fauzia; Cothren, Shiyoko; Purichia, Heather; Bouder, James N; Petersen, Christopher

    2009-12-01

    Reliability and validity for three autism instruments were compared for 190 children with low functioning autism (LFA), 190 children with high functioning autism or Asperger's disorder (HFA), 76 children with attention deficit hyperactivity disorder (ADHD), and 64 typical children. The instruments were the Checklist for Autism Spectrum Disorder (designed for children with LFA and HFA), Childhood Autism Rating Scale (CARS) for children with LFA, and Gilliam Asperger's Disorder Scale (GADS). For children with LFA or ADHD, classification accuracy was 100% for the Checklist and 98% for the CARS clinician scores. For children with HFA or ADHD, classification accuracy was 99% for the Checklist and 93% for the GADS clinician scores. Clinician-parent diagnostic agreement was high (90% Checklist, 90% CARS, and 84% GADS).

  20. Cross-cultural adaptation and validation of the Turkish version of the Hip disability and Osteoarthritis Outcome Score-Physical function Short-form (HOOS-PS).

    PubMed

    Yilmaz, Ozlem; Gul, Ebru Demir; Bodur, Hatice

    2014-01-01

    The purpose of this study is to adapt the Hip disability and Osteoarthritis Outcome Score-Physical function Short-form (HOOS-PS) to Turkish language and to evaluate the psychometric properties of the Turkish version in patients with primary hip osteoarthritis. After the translation from the source language (English) to the target language (Turkish), synthesis, back translation, revision, and pretest stages were done. Next, 50 patients with primary hip osteoarthritis were asked to fill out the Turkish version of the HOOS-PS two times with one week interval. Internal consistency was tested using the Cronbach's alpha coefficient, and test-retest reliability was assessed by calculating the intra-class correlation coefficient (ICC). Construct validity was investigated by comparing the results of the HOOS-PS and WOMAC, Lequesne questionnaries using Spearman's rank correlation coefficient. Internal consistency was good with a Cronbach's alpha of 0.778 (>0.7) and ICC was 0.911 (>0.7). Both scores verify that the Turkish HOOS-PS is a reliable tool. Spearman's rank correlation coefficients between the HOOS-PS and overall WOMAC (r = 0.653), WOMAC physical functions (r = 0.626), WOMAC pain (r = 0.629) subscales, overall Lequesne (r = 0.650), and Lequesne daily living activities (r = 0.620) subscales were high (r > 0.6), and moderate correlations were found between the HOOS-PS and WOMAC stiffness (r = 0.511), Lequesne pain (r = 0.569), and Lequesne-walking distance (r = 0.578) subscales (0.6 > r > 0.2), thus providing proof for the validity of the Turkish form. The Turkish HOOS-PS was found to be reliable and valid for patients with primary hip osteoarthritis. PMID:24026527

  1. An update on pediatric bleeding disorders: bleeding scores, benign joint hypermobility, and platelet function testing in the evaluation of the child with bleeding symptoms.

    PubMed

    O'Brien, Sarah H

    2012-05-01

    Evaluating a child with symptoms of easy bruising and/or bleeding remains a challenge in pediatric hematology, and there is no "one size fits all" approach. This review focuses on recent research in three elements of the evaluation of a child with a suspected bleeding disorder. We will first discuss the development of the standardized Pediatric Bleeding Questionnaire, and its applications in research and clinical settings. We will then discuss the relationship between benign hypermobility syndromes and hemostasis, and the importance of including a Beighton Score in the physical examination of any child presenting with unusual bruising or bleeding. While prolonged bleeding times and abnormal platelet aggregation are common findings in children with benign hypermobility, normal coagulation studies do not exclude the presence of a connective tissue disorder in a child presenting with easy bleeding and joint hypermobility on examination. Finally, we will discuss the current state of knowledge regarding the laboratory evaluation of platelet function in children. Platelet function disorders are among the most common inherited bleeding disorders. However, testing for such disorders is time-consuming and requires a step-wise approach. We will review the indications for and limitations of the most commonly utilized platelet function laboratory studies.

  2. Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains.

    PubMed

    Ishikawa, Fumihiro; Miyamoto, Kengo; Konno, Sho; Kasai, Shota; Kakeya, Hideaki

    2015-12-18

    A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique

  3. Cocoa flavanol intake improves endothelial function and Framingham Risk Score in healthy men and women: a randomised, controlled, double-masked trial: the Flaviola Health Study.

    PubMed

    Sansone, Roberto; Rodriguez-Mateos, Ana; Heuel, Jan; Falk, David; Schuler, Dominik; Wagstaff, Rabea; Kuhnle, Gunter G C; Spencer, Jeremy P E; Schroeter, Hagen; Merx, Marc W; Kelm, Malte; Heiss, Christian

    2015-10-28

    Cocoa flavanol (CF) intake improves endothelial function in patients with cardiovascular risk factors and disease. We investigated the effects of CF on surrogate markers of cardiovascular health in low risk, healthy, middle-aged individuals without history, signs or symptoms of CVD. In a 1-month, open-label, one-armed pilot study, bi-daily ingestion of 450 mg of CF led to a time-dependent increase in endothelial function (measured as flow-mediated vasodilation (FMD)) that plateaued after 2 weeks. Subsequently, in a randomised, controlled, double-masked, parallel-group dietary intervention trial (Clinicaltrials.gov: NCT01799005), 100 healthy, middle-aged (35-60 years) men and women consumed either the CF-containing drink (450 mg) or a nutrient-matched CF-free control bi-daily for 1 month. The primary end point was FMD. Secondary end points included plasma lipids and blood pressure, thus enabling the calculation of Framingham Risk Scores and pulse wave velocity. At 1 month, CF increased FMD over control by 1·2 % (95 % CI 1·0, 1·4 %). CF decreased systolic and diastolic blood pressure by 4·4 mmHg (95 % CI 7·9, 0·9 mmHg) and 3·9 mmHg (95 % CI 6·7, 0·9 mmHg), pulse wave velocity by 0·4 m/s (95 % CI 0·8, 0·04 m/s), total cholesterol by 0·20 mmol/l (95 % CI 0·39, 0·01 mmol/l) and LDL-cholesterol by 0·17 mmol/l (95 % CI 0·32, 0·02 mmol/l), whereas HDL-cholesterol increased by 0·10 mmol/l (95 % CI 0·04, 0·17 mmol/l). By applying the Framingham Risk Score, CF predicted a significant lowering of 10-year risk for CHD, myocardial infarction, CVD, death from CHD and CVD. In healthy individuals, regular CF intake improved accredited cardiovascular surrogates of cardiovascular risk, demonstrating that dietary flavanols have the potential to maintain cardiovascular health even in low-risk subjects.

  4. Cocoa flavanol intake improves endothelial function and Framingham Risk Score in healthy men and women: a randomised, controlled, double-masked trial: the Flaviola Health Study.

    PubMed

    Sansone, Roberto; Rodriguez-Mateos, Ana; Heuel, Jan; Falk, David; Schuler, Dominik; Wagstaff, Rabea; Kuhnle, Gunter G C; Spencer, Jeremy P E; Schroeter, Hagen; Merx, Marc W; Kelm, Malte; Heiss, Christian

    2015-10-28

    Cocoa flavanol (CF) intake improves endothelial function in patients with cardiovascular risk factors and disease. We investigated the effects of CF on surrogate markers of cardiovascular health in low risk, healthy, middle-aged individuals without history, signs or symptoms of CVD. In a 1-month, open-label, one-armed pilot study, bi-daily ingestion of 450 mg of CF led to a time-dependent increase in endothelial function (measured as flow-mediated vasodilation (FMD)) that plateaued after 2 weeks. Subsequently, in a randomised, controlled, double-masked, parallel-group dietary intervention trial (Clinicaltrials.gov: NCT01799005), 100 healthy, middle-aged (35-60 years) men and women consumed either the CF-containing drink (450 mg) or a nutrient-matched CF-free control bi-daily for 1 month. The primary end point was FMD. Secondary end points included plasma lipids and blood pressure, thus enabling the calculation of Framingham Risk Scores and pulse wave velocity. At 1 month, CF increased FMD over control by 1·2 % (95 % CI 1·0, 1·4 %). CF decreased systolic and diastolic blood pressure by 4·4 mmHg (95 % CI 7·9, 0·9 mmHg) and 3·9 mmHg (95 % CI 6·7, 0·9 mmHg), pulse wave velocity by 0·4 m/s (95 % CI 0·8, 0·04 m/s), total cholesterol by 0·20 mmol/l (95 % CI 0·39, 0·01 mmol/l) and LDL-cholesterol by 0·17 mmol/l (95 % CI 0·32, 0·02 mmol/l), whereas HDL-cholesterol increased by 0·10 mmol/l (95 % CI 0·04, 0·17 mmol/l). By applying the Framingham Risk Score, CF predicted a significant lowering of 10-year risk for CHD, myocardial infarction, CVD, death from CHD and CVD. In healthy individuals, regular CF intake improved accredited cardiovascular surrogates of cardiovascular risk, demonstrating that dietary flavanols have the potential to maintain cardiovascular health even in low-risk subjects. PMID:26348767

  5. Accurate Prediction of Hyperfine Coupling Constants in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method.

    PubMed

    Yamada, Kenta; Kawashima, Yukio; Tachikawa, Masanori

    2014-05-13

    We performed ab initio path integral molecular dynamics (PIMD) simulations with a density functional theory (DFT) method to accurately predict hyperfine coupling constants (HFCCs) in the ethyl radical (CβH3-CαH2) and its Mu-substituted (muoniated) compound (CβH2Mu-CαH2). The substitution of a Mu atom, an ultralight isotope of the H atom, with larger nuclear quantum effect is expected to strongly affect the nature of the ethyl radical. The static conventional DFT calculations of CβH3-CαH2 find that the elongation of one Cβ-H bond causes a change in the shape of potential energy curve along the rotational angle via the imbalance of attractive and repulsive interactions between the methyl and methylene groups. Investigation of the methyl-group behavior including the nuclear quantum and thermal effects shows that an unbalanced CβH2Mu group with the elongated Cβ-Mu bond rotates around the Cβ-Cα bond in a muoniated ethyl radical, quite differently from the CβH3 group with the three equivalent Cβ-H bonds in the ethyl radical. These rotations couple with other molecular motions such as the methylene-group rocking motion (inversion), leading to difficulties in reproducing the corresponding barrier heights. Our PIMD simulations successfully predict the barrier heights to be close to the experimental values and provide a significant improvement in muon and proton HFCCs given by the static conventional DFT method. Further investigation reveals that the Cβ-Mu/H stretching motion, methyl-group rotation, methylene-group rocking motion, and HFCC values deeply intertwine with each other. Because these motions are different between the radicals, a proper description of the structural fluctuations reflecting the nuclear quantum and thermal effects is vital to evaluate HFCC values in theory to be comparable to the experimental ones. Accordingly, a fundamental difference in HFCC between the radicals arises from their intrinsic molecular motions at a finite temperature, in

  6. Methods for accurate homology modeling by global optimization.

    PubMed

    Joo, Keehyoung; Lee, Jinwoo; Lee, Jooyoung

    2012-01-01

    High accuracy protein modeling from its sequence information is an important step toward revealing the sequence-structure-function relationship of proteins and nowadays it becomes increasingly more useful for practical purposes such as in drug discovery and in protein design. We have developed a protocol for protein structure prediction that can generate highly accurate protein models in terms of backbone structure, side-chain orientation, hydrogen bonding, and binding sites of ligands. To obtain accurate protein models, we have combined a powerful global optimization method with traditional homology modeling procedures such as multiple sequence alignment, chain building, and side-chain remodeling. We have built a series of specific score functions for these steps, and optimized them by utilizing conformational space annealing, which is one of the most successful combinatorial optimization algorithms currently available.

  7. An Equipercentile Version of the Levine Linear Observed-Score Equating Function Using the Methods of Kernel Equating. Research Report. ETS RR-07-14

    ERIC Educational Resources Information Center

    von Davier, Alina A.; Fournier-Zajac, Stephanie; Holland, Paul W.

    2007-01-01

    In the nonequivalent groups with anchor test (NEAT) design, there are several ways to use the information provided by the anchor in the equating process. One of the NEAT-design equating methods is the linear observed-score Levine method (Kolen & Brennan, 2004). It is based on a classical test theory model of the true scores on the test forms…

  8. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  9. Effect of a community intervention programme promoting social interactions on functional disability prevention for older adults: propensity score matching and instrumental variable analyses, JAGES Taketoyo study

    PubMed Central

    Hikichi, Hiroyuki; Kondo, Naoki; Kondo, Katsunori; Aida, Jun; Takeda, Tokunori; Kawachi, Ichiro

    2015-01-01

    Background The efficacy of promoting social interactions to improve the health of older adults is not fully established due to residual confounding and selection bias. Methods The government of Taketoyo town, Aichi Prefecture, Japan, developed a resident-centred community intervention programme called ‘community salons’, providing opportunities for social interactions among local older residents. To evaluate the impact of the programme, we conducted questionnaire surveys for all older residents of Taketoyo. We carried out a baseline survey in July 2006 (prior to the introduction of the programme) and assessed the onset of functional disability during March 2012. We analysed the data of 2421 older people. In addition to the standard Cox proportional hazard regression, we conducted Cox regression with propensity score matching (PSM) and an instrumental variable (IV) analysis, using the number of community salons within a radius of 350 m from the participant's home as an instrument. Results In the 5 years after the first salon was launched, the salon participants showed a 6.3% lower incidence of functional disability compared with non-participants. Even adjusting for sex, age, equivalent income, educational attainment, higher level activities of daily living and depression, the Cox adjusted HR for becoming disabled was 0.49 (95% CI 0.33 to 0.72). Similar results were observed using PSM (HR 0.52, 95% CI 0.33 to 0.83) and IV-Cox analysis (HR 0.50, 95% CI 0.34 to 0.74). Conclusions A community health promotion programme focused on increasing social interactions among older adults may be effective in preventing the onset of disability. PMID:25888596

  10. In early returns scoring scores big.

    PubMed

    Butman, Samuel M

    2016-07-01

    A scoring or cutting balloon is always useful in preventing slippage during therapy of in-stent restenosis. A drug-coated scoring balloon for in-stent restenosis may be an alternative to a drug-coated balloon Definitive comparison trials are needed and likely to help define their exact role in patients with in-stent restenosis. PMID:27400636

  11. EVALUATION OF ANATOMICAL INTEGRITY USING ULTRASOUND EXAMINATION, AND FUNCTIONAL INTEGRITY USING THE CONSTANT & MURLEY SCORE, OF THE ROTATOR CUFF FOLLOWING ARTHROSCOPIC REPAIR

    PubMed Central

    Godinho, Glaydson Gomes; França, Flavio de Oliveira; Alves, Freitas José Marcio; Watanabe, Fábio Nagato; Nobre, Leonardo Oliveira; De Almeida Neto, Manoel Augusto; Mendes Da Silva, Marcos André

    2015-01-01

    Objective: To evaluate the functional and anatomical results from surgical treatment via arthroscopy in cases of complete rupture of the rotator cuff, using ultrasound images and the Constant and Murley functional index to investigate the correlation between them. Methods: 100 patients (110 shoulders) were evaluated. The mean follow-up was 48.8 ± 33.28 months (12 to 141 months). The mean age was 60.25 ± 10.09 (36 to 81 years). Rupture of the supraspinal tendon alone occurred in 85 cases (77%), and in association with the infraspinatus in 20 cases (18%) and subscapularis in four shoulders (4%). An association of supraspinatus, infraspinatus and subscapularis lesions was found in one shoulder (1%). The lesions were classified according to DeOrio and Cofield scores as small/medium in 85 shoulders (77%) and large/extensive in 25 (23%). The clinical results were assessed in accordance with the Constant and Murley criteria. The ultrasound results relate to reports issued by different radiologists. Statistical analysis was carried out using the chi-square test, Fisher's exact test, Student's t test, Pearson's correlation, Kruskal-Wallis correlation and logistic regression (significance: p < 0.05). Results: The mean Constant evaluation was 85.3 ± 10.06 in the normal shoulders and 83.96 ± 8.67 in the operated shoulders (p = 0.224). Excellent and good results were found in 74 shoulders (67%), satisfactory and moderate results in 32 (29%) and poor results in four (4%). The ultrasound evaluation showed 38 shoulders with re-rupture (35%) and absence of rupture in 71 (65%). Among the 74 shoulders (67%) with excellent/good results, 22 (30%) presented re-rupture in the ultrasound report (p = 0.294). Among the four shoulders (4%) with poor results, two (50%) presented reports of intact tendons (p = 0.294). Conclusion: There was no statistically valid correlation between the ultrasound diagnosis and the clinical evaluation of results among the patients who underwent arthroscopic

  12. The lung function score and its components as predictors of overall survival and chronic graft-vs-host disease after allogeneic stem cell transplantation

    PubMed Central

    Ditz, Diana; Rabanus, Robert; Schulz, Christian; Wolff, Daniel; Holler, Barbara; Holler, Ernst; Hildebrandt, Gerhard Carl

    2016-01-01

    Aim To retrospectively assess if the modified lung function score (LFS) and/or its components, forced expiratory volume within the first second (FEV1) and diffusion capacity for carbon monoxide corrected for hemoglobin level (cDLCO), predict overall survival (OS) and chronic graft-vs-host-disease (cGvHD). Methods We evaluated 241 patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT) at the University of Regensburg Transplant Center between June 1998 and July 2005 in relation to their LFS, FEV1 and cDLCO, before and after HSCT. Results Decreased OS after allo-HSCT was related to decreased pre-transplantation values of FEV1<60% (P = 0.040), cDLCO<50% of predicted value (P = 0.025), and LFS≥III (P = 0.037). It was also related to decreased FEV1 at 3 and 12 months after HSCT (P < 0.001 and P = 0.001, respectively) and increased LFS at 3 and 12 months after HSCT (P = 0.028 and P = 0.002, respectively), but not to changes of cDLCO. A higher incidence of cGvHD was related to decreased FEV1 at 6, 12, and 18 months (P = 0.069, P = 0.054, and P = 0.009, respectively) and increased LFS at 12 months (P = 0.002), but not to changes in cDLCO. Conclusions OS was related to both LFS and FEV1, but cGvHD had a stronger relation to FEV1 than to cDLCO or LFS. FEV1 alone offered more information on the outcome after allo-HSCT than LFS or cDLCO, suggesting limited value of LFS for the patients’ assessment after allo-HSCT. PMID:26935611

  13. Genetic Interaction Scoring Procedure for Bacterial Species.

    PubMed

    Wagih, Omar; Parts, Leopold

    2015-01-01

    A genetic interaction occurs when the phenotype of an organism carrying two mutant genes differs from what should have been observed given their independent influence. Such unexpected outcome indicates a mechanistic connection between the perturbed genes, providing a key source of functional information about the cell. Large-scale screening for genetic interactions involves measuring phenotypes of single and double mutants, which for microorganisms is usually done by automated analysis of images of ordered colonies. Obtaining accurate colony sizes, and using them to identify genetic interactions from such screens remains a challenging and time-consuming task. Here, we outline steps to compute genetic interaction scores in E. coli by measuring colony sizes from plate images, performing normalisation, and quantifying the strength of the effect. PMID:26621468

  14. Ligand Identification Scoring Algorithm (LISA)

    PubMed Central

    Zheng, Zheng; Merz, Kenneth M.

    2011-01-01

    A central problem in de novo drug design is determining the binding affinity of a ligand with a receptor. A new scoring algorithm is presented that estimates the binding affinity of a protein-ligand complex given a three-dimensional structure. The method, LISA (Ligand Identification Scoring Algorithm), uses an empirical scoring function to describe the binding free energy. Interaction terms have been designed to account for van der Waals (VDW) contacts, hydrogen bonding, desolvation effects and metal chelation to model the dissociation equilibrium constants using a linear model. Atom types have been introduced to differentiate the parameters for VDW, H-bonding interactions and metal chelation between different atom pairs. A training set of 492 protein-ligand complexes was selected for the fitting process. Different test sets have been examined to evaluate its ability to predict experimentally measured binding affinities. By comparing with other well known scoring functions, the results show that LISA has advantages over many existing scoring functions in simulating protein-ligand binding affinity, especially metalloprotein-ligand binding affinity. Artificial Neural Network (ANN) was also used in order to demonstrate that the energy terms in LISA are well designed and do not require extra cross terms. PMID:21561101

  15. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods.

    PubMed

    Kapil, V; VandeVondele, J; Ceriotti, M

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  16. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    NASA Astrophysics Data System (ADS)

    Kapil, V.; VandeVondele, J.; Ceriotti, M.

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  17. The Apgar Score.

    PubMed

    2015-10-01

    The Apgar score provides an accepted and convenient method for reporting the status of the newborn infant immediately after birth and the response to resuscitation if needed. The Apgar score alone cannot be considered as evidence of, or a consequence of, asphyxia; does not predict individual neonatal mortality or neurologic outcome; and should not be used for that purpose. An Apgar score assigned during resuscitation is not equivalent to a score assigned to a spontaneously breathing infant. The American Academy of Pediatrics and the American College of Obstetricians and Gynecologists encourage use of an expanded Apgar score reporting form that accounts for concurrent resuscitative interventions.

  18. The Reliability and Precision of Total Scores and IRT Estimates as a Function of Polytomous IRT Parameters and Latent Trait Distribution

    ERIC Educational Resources Information Center

    Culpepper, Steven Andrew

    2013-01-01

    A classic topic in the fields of psychometrics and measurement has been the impact of the number of scale categories on test score reliability. This study builds on previous research by further articulating the relationship between item response theory (IRT) and classical test theory (CTT). Equations are presented for comparing the reliability and…

  19. Validity of the General Conceptual Ability Score from the Differential Ability Scales as a Function of Significant and Rare Interfactor Variability

    ERIC Educational Resources Information Center

    Kotz, Kasey M.; Watkins, Marley W.; McDermott, Paul A.

    2008-01-01

    Some researchers have argued that discrepant broad index scores invalidate IQs, but others have questioned the fundamental logic of that argument. To resolve this debate, the present study used a nationally representative sample of children (N = 1,200) who were matched individually for IQ. Children with significantly uneven broad index score…

  20. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2016-09-13

    The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.

  1. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2016-09-13

    The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses. PMID:27537680

  2. Overestimation Bias in Self-Reported SAT Scores

    ERIC Educational Resources Information Center

    Mayer, Richard E.; Stull, Andrew T.; Campbell, Julie; Almeroth, Kevin; Bimber, Bruce; Chun, Dorothy; Knight, Allan

    2007-01-01

    The authors analyzed self-reported SAT scores and actual SAT scores for five different samples of college students (N = 650). Students overestimated their actual SAT scores by an average of 25 points (SD = 81, d = 0.31), with 10% under-reporting, 51% reporting accurately, and 39% over-reporting, indicating a systematic bias towards over-reporting.…

  3. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.

  4. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol. PMID:19603962

  5. An Outcome Measure of Functionality and Pain in Patients with Low Back Disorder: A Validation Study of the Iranian version of Low Back Outcome Score

    PubMed Central

    Nayeb Aghaei, Hossein; Azhari, Shirzad; Shazadi, Sohrab; Khayat Kashany, Hamid; Mohammadi, Hassan Reza; Montazeri, Ali

    2016-01-01

    Study Design Cross-sectional study. Purpose This study aimed to cross-culturally translate and validate the low back outcome score (LBOS) in Iran. Overview of Literature Lumbar disc hernia (LDH) is the most common diagnoses of low back pain and imposes a heavy burden on both individual and society. Instruments measuring patient reported outcomes should satisfy cetain psychometric properties. Methods The translation and cross-cultural adaptation of the original questionnaire was performed using Beaton's guideline. A total of 163 patients with LDH were asked to respond to the questionnaire at three points in time: preoperative and twice within 1-week interval after surgery assessments. The Oswestry disabilty index (ODI) was also completed. The internal consistency, test-retest, convergent validity, and responsiveness to change were assessed. Responsiveness to change also was assessed comparing patients' pre- and postoperative scores. Results The mean age of the cohort was 49.8 years (standard deviation=10.1). The Cronbach's alpha coefficients for the LBOS at preoperative and postoperative assessments ranged from 0.77 to 0.79, indicating good internal consistency. Test-retest reliability as performed by intraclass correlation coefficient was found to be 0.82 (0.62–0.91). The instrument discriminated well between sub-groups of patients who differed in the Finneson-Cooper score. The ODI correlated strongly with the LBOS score, lending support to its good convergent validity (r=––0.83; p<0.001). Further analysis also indicated that the questionnaire was responsive to change (p<0.001). Conclusions The Iranian version of LBOS performed well and the findings suggest that it is a valid measure of back pain treatment evaluation among LDH patients. PMID:27559453

  6. Recursive Partitioning to Identify Potential Causes of Differential Item Functioning in Cross-National Data

    ERIC Educational Resources Information Center

    Finch, W. Holmes; Hernández Finch, Maria E.; French, Brian F.

    2016-01-01

    Differential item functioning (DIF) assessment is key in score validation. When DIF is present scores may not accurately reflect the construct of interest for some groups of examinees, leading to incorrect conclusions from the scores. Given rising immigration, and the increased reliance of educational policymakers on cross-national assessments…

  7. Stability of emotionality scores.

    PubMed

    Campos, A; Sueiro, E

    1991-12-01

    We hypothesized the stability of scores on emotionality given by 111 young adults, whose mean age was 16.6 yr, 132 adults, whose mean age was 29.9 yr., and 48 older adults, whose mean age was 53.3 yr. Significant correlations were obtained between scores given to 210 words across age and sex groups. Pearson correlations were calculated over words and not over subjects. The correlations between scores of young people and adults were .90, between young and older people .80, and between adults and older people .87. Men's and women's scores correlated .89.

  8. Metabolic changes assessed by MRS accurately reflect brain function during drug-induced epilepsy in mice in contrast to fMRI-based hemodynamic readouts.

    PubMed

    Seuwen, Aline; Schroeter, Aileen; Grandjean, Joanes; Rudin, Markus

    2015-10-15

    Functional proton magnetic resonance spectroscopy (1H-MRS) enables the non-invasive assessment of neural activity by measuring signals arising from endogenous metabolites in a time resolved manner. Proof-of-principle of this approach has been demonstrated in humans and rats; yet functional 1H-MRS has not been applied in mice so far, although it would be of considerable interest given the many genetically engineered models of neurological disorders established in this species only. Mouse 1H-MRS is challenging as the high demands on spatial resolution typically result in long data acquisition times not commensurable with functional studies. Here, we propose an approach based on spectroscopic imaging in combination with the acquisition of the free induction decay to maximize signal intensity. Highly resolved metabolite maps have been recorded from mouse brain with 12 min temporal resolution. This enabled monitoring of metabolic changes following the administration of bicuculline, a GABA-A receptor antagonist. Changes in levels of metabolites involved in energy metabolism (lactate and phosphocreatine) and neurotransmitters (glutamate) were investigated in a region-dependent manner and shown to scale with the bicuculline dose. GABAergic inhibition induced spectral changes characteristic for increased neurotransmitter turnover and oxidative stress. In contrast to metabolic readouts, BOLD and CBV fMRI responses did not scale with the bicuculline dose indicative of the failure of neurovascular coupling. Nevertheless fMRI measurements supported the notion of increased oxidative stress revealed by functional MRS. Hence, the combined analysis of metabolic and hemodynamic changes in response to stimulation provides complementary insight into processes associated with neural activity.

  9. Metabolic changes assessed by MRS accurately reflect brain function during drug-induced epilepsy in mice in contrast to fMRI-based hemodynamic readouts.

    PubMed

    Seuwen, Aline; Schroeter, Aileen; Grandjean, Joanes; Rudin, Markus

    2015-10-15

    Functional proton magnetic resonance spectroscopy (1H-MRS) enables the non-invasive assessment of neural activity by measuring signals arising from endogenous metabolites in a time resolved manner. Proof-of-principle of this approach has been demonstrated in humans and rats; yet functional 1H-MRS has not been applied in mice so far, although it would be of considerable interest given the many genetically engineered models of neurological disorders established in this species only. Mouse 1H-MRS is challenging as the high demands on spatial resolution typically result in long data acquisition times not commensurable with functional studies. Here, we propose an approach based on spectroscopic imaging in combination with the acquisition of the free induction decay to maximize signal intensity. Highly resolved metabolite maps have been recorded from mouse brain with 12 min temporal resolution. This enabled monitoring of metabolic changes following the administration of bicuculline, a GABA-A receptor antagonist. Changes in levels of metabolites involved in energy metabolism (lactate and phosphocreatine) and neurotransmitters (glutamate) were investigated in a region-dependent manner and shown to scale with the bicuculline dose. GABAergic inhibition induced spectral changes characteristic for increased neurotransmitter turnover and oxidative stress. In contrast to metabolic readouts, BOLD and CBV fMRI responses did not scale with the bicuculline dose indicative of the failure of neurovascular coupling. Nevertheless fMRI measurements supported the notion of increased oxidative stress revealed by functional MRS. Hence, the combined analysis of metabolic and hemodynamic changes in response to stimulation provides complementary insight into processes associated with neural activity. PMID:26166624

  10. Cut Scores: Results May Vary. NBETPP Monographs, Volume 1, Number 1.

    ERIC Educational Resources Information Center

    Horn, Catherine; Ramos, Miguel; Blumer, Irwin; Madaus, George

    This paper discusses how cut scores are set and used and how accurately they reflect student achievement. Regardless of the method used, the cut-score setting process is subjective. The cut score is the point on a score scale that separates one performance standard from another. Cut scores may also be used to set performance levels for…

  11. SCORE - A DESCRIPTION.

    ERIC Educational Resources Information Center

    SLACK, CHARLES W.

    REINFORCEMENT AND ROLE-REVERSAL TECHNIQUES ARE USED IN THE SCORE PROJECT, A LOW-COST PROGRAM OF DELINQUENCY PREVENTION FOR HARD-CORE TEENAGE STREET CORNER BOYS. COMMITTED TO THE BELIEF THAT THE BOYS HAVE THE POTENTIAL FOR ETHICAL BEHAVIOR, THE SCORE WORKER FOLLOWS B.F. SKINNER'S THEORY OF OPERANT CONDITIONING AND REINFORCES THE DELINQUENT'S GOOD…

  12. Home Energy Score

    SciTech Connect

    2011-12-16

    The Home Energy Score allows a homeowner to compare her or his home's energy consumption to that of other homes, similar to a vehicle's mile-per-gallon rating. A home energy assessor will collect energy information during a brief home walk-through and then score that home on a scale of 1 to 10.

  13. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  14. Density functional computational thermochemistry: Accurate determination of the enthalpy of formation of perfluoropropane from DFT and ab initio calculations on isodesmic reactions

    NASA Astrophysics Data System (ADS)

    Ventura, Oscar N.; Segovia, Marc

    2005-02-01

    The experimental enthalpy of formation of perfluoropropane (C 3F 8), reported originally as -1729 kJ/mol and latter corrected to -1784.7 kJ/mol, is reexamined at the light of density functional and model chemistry (G3, CBS-4, CBS-Q) calculations of several isodesmic reactions relating C 3F 8 to smaller fluoroalkanes. The average enthalpy of formation of C 3F 8 obtained from all reactions studied was -1739 ± 12 kJ/mol at the DFT level and -1748 ± 12 kJ/mol at the ab initio level, thus ruling out the larger experimental value. A value of -1732 ± 5 kJ/mol is recommended from careful analysis of the theoretical results.

  15. Refining similarity scoring to enable decoy-free validation in spectral library searching.

    PubMed

    Shao, Wenguang; Zhu, Kan; Lam, Henry

    2013-11-01

    Spectral library searching is a maturing approach for peptide identification from MS/MS, offering an alternative to traditional sequence database searching. Spectral library searching relies on direct spectrum-to-spectrum matching between the query data and the spectral library, which affords better discrimination of true and false matches, leading to improved sensitivity. However, due to the inherent diversity of the peak location and intensity profiles of real spectra, the resulting similarity score distributions often take on unpredictable shapes. This makes it difficult to model the scores of the false matches accurately, necessitating the use of decoy searching to sample the score distribution of the false matches. Here, we refined the similarity scoring in spectral library searching to enable the validation of spectral search results without the use of decoys. We rank-transformed the peak intensities to standardize all spectra, making it possible to fit a parametric distribution to the scores of the nontop-scoring spectral matches. The statistical significance of the top-scoring match can then be estimated in a rigorous manner according to Extreme Value Theory. The overall result is a more robust and interpretable measure of the quality of the spectral match, which can be obtained without decoys. We tested this refined similarity scoring function on real datasets and demonstrated its effectiveness. This approach reduces search time, increases sensitivity, and extends spectral library searching to situations where decoy spectra cannot be readily generated, such as in searching unidentified and nonpeptide spectral libraries.

  16. Smoothing and Equating Methods Applied to Different Types of Test Score Distributions and Evaluated with Respect to Multiple Equating Criteria. Research Report. ETS RR-11-20

    ERIC Educational Resources Information Center

    Moses, Tim; Liu, Jinghua

    2011-01-01

    In equating research and practice, equating functions that are smooth are typically assumed to be more accurate than equating functions with irregularities. This assumption presumes that population test score distributions are relatively smooth. In this study, two examples were used to reconsider common beliefs about smoothing and equating. The…

  17. A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans

    PubMed Central

    Bigdeli, T. Bernard; Lee, Donghyung; Webb, Bradley Todd; Riley, Brien P.; Vladimirov, Vladimir I.; Fanous, Ayman H.; Kendler, Kenneth S.; Bacanu, Silviu-Alin

    2016-01-01

    Motivation: For genetic studies, statistically significant variants explain far less trait variance than ‘sub-threshold’ association signals. To dimension follow-up studies, researchers need to accurately estimate ‘true’ effect sizes at each SNP, e.g. the true mean of odds ratios (ORs)/regression coefficients (RRs) or Z-score noncentralities. Naïve estimates of effect sizes incur winner’s curse biases, which are reduced only by laborious winner’s curse adjustments (WCAs). Given that Z-scores estimates can be theoretically translated on other scales, we propose a simple method to compute WCA for Z-scores, i.e. their true means/noncentralities. Results:WCA of Z-scores shrinks these towards zero while, on P-value scale, multiple testing adjustment (MTA) shrinks P-values toward one, which corresponds to the zero Z-score value. Thus, WCA on Z-scores scale is a proxy for MTA on P-value scale. Therefore, to estimate Z-score noncentralities for all SNPs in genome scans, we propose FDR Inverse Quantile Transformation (FIQT). It (i) performs the simpler MTA of P-values using FDR and (ii) obtains noncentralities by back-transforming MTA P-values on Z-score scale. When compared to competitors, realistic simulations suggest that FIQT is more (i) accurate and (ii) computationally efficient by orders of magnitude. Practical application of FIQT to Psychiatric Genetic Consortium schizophrenia cohort predicts a non-trivial fraction of sub-threshold signals which become significant in much larger supersamples. Conclusions: FIQT is a simple, yet accurate, WCA method for Z-scores (and ORs/RRs, via simple transformations). Availability and Implementation: A 10 lines R function implementation is available at https://github.com/bacanusa/FIQT. Contact: sabacanu@vcu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27187203

  18. VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing

    PubMed Central

    Medina, Ignacio; De Maria, Alejandro; Bleda, Marta; Salavert, Francisco; Alonso, Roberto; Gonzalez, Cristina Y.; Dopazo, Joaquin

    2012-01-01

    The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at: http://variant.bioinfo.cipf.es. PMID:22693211

  19. Reporting Valid and Reliable Overall Scores and Domain Scores

    ERIC Educational Resources Information Center

    Yao, Lihua

    2010-01-01

    In educational assessment, overall scores obtained by simply averaging a number of domain scores are sometimes reported. However, simply averaging the domain scores ignores the fact that different domains have different score points, that scores from those domains are related, and that at different score points the relationship between overall…

  20. Accurate identification of the frequency response functions for the rotor-bearing-foundation system using the modified pseudo mode shape method

    NASA Astrophysics Data System (ADS)

    Chen, Yeong-Shu; Cheng, Ye-Dar; Yang, Tachung; Koai, Kwang-Lu

    2010-03-01

    In this paper, an identification technique in the dynamic analyses of rotor-bearing-foundation systems called the pseudo mode shape method (PMSM) was improved in order to enhance the accuracy of the identified dynamic characteristic matrices of its foundation models. Two procedures, namely, phase modification and numerical optimisation, were proposed in the algorithm of PMSM to effectively improve its accuracy. Generally, it is always necessary to build the whole foundation model in studying the dynamics of a rotor system through the finite element analysis method. This is either unfeasible or impractical when the foundation is too complicated. Instead, the PMSM uses the frequency response function (FRF) data of joint positions between the rotor and the foundation to establish the equivalent mass, damping, and stiffness matrices of the foundation without having to build the physical model. However, the accuracy of the obtained system's FRF is still unsatisfactory, especially at those higher modes. In order to demonstrate the effectiveness of the presented methods, a solid foundation was solved for its FRF by using both the original and modified PMSM, as well as the finite element (ANSYS) model for comparisons. The results showed that the accuracy of the obtained FRF was improved remarkably with the modified PMSM based on the results of the ANSYS. In addition, an induction motor resembling a rotor-bearing-foundation system, with its housing treated as the foundation, was taken as an example to verify the algorithm experimentally. The FRF curves at the bearing supports of the rotor (armature) were obtained through modal testing to estimate the above-mentioned equivalent matrices of the housing. The FRF of the housing, which was calculated from the equivalent matrices with the modified PMSM, showed satisfactory consistency with that from the modal testing.

  1. Recalibration of the HAS-BLED Score: Should Hemorrhagic Stroke Account for One or Two Points?

    PubMed

    Nielsen, Peter Brønnum; Larsen, Torben Bjerregaard; Lip, Gregory Y H

    2016-02-01

    After a hemorrhagic stroke, it is uncertain whether this event scores one point (either for stroke or bleeding) or two points (one point each for stroke and bleeding) on the bleeding risk score termed HAS-BLED (hypertension, abnormal renal/liver function [one or two points], stroke, bleeding history or predisposition, labile international normalized ratio [INR], elderly [> 65 years], drugs/alcohol concomitantly [one or two points]). We investigated the value of a recalibration of the HAS-BLED score to account for two points from a hemorrhagic stroke. Data were analyzed from the Danish nationwide cohort of patients with incident atrial fibrillation (AF) from January 1999 to December 2013. The primary outcome in this observational study was major bleeding. The original and the recalibrated HAS-BLED scores were assessed, and the event rates of major bleeding were calculated. The predictive accuracy of major bleeding was compared by using C-statistics, the net reclassification index (NRI), and integrated discrimination improvement (IDI). An event rate for major bleeding of 4.3 per 100 person-years was recorded in the 210,299 patients with AF. The C-statistics for the two scores were modest: 0.613 (95% CI, 0.607-0.619) for the original score and 0.616 (95% CI, 0.610-0.622) for the recalibrated score. The NRI was 10.0% (95% CI, 7.6-12.4). The relative IDI was 23.6% (95% CI, 15.7-31.5), reflecting that the recalibrated HAS-BLED score more accurately predicted bleeding events. Recalibration of the "S" component in the HAS-BLED score (counting two points for a hemorrhagic stroke) resulted in an increase in the C-statistics, NRI, and IDI. This approach could potentially aid physicians in more accurate assessments of bleeding risk in patients with AF. PMID:26356508

  2. Psychometrics evaluation of Charcot-Marie-Tooth Neuropathy Score (CMTNSv2) second version, using Rasch analysis.

    PubMed

    Sadjadi, Reza; Reilly, Mary M; Shy, Michael E; Pareyson, Davide; Laura, Matilde; Murphy, Sinead; Feely, Shawna M E; Grider, Tiffany; Bacon, Chelsea; Piscosquito, Giuseppe; Calabrese, Daniela; Burns, Ted M

    2014-09-01

    Charcot-Marie-Tooth Neuropathy Score second version (CMTNSv2) is a validated clinical outcome measure developed for use in clinical trials to monitor disease impairment and progression in affected CMT patients. Currently, all items of CMTNSv2 have identical contribution to the total score. We used Rasch analysis to further explore psychometric properties of CMTNSv2, and in particular, category response functioning, and their weight on the overall disease progression. Weighted category responses represent a more accurate estimate of actual values measuring disease severity and therefore could potentially be used in improving the current version.

  3. Psychometrics evaluation of Charcot-Marie-Tooth Neuropathy Score (CMTNSv2) second version, using Rasch analysis

    PubMed Central

    Sadjadi, Reza; Reilly, Mary M.; Shy, Michael E.; Pareyson, Davide; Laura, Matilde; Murphy, Sinead; Feely, Shawna M.E.; Grider, Tiffany; Bacon, Chelsea; Piscosquito, Giuseppe; Calabrese, Daniela; Burns, Ted M.

    2015-01-01

    Charcot-Marie-Tooth Neuropathy Score second version (CMTNSv2) is a validated clinical outcome measure developed for use in clinical trials to monitor disease impairment and progression in affected CMT patients. Currently, all items of CMTNSv2 have identical contribution to the total score. We used Rasch analysis to further explore psychometric properties of CMTNSv2, and in particular, category response functioning and their weight on the overall disease progression. Weighted category responses represent a more accurate estimate of actual values measuring disease severity and therefore could potentially be used in improving the current version. PMID:25400013

  4. Volleyball Scoring Systems.

    ERIC Educational Resources Information Center

    Calhoun, William; Dargahi-Noubary, G. R.; Shi, Yixun

    2002-01-01

    The widespread interest in sports in our culture provides an excellent opportunity to catch students' attention in mathematics and statistics classes. One mathematically interesting aspect of volleyball, which can be used to motivate students, is the scoring system. (MM)

  5. Nutrient Density Scores.

    ERIC Educational Resources Information Center

    Dickinson, Annette; Thompson, William T.

    1979-01-01

    Announces a nutrient density food scoring system called the Index of Nutritional Quality (INQ). It expresses the ratio between the percent RDA of a nutrient and the percent daily allowance of calories in a food. (Author/SA)

  6. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    NASA Technical Reports Server (NTRS)

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds

    2005-01-01

    High frequency (HF, 150-250 Hz) analysis over the entire QRS interval of the ECG is more sensitive than conventional ECG for detecting myocardial ischemia. However, the accuracy of HF QRS ECG for detecting cardiomyopathy is unknown. We obtained simultaneous resting conventional and HF QRS 12-lead ECGs in 66 patients with cardiomyopathy (EF = 23.2 plus or minus 6.l%, mean plus or minus SD) and in 66 age- and gender-matched healthy controls using PC-based ECG software recently developed at NASA. The single most accurate ECG parameter for detecting cardiomyopathy was an HF QRS morphological score that takes into consideration the total number and severity of reduced amplitude zones (RAZs) present plus the clustering of RAZs together in contiguous leads. This RAZ score had an area under the receiver operator curve (ROC) of 0.91, and was 88% sensitive, 82% specific and 85% accurate for identifying cardiomyopathy at optimum score cut-off of 140 points. Although conventional ECG parameters such as the QRS and QTc intervals were also significantly longer in patients than controls (P less than 0.001, BBBs excluded), these conventional parameters were less accurate (area under the ROC = 0.77 and 0.77, respectively) than HF QRS morphological parameters for identifying underlying cardiomyopathy. The total amplitude of the HF QRS complexes, as measured by summed root mean square voltages (RMSVs), also differed between patients and controls (33.8 plus or minus 11.5 vs. 41.5 plus or minus 13.6 mV, respectively, P less than 0.003), but this parameter was even less accurate in distinguishing the two groups (area under ROC = 0.67) than the HF QRS morphologic and conventional ECG parameters. Diagnostic accuracy was optimal (86%) when the RAZ score from the HF QRS ECG and the QTc interval from the conventional ECG were used simultaneously with cut-offs of greater than or equal to 40 points and greater than or equal to 445 ms, respectively. In conclusion 12-lead HF QRS ECG employing

  7. Prediction of {sup 2}D Rydberg energy levels of {sup 6}Li and {sup 7}Li based on very accurate quantum mechanical calculations performed with explicitly correlated Gaussian functions

    SciTech Connect

    Bubin, Sergiy; Sharkey, Keeper L.; Adamowicz, Ludwik

    2013-04-28

    Very accurate variational nonrelativistic finite-nuclear-mass calculations employing all-electron explicitly correlated Gaussian basis functions are carried out for six Rydberg {sup 2}D states (1s{sup 2}nd, n= 6, Horizontal-Ellipsis , 11) of the {sup 7}Li and {sup 6}Li isotopes. The exponential parameters of the Gaussian functions are optimized using the variational method with the aid of the analytical energy gradient determined with respect to these parameters. The experimental results for the lower states (n= 3, Horizontal-Ellipsis , 6) and the calculated results for the higher states (n= 7, Horizontal-Ellipsis , 11) fitted with quantum-defect-like formulas are used to predict the energies of {sup 2}D 1s{sup 2}nd states for {sup 7}Li and {sup 6}Li with n up to 30.

  8. Scoring docking conformations using predicted protein interfaces

    PubMed Central

    2014-01-01

    Background Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). Results First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. Conclusion Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations. PMID:24906633

  9. Estimating one's own personality and intelligence scores.

    PubMed

    Furnham, Adrian; Chamorro-Premuzic, Tomas

    2004-05-01

    One hundred and eighty-seven university students completed the full NEO-PI-R assessing the five super-traits and 30 primary traits, and the Wonderlic Personnel Test of general intelligence. Two months later (before receiving feedback on their psychometric scores), they estimated their own scores on these variables. Results at the super-factor level indicated that participants could significantly predict/estimate their own Neuroticism, Extraversion, and Conscientiousness scores. The correlation between estimated and psychometrically measured IQ was r=.30, showing that participants could, to some extent, accurately estimate their intelligence. In addition, there were a number of significant correlations between estimated intelligence and psychometrically assessed personality (particularly Neuroticism, Agreeableness and Extraversion). Disagreeable people tended to award themselves higher self-estimated intelligence scores. Similarly, stable people tended to award themselves higher estimates of intelligence (even when other variables were controlled). Regressing both estimated and psychometric IQ scores onto estimated and psychometric personality scores indicated that the strongest significant effect was the relationship between trait scores and self-estimated intelligence. PMID:15142299

  10. Interpreting Standardized Test Scores: Some Fine Points.

    ERIC Educational Resources Information Center

    Hunter, William J.

    1980-01-01

    An essential function of the school guidance worker is the translation of test results into plain language and/or concrete recommendations. To do so requires a thorough understanding of the various test scores publishers provide. (Author)

  11. Applying Computerized-Scoring Models of Written Biological Explanations across Courses and Colleges: Prospects and Limitations

    PubMed Central

    Ha, Minsu; Nehm, Ross H.; Urban-Lurain, Mark; Merrill, John E.

    2011-01-01

    Our study explored the prospects and limitations of using machine-learning software to score introductory biology students’ written explanations of evolutionary change. We investigated three research questions: 1) Do scoring models built using student responses at one university function effectively at another university? 2) How many human-scored student responses are needed to build scoring models suitable for cross-institutional application? 3) What factors limit computer-scoring efficacy, and how can these factors be mitigated? To answer these questions, two biology experts scored a corpus of 2556 short-answer explanations (from biology majors and nonmajors) at two universities for the presence or absence of five key concepts of evolution. Human- and computer-generated scores were compared using kappa agreement statistics. We found that machine-learning software was capable in most cases of accurately evaluating the degree of scientific sophistication in undergraduate majors’ and nonmajors’ written explanations of evolutionary change. In cases in which the software did not perform at the benchmark of “near-perfect” agreement (kappa > 0.80), we located the causes of poor performance and identified a series of strategies for their mitigation. Machine-learning software holds promise as an assessment tool for use in undergraduate biology education, but like most assessment tools, it is also characterized by limitations. PMID:22135372

  12. Prepartum concentrate supplementation of a diet based on medium-quality grass silage: Effects on performance, health, fertility, metabolic function, and immune function of low body condition score cows.

    PubMed

    Little, M W; O'Connell, N E; Welsh, M D; Barley, J; Meade, K G; Ferris, C P

    2016-09-01

    When cows with a "higher" body condition score (BCS) are oversupplied with energy during the dry period, postpartum energy balance is normally reduced, which can have a detrimental effect on immune competence and increase the infectious disease risk. However, within grassland-based systems higher yielding cows frequently have a low BCS at drying off. The effects on performance, health, and metabolic and immune functions of providing additional energy to cows with low BCS during the dry period is less certain. To address this uncertainty, 53 multiparous Holstein-Friesian cows (mean BCS of 2.5; 1-5 scale) were allocated to 1 of 2 treatments at dry-off: silage only or silage plus concentrates. Cows on the silage-only treatment were offered ad libitum access to medium-quality grass silage. Cows on the silage-plus-concentrate treatment were offered ad libitum access to a mixed ration comprising the same grass silage plus concentrates [in a 75:25 dry matter (DM) ratio], which provided a mean concentrate DM intake of 3.0kg/cow per day. Postpartum, cows were offered a common mixed ration comprising grass silage and concentrates (in a 40:60 DM ratio) for a 70-d period. Offering concentrates during the dry period increased DM intake, tended to increase energy balance, and increased body weight (BW) and BCS gain prepartum. Offering concentrates during the dry period increased BW and BCS loss postpartum and tended to increase milk fat percentage and serum nonesterified fatty acid concentration, but it did not affect postpartum DM intake, energy balance, and milk yield. Although the percentage of phagocytosis-positive neutrophils did not differ, neutrophils from cows on the silage-plus-concentrate treatment had higher phagocytic fluorescence intensity at 1 and 2 wk postpartum and higher phagocytic index at 1 wk postpartum. Serum haptoglobin concentrations and IFN-γ production by pokeweed mitogen stimulated whole blood culture were unaffected by treatment, although haptoglobin

  13. Prepartum concentrate supplementation of a diet based on medium-quality grass silage: Effects on performance, health, fertility, metabolic function, and immune function of low body condition score cows.

    PubMed

    Little, M W; O'Connell, N E; Welsh, M D; Barley, J; Meade, K G; Ferris, C P

    2016-09-01

    When cows with a "higher" body condition score (BCS) are oversupplied with energy during the dry period, postpartum energy balance is normally reduced, which can have a detrimental effect on immune competence and increase the infectious disease risk. However, within grassland-based systems higher yielding cows frequently have a low BCS at drying off. The effects on performance, health, and metabolic and immune functions of providing additional energy to cows with low BCS during the dry period is less certain. To address this uncertainty, 53 multiparous Holstein-Friesian cows (mean BCS of 2.5; 1-5 scale) were allocated to 1 of 2 treatments at dry-off: silage only or silage plus concentrates. Cows on the silage-only treatment were offered ad libitum access to medium-quality grass silage. Cows on the silage-plus-concentrate treatment were offered ad libitum access to a mixed ration comprising the same grass silage plus concentrates [in a 75:25 dry matter (DM) ratio], which provided a mean concentrate DM intake of 3.0kg/cow per day. Postpartum, cows were offered a common mixed ration comprising grass silage and concentrates (in a 40:60 DM ratio) for a 70-d period. Offering concentrates during the dry period increased DM intake, tended to increase energy balance, and increased body weight (BW) and BCS gain prepartum. Offering concentrates during the dry period increased BW and BCS loss postpartum and tended to increase milk fat percentage and serum nonesterified fatty acid concentration, but it did not affect postpartum DM intake, energy balance, and milk yield. Although the percentage of phagocytosis-positive neutrophils did not differ, neutrophils from cows on the silage-plus-concentrate treatment had higher phagocytic fluorescence intensity at 1 and 2 wk postpartum and higher phagocytic index at 1 wk postpartum. Serum haptoglobin concentrations and IFN-γ production by pokeweed mitogen stimulated whole blood culture were unaffected by treatment, although haptoglobin

  14. A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference.

    PubMed

    Gao, Nan; Zhang, Yan; Feng, Bing; Tang, Jijun

    2015-01-01

    Recent advances of technology have made it easy to obtain and compare whole genomes. Rearrangements of genomes through operations such as reversals and transpositions are rare events that enable researchers to reconstruct deep evolutionary history among species. Some of the popular methods need to search a large tree space for the best scored tree, thus it is desirable to have a fast and accurate method that can score a given tree efficiently. During the tree scoring procedure, the genomic structures of internal tree nodes are also provided, which provide important information for inferring ancestral genomes and for modeling the evolutionary processes. However, computing tree scores and ancestral genomes are very difficult and a lot of researchers have to rely on heuristic methods which have various disadvantages. In this paper, we describe the first genetic algorithm for tree scoring and ancestor inference, which uses a fitness function considering co-evolution, adopts different initial seeding methods to initialize the first population pool, and utilizes a sorting-based approach to realize evolution. Our extensive experiments show that compared with other existing algorithms, this new method is more accurate and can infer ancestral genomes that are much closer to the true ancestors. PMID:26671797

  15. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  16. Widening clinical applications of the SYNTAX Score.

    PubMed

    Farooq, Vasim; Head, Stuart J; Kappetein, Arie Pieter; Serruys, Patrick W

    2014-02-01

    The SYNTAX Score (http://www.syntaxscore.com) has established itself as an anatomical based tool for objectively determining the complexity of coronary artery disease and guiding decision-making between coronary artery bypass graft (CABG) surgery and percutaneous coronary intervention (PCI). Since the landmark SYNTAX (Synergy between PCI with Taxus and Cardiac Surgery) Trial comparing CABG with PCI in patients with complex coronary artery disease (unprotected left main or de novo three vessel disease), numerous validation studies have confirmed the clinical validity of the SYNTAX Score for identifying higher-risk subjects and aiding decision-making between CABG and PCI in a broad range of patient types. The SYNTAX Score is now advocated in both the European and US revascularisation guidelines for decision-making between CABG and PCI as part of a SYNTAX-pioneered heart team approach. Since establishment of the SYNTAX Score, widening clinical applications of this clinical tool have emerged. The purpose of this review is to systematically examine the widening applications of tools based on the SYNTAX Score: (1) by improving the diagnostic accuracy of the SYNTAX Score by adding a functional assessment of lesions; (2) through amalgamation of the anatomical SYNTAX Score with clinical variables to enhance decision-making between CABG and PCI, culminating in the development and validation of the SYNTAX Score II, in which objective and tailored decisions can be made for the individual patient; (3) through assessment of completeness of revascularisation using the residual and post-CABG SYNTAX Scores for PCI and CABG patients, respectively. Finally, the future direction of the SYNTAX Score is covered through discussion of the ongoing development of a non-invasive, functional SYNTAX Score and review of current and planned clinical trials.

  17. Pre-Transplant CDKN2A Expression in Kidney Biopsies Predicts Renal Function and Is a Future Component of Donor Scoring Criteria

    PubMed Central

    Gingell-Littlejohn, Marc; McGuinness, Dagmara; McGlynn, Liane M.; Kingsmore, David; Stevenson, Karen S.; Koppelstaetter, Christian; Clancy, Marc J.; Shiels, Paul G.

    2013-01-01

    CDKN2A is a proven and validated biomarker of ageing which acts as an off switch for cell proliferation. We have demonstrated previously that CDKN2A is the most robust and the strongest pre-transplant predictor of post- transplant serum creatinine when compared to “Gold Standard” clinical factors, such as cold ischaemic time and donor chronological age. This report shows that CDKN2A is better than telomere length, the most celebrated biomarker of ageing, as a predictor of post-transplant renal function. It also shows that CDKN2A is as strong a determinant of post-transplant organ function when compared to extended criteria (ECD) kidneys. A multivariate analysis model was able to predict up to 27.1% of eGFR at one year post-transplant (p = 0.008). Significantly, CDKN2A was also able to strongly predict delayed graft function. A pre-transplant donor risk classification system based on CDKN2A and ECD criteria is shown to be feasible and commendable for implementation in the near future. PMID:23861858

  18. Developing Scoring Algorithms

    Cancer.gov

    We developed scoring procedures to convert screener responses to estimates of individual dietary intake for fruits and vegetables, dairy, added sugars, whole grains, fiber, and calcium using the What We Eat in America 24-hour dietary recall data from the 2003-2006 NHANES.

  19. Syncopation and the Score

    PubMed Central

    Song, Chunyang; Simpson, Andrew J. R.; Harte, Christopher A.; Pearce, Marcus T.; Sandler, Mark B.

    2013-01-01

    The score is a symbolic encoding that describes a piece of music, written according to the conventions of music theory, which must be rendered as sound (e.g., by a performer) before it may be perceived as music by the listener. In this paper we provide a step towards unifying music theory with music perception in terms of the relationship between notated rhythm (i.e., the score) and perceived syncopation. In our experiments we evaluated this relationship by manipulating the score, rendering it as sound and eliciting subjective judgments of syncopation. We used a metronome to provide explicit cues to the prevailing rhythmic structure (as defined in the time signature). Three-bar scores with time signatures of 4/4 and 6/8 were constructed using repeated one-bar rhythm-patterns, with each pattern built from basic half-bar rhythm-components. Our manipulations gave rise to various rhythmic structures, including polyrhythms and rhythms with missing strong- and/or down-beats. Listeners (N = 10) were asked to rate the degree of syncopation they perceived in response to a rendering of each score. We observed higher degrees of syncopation in time signatures of 6/8, for polyrhythms, and for rhythms featuring a missing down-beat. We also found that the location of a rhythm-component within the bar has a significant effect on perceived syncopation. Our findings provide new insight into models of syncopation and point the way towards areas in which the models may be improved. PMID:24040323

  20. The Relation between Factor Score Estimates, Image Scores, and Principal Component Scores

    ERIC Educational Resources Information Center

    Velicer, Wayne F.

    1976-01-01

    Investigates the relation between factor score estimates, principal component scores, and image scores. The three methods compared are maximum likelihood factor analysis, principal component analysis, and a variant of rescaled image analysis. (RC)

  1. Accurate, Analytic, Empirical Potentials and Born-Oppenheimer Breakdown Functions for the X(1^1Σ)-STATES of BeH, BeD, and BeT

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.; Welsh, Staszek

    2014-06-01

    Being the simplest neutral open shell molecule, BeH is a very important benchmark system for ab initio calculations. However, the most accurate empirical potentials and Born-Oppenheimer breakdown (BOB) functions for this system are nearly a decade old and are not reliable in the long-range region. Particularly, the uncertainties in their dissociation energies were about ±200 cm-1, and even the number of vibrational levels predicted was at the time very questionable, meaning that no good benchmark exists for ab initio calculations on neutral open shell molecules. We build new empirical potentials for BeH, BeD, and BeT that are much more reliable in the long-range. Being the second lightest heteronuclear molecule with a stable ground electronic state, BeH is also very important for the study of isotope effects, such as BOB. We extensively study isotope effects in this system, and we show that the empirical BOB functions fitted from the data of any two isotopologues, is sufficient to predict crucial properties of the third isotopologue.

  2. [The use of scores in general medicine].

    PubMed

    Huber, Ursula; Rösli, Andreas; Ballmer, Peter E; Rippin, Sarah Jane

    2013-10-01

    Scores are tools to combine complex information into a numerical value. In General Medicine, there are scores to assist in making diagnoses and prognoses, scores to assist therapeutic decision making and to evaluate therapeutic results and scores to help physicians when informing and advising patients. We review six of the scoring systems that have the greatest utility for the General Physician in hospital-based care and in General Practice. The Nutritional Risk Screening (NRS 2002) tool is designed to identify hospital patients in danger of malnutrition. The aim is to improve the nutritional status of these patients. The CURB-65 score predicts 30-day mortality in patients with community acquired pneumonia. Patients with a low score can be considered for home treatment, patients with an elevated score require hospitalisation and those with a high score should be treated as having severe pneumonia; treatment in the intensive care unit should be considered. The IAS-AGLA score of the Working Group on Lipids and Atherosclerosis of the Swiss Society of Cardiology calculates the 10-year risk of a myocardial infarction for people living in Switzerland. The working group makes recommendations for preventative treatment according to the calculated risk status. The Body Mass Index, which is calculated by dividing the body weight in kilograms by the height in meters squared and then divided into weight categories, is used to classify people as underweight, of normal weight, overweight or obese. The prognostic value of this classification is discussed. The Mini-Mental State Examination allows the physician to assess important cognitive functions in a simple and standardised form. The Glasgow Coma Scale is used to classify the level of consciousness in patients with head injury. It can be used for triage and correlates with prognosis.

  3. The Oxford Knee Score; problems and pitfalls.

    PubMed

    Whitehouse, Sarah L; Blom, Ashley W; Taylor, Adrian H; Pattison, Giles T R; Bannister, Gordon C

    2005-08-01

    The Oxford Knee Score is a self-completed patient based outcome score. We audited the outcome of total knee arthroplasty at our unit using the Oxford Knee Score. The hypothesis of this study is that the OKS can be easily and accurately completed by unassisted patients. Of 856 patients who had undergone total knee arthroplasty and were given questionnaires, 769 (90%) responded. 624 (81%) of the respondents managed to complete the questionnaire. A number of the 12 items composing the questionnaire posed problems for the patients and a number of items were left blank. Item 4 (concerning walking time) was omitted in 82 (13%) of the 624 completed questionnaires. Calculation of Cronbach's alpha for internal consistency suggests that there are redundancies within the Score. Limitations in some of the items of the scale suggest the need for reconsideration and reformulation of questions and response categories. This study suggests that where detailed assessment of outcome is required, such as for outcome studies or controlled trials, the Oxford Knee Score, in its present form, is not ideal for use as a postal questionnaire.

  4. Verbal Reasoning Test Scores and Their Stability over Time.

    ERIC Educational Resources Information Center

    Primrose, Alison F.; Fuller, Mary; Littledyke, Michael

    2000-01-01

    Stability of verbal reasoning test scores was measured for 146 students aged 8-13. Results suggest that reasoning test scores are not constant and vary considerably over time. Scores are not finite measures of intellectual capacity but of current verbal functioning, reflecting education and experiences to that point. (SK)

  5. Statistical Assessment of Estimated Transformations in Observed-Score Equating

    ERIC Educational Resources Information Center

    Wiberg, Marie; González, Jorge

    2016-01-01

    Equating methods make use of an appropriate transformation function to map the scores of one test form into the scale of another so that scores are comparable and can be used interchangeably. The equating literature shows that the ways of judging the success of an equating (i.e., the score transformation) might differ depending on the adopted…

  6. Can Administrative Claim File Review Be Used to Gather Physical Therapy, Occupational Therapy, and Psychology Payment Data and Functional Independence Measure Scores? Implications for Rehabilitation Providers in the Private Health Sector

    PubMed Central

    Jaglal, Susan; Boschen, Kathryn; Walker, Jan; Verrier, Molly

    2011-01-01

    ABSTRACT Purpose: Rehabilitation costs for spinal-cord injury (SCI) are increasingly borne by Canada's private health system. Because of poor outcomes, payers are questioning the value of their expenditures, but there is a paucity of data informing analysis of rehabilitation costs and outcomes. This study evaluated the feasibility of using administrative claim file review to extract rehabilitation payment data and functional status for a sample of persons with work-related SCI. Methods: Researchers reviewed 28 administrative e-claim files for persons who sustained a work-related SCI between 1996 and 2000. Payment data were extracted for physical therapy (PT), occupational therapy (OT), and psychology services. Functional Independence Measure (FIM) scores were targeted as a surrogate measure for functional outcome. Feasibility was tested using an existing approach for evaluating health services data. Results: The process of administrative e-claim file review was not practical for extraction of the targeted data. Conclusions: While administrative claim files contain some rehabilitation payment and outcome data, in their present form the data are not suitable to inform rehabilitation services research. A new strategy to standardize collection, recording, and sharing of data in the rehabilitation industry should be explored as a means of promoting best practices. PMID:22654238

  7. Pharmacophore-Based Similarity Scoring for DOCK

    PubMed Central

    2015-01-01

    Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein–ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK. PMID:25229837

  8. Fingerprinting of music scores

    NASA Astrophysics Data System (ADS)

    Irons, Jonathan; Schmucker, Martin

    2004-06-01

    Publishers of sheet music are generally reluctant in distributing their content via the Internet. Although online sheet music distribution's advantages are numerous the potential risk of Intellectual Property Rights (IPR) infringement, e.g. illegal online distributions, disables any innovation propensity. While active protection techniques only deter external risk factors, additional technology is necessary to adequately treat further risk factors. For several media types including music scores watermarking technology has been developed, which ebeds information in data by suitable data modifications. Furthermore, fingerprinting or perceptual hasing methods have been developed and are being applied especially for audio. These methods allow the identification of content without prior modifications. In this article we motivate the development of watermarking and fingerprinting technologies for sheet music. Outgoing from potential limitations of watermarking methods we explain why fingerprinting methods are important for sheet music and address potential applications. Finally we introduce a condept for fingerprinting of sheet music.

  9. Relationship of Apgar Scores and Bayley Mental and Motor Scores

    ERIC Educational Resources Information Center

    Serunian, Sally A.; Broman, Sarah H.

    1975-01-01

    Examined the relationship of newborns' 1-minute Apgar scores to their 8-month Bayley mental and motor scores and to 8-month classifications of their development as normal, suspect, or abnormal. Also investigated relationships between Apgar scores and race, longevity, and birth weight. (JMB)

  10. Automated Essay Scoring versus Human Scoring: A Comparative Study

    ERIC Educational Resources Information Center

    Wang, Jinhao; Brown, Michelle Stallone

    2007-01-01

    The current research was conducted to investigate the validity of automated essay scoring (AES) by comparing group mean scores assigned by an AES tool, IntelliMetric [TM] and human raters. Data collection included administering the Texas version of the WriterPlacer "Plus" test and obtaining scores assigned by IntelliMetric [TM] and by human…

  11. Comparison of Scores on the Checklist for Autism Spectrum Disorder, Childhood Autism Rating Scale, and Gilliam Asperger's Disorder Scale for Children with Low Functioning Autism, High Functioning Autism, Asperger's Disorder, ADHD, and Typical Development

    ERIC Educational Resources Information Center

    Mayes, Susan Dickerson; Calhoun, Susan L.; Murray, Michael J.; Morrow, Jill D.; Yurich, Kirsten K. L.; Mahr, Fauzia; Cothren, Shiyoko; Purichia, Heather; Bouder, James N.; Petersen, Christopher

    2009-01-01

    Reliability and validity for three autism instruments were compared for 190 children with low functioning autism (LFA), 190 children with high functioning autism or Asperger's disorder (HFA), 76 children with attention deficit hyperactivity disorder (ADHD), and 64 typical children. The instruments were the Checklist for Autism Spectrum Disorder…

  12. Automated sleep scoring and sleep apnea detection in children

    NASA Astrophysics Data System (ADS)

    Baraglia, David P.; Berryman, Matthew J.; Coussens, Scott W.; Pamula, Yvonne; Kennedy, Declan; Martin, A. James; Abbott, Derek

    2005-12-01

    This paper investigates the automated detection of a patient's breathing rate and heart rate from their skin conductivity as well as sleep stage scoring and breathing event detection from their EEG. The software developed for these tasks is tested on data sets obtained from the sleep disorders unit at the Adelaide Women's and Children's Hospital. The sleep scoring and breathing event detection tasks used neural networks to achieve signal classification. The Fourier transform and the Higuchi fractal dimension were used to extract features for input to the neural network. The filtered skin conductivity appeared visually to bear a similarity to the breathing and heart rate signal, but a more detailed evaluation showed the relation was not consistent. Sleep stage classification was achieved with and accuracy of around 65% with some stages being accurately scored and others poorly scored. The two breathing events hypopnea and apnea were scored with varying degrees of accuracy with the highest scores being around 75% and 30%.

  13. Olympic Scoring of English Compositions

    ERIC Educational Resources Information Center

    Follman, John; Panther, Edward

    1974-01-01

    Examines empirically the efficacy of utilizing Olympic diving and gymnastic scoring systems for grading graduate students' English compositions. Results indicated that such scoring rules do not produce ratings different in reliability or in level from conventional letter grades. (ED)

  14. Line Lengths and Starch Scores.

    ERIC Educational Resources Information Center

    Moriarty, Sandra E.

    1986-01-01

    Investigates readability of different line lengths in advertising body copy, hypothesizing a normal curve with lower scores for shorter and longer lines, and scores above the mean for lines in the middle of the distribution. Finds support for lower scores for short lines and some evidence of two optimum line lengths rather than one. (SKC)

  15. Impact of adherence to GOLD guidelines on 6-minute walk distance, MRC dyspnea scale score, lung function decline, quality of life, and quality-adjusted life years in a Shanghai suburb.

    PubMed

    Jiang, Y Q; Zhu, Y X; Chen, X L; Xu, X; Li, F; Fu, H J; Shen, C Y; Lu, Y Y; Zhuang, Q J; Xu, G; Cai, Y Y; Zhang, Y; Liu, S S; Zhu, M Y; Li, S H

    2015-01-01

    We performed a 1-year cluster-randomized field trial to assess the effect of standardized management of chronic obstructive pulmonary disease (COPD) on lung function and quality of life (QOL) measures in patients in China. We used the Global Initiative for Chronic Obstructive Lung Disease (GOLD) treatment guidelines and assessed indexes including pulmonary function, QOL, quality-adjusted life years (QALY), Medical Research Council (MRC) dyspnea scale, 6-min walk distance (6-MWD), number of emergency visits, and frequency of hospitalization. Of a total of 711 patients with chronic cough and asthma, 132 were diagnosed as having COPD and 102 participated in this study [intervention group (N = 47); control group (N = 55)]. We found that adherence to GOLD guidelines had a perceivable impact on 6-MWD, MRC dyspnea scale score, and QOL. The average QALY increased by 1.42/person/year in the intervention group, but declined by 0.95/person/year in the control group. We conclude that standardized management improves disease severity, QOL, and QALY in COPD patients when treatment protocols adhere to GOLD guidelines.

  16. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  17. Higher maternal plasma folate but not vitamin B-12 concentrations during pregnancy are associated with better cognitive function scores in 9-10 year old children in South-India1-3

    PubMed Central

    Veena, Sargoor R; Krishnaveni, Ghattu V; Srinivasan, Krishnamachari; Wills, Andrew K; Muthayya, Sumithra; Kurpad, Anura V; Yajnik, Chittaranjan S; Fall, Caroline HD

    2012-01-01

    Folate and vitamin B-12 (B-12) are essential for normal brain development. Few studies have examined the relationship of maternal folate and B-12 status during pregnancy to offspring cognitive function. To test the hypothesis that lower maternal plasma folate and B-12 concentrations and higher plasma homocysteine concentrations during pregnancy, are associated with poorer neurodevelopment, cognitive function was assessed during 2007-2008 among 536 children (aged 9-10 y) from the Mysore Parthenon birth cohort. Maternal folate, B-12 and homocysteine concentrations were measured in stored plasma samples taken at 30±2 wk gestation. The children’s cognitive function was measured using 3 core tests from the Kaufman Assessment Battery and additional tests measuring learning ability, long-term storage/retrieval, attention and concentration, visuo-spatial and verbal abilities. During pregnancy 4% of mothers had low folate concentrations (<7 nmol/L), 42.5% had low B-12 concentrations (<150 pmol/L) and 3% had hyperhomocysteinemia (>10 μmol/L). There was a 0.1-0.2 SD increase in the children’s cognitive scores per SD increase in maternal folate concentration (p<0.001 for all tests). The associations with learning ability and long-term storage/retrieval, visuo-spatial ability, attention and concentration were independent of maternal age, BMI, parity, the parents’ education, socio-economic status, rural/urban residence, religion, the child’s gestational age, birth size, sex and the children’s size, educational level and folate and B-12 concentrations at 9.5 y. There were no consistent associations of maternal B-12 and homocysteine concentrations with childhood cognitive performance. Conclusions In this Indian population higher maternal folate, but not vitamin B-12 concentrations during pregnancy, predicted better childhood cognitive ability. PMID:20335637

  18. Equating Scores from Adaptive to Linear Tests

    ERIC Educational Resources Information Center

    van der Linden, Wim J.

    2006-01-01

    Two local methods for observed-score equating are applied to the problem of equating an adaptive test to a linear test. In an empirical study, the methods were evaluated against a method based on the test characteristic function (TCF) of the linear test and traditional equipercentile equating applied to the ability estimates on the adaptive test…

  19. Higher maternal plasma folate but not vitamin B-12 concentrations during pregnancy are associated with better cognitive function scores in 9- to 10- year-old children in South India.

    PubMed

    Veena, Sargoor R; Krishnaveni, Ghattu V; Srinivasan, Krishnamachari; Wills, Andrew K; Muthayya, Sumithra; Kurpad, Anura V; Yajnik, Chittaranjan S; Fall, Caroline H D

    2010-05-01

    Folate and vitamin B-12 are essential for normal brain development. Few studies have examined the relationship of maternal folate and vitamin B-12 status during pregnancy and offspring cognitive function. To test the hypothesis that lower maternal plasma folate and vitamin B-12 concentrations and higher plasma homocysteine concentrations during pregnancy are associated with poorer neurodevelopment, 536 children (aged 9-10 y) from the Mysore Parthenon birth cohort underwent cognitive function assessment during 2007-2008 using 3 core tests from the Kaufman Assessment Battery, and additional tests measuring learning, long-term storage/retrieval, attention and concentration, and visuo-spatial and verbal abilities. Maternal folate, vitamin B-12, and homocysteine concentrations were measured at 30 +/- 2 wk gestation. During pregnancy, 4% of mothers had low folate concentrations (<7 nmol/L), 42.5% had low vitamin B-12 concentrations (<150 pmol/L), and 3% had hyperhomocysteinemia (>10 micromol/L). The children's cognitive test scores increased by 0.1-0.2 SD per SD increase across the entire range of maternal folate concentrations (P < 0.001 for all), with no apparent associations at the deficiency level. The associations with learning, long-term storage/retrieval, visuo-spatial ability, attention, and concentration were independent of the parents' education, socioeconomic status, religion, and the child's sex, age, current size, and folate and vitamin B-12 concentrations. There were no consistent associations of maternal vitamin B-12 and homocysteine concentrations with childhood cognitive performance. In this Indian population, higher maternal folate, but not vitamin B-12, concentrations during pregnancy predicted better childhood cognitive ability. It also suggests that, in terms of neurodevelopment, the concentration used to define folate deficiency may be set too low. PMID:20335637

  20. Higher maternal plasma folate but not vitamin B-12 concentrations during pregnancy are associated with better cognitive function scores in 9- to 10- year-old children in South India.

    PubMed

    Veena, Sargoor R; Krishnaveni, Ghattu V; Srinivasan, Krishnamachari; Wills, Andrew K; Muthayya, Sumithra; Kurpad, Anura V; Yajnik, Chittaranjan S; Fall, Caroline H D

    2010-05-01

    Folate and vitamin B-12 are essential for normal brain development. Few studies have examined the relationship of maternal folate and vitamin B-12 status during pregnancy and offspring cognitive function. To test the hypothesis that lower maternal plasma folate and vitamin B-12 concentrations and higher plasma homocysteine concentrations during pregnancy are associated with poorer neurodevelopment, 536 children (aged 9-10 y) from the Mysore Parthenon birth cohort underwent cognitive function assessment during 2007-2008 using 3 core tests from the Kaufman Assessment Battery, and additional tests measuring learning, long-term storage/retrieval, attention and concentration, and visuo-spatial and verbal abilities. Maternal folate, vitamin B-12, and homocysteine concentrations were measured at 30 +/- 2 wk gestation. During pregnancy, 4% of mothers had low folate concentrations (<7 nmol/L), 42.5% had low vitamin B-12 concentrations (<150 pmol/L), and 3% had hyperhomocysteinemia (>10 micromol/L). The children's cognitive test scores increased by 0.1-0.2 SD per SD increase across the entire range of maternal folate concentrations (P < 0.001 for all), with no apparent associations at the deficiency level. The associations with learning, long-term storage/retrieval, visuo-spatial ability, attention, and concentration were independent of the parents' education, socioeconomic status, religion, and the child's sex, age, current size, and folate and vitamin B-12 concentrations. There were no consistent associations of maternal vitamin B-12 and homocysteine concentrations with childhood cognitive performance. In this Indian population, higher maternal folate, but not vitamin B-12, concentrations during pregnancy predicted better childhood cognitive ability. It also suggests that, in terms of neurodevelopment, the concentration used to define folate deficiency may be set too low.

  1. Utilizing signature-score to identify oncogenic pathways of cholangiocarcinoma

    PubMed Central

    Hsiao, Tzu-Hung; Chen, Hung-I Harry; Lu, Jo-Yang; Lin, Pei-Ying; Keller, Charles; Comerford, Sarah; Tomlinson, Gail E.; Chen, Yidong

    2013-01-01

    Extracting maximal information from gene signature sets (GSSs) via microarray-based transcriptional profiling involves assigning function to up and down regulated genes. Here we present a novel sample scoring method called Signature-score (S-score) which can be used to quantify the expression pattern of tumor samples from previously identified gene signature sets. A simulation result demonstrated an improved accuracy and robustness by S-score method comparing with other scoring methods. By applying the S-score method to cholangiocarcinoma (CAC), an aggressive hepatic cancer that arises from bile ducts cells, we identified enriched oncogenic pathways in two large CAC data sets. Thirteen pathways were enriched in CAC compared with normal liver and bile duct. Moreover, using S-score, we were able to dissect correlations between CAC-associated oncogenic pathways and Gene Ontology function. Two major oncogenic clusters and associated functions were identified. Cluster 1, which included beta-catenin and Ras, showed a positive correlation with the cell cycle, while cluster 2, which included TGF-beta, cytokeratin 19 and EpCAM was inversely correlated with immune function. We also used S-score to identify pathways that are differentially expressed in CAC and hepatocellular carcinoma (HCC), the more common subtype of liver cancer. Our results demonstrate the utility and effectiveness of S-score in assigning functional roles to tumor-associated gene signature sets and in identifying potential therapeutic targets for specific liver cancer subtypes. PMID:23905013

  2. Use of the Childhood Autism Rating Scale (CARS) for Children with High Functioning Autism or Asperger Syndrome

    ERIC Educational Resources Information Center

    Mayes, Susan Dickerson; Calhoun, Susan L.; Murray, Michael J.; Morrow, Jill D.; Yurich, Kirsten K. L.; Cothren, Shiyoko; Purichia, Heather; Mahr, Fauzia; Bouder, James N.; Petersen, Christopher

    2012-01-01

    The authors of the "Childhood Autism Rating Scale" (CARS) state in the manual that the best cutoff score for distinguishing low functioning autism (LFA) from intellectual disability is 30 for children and 28 for adolescents and adults. This study determined that a cutoff score of 25.5 was most accurate in differentiating between high functioning…

  3. Automated Essay Scoring versus Human Scoring: A Correlational Study

    ERIC Educational Resources Information Center

    Wang, Jinhao; Brown, Michelle Stallone

    2008-01-01

    The purpose of the current study was to analyze the relationship between automated essay scoring (AES) and human scoring in order to determine the validity and usefulness of AES for large-scale placement tests. Specifically, a correlational research design was used to examine the correlations between AES performance and human raters' performance.…

  4. Accurate calculation of diffraction-limited encircled and ensquared energy.

    PubMed

    Andersen, Torben B

    2015-09-01

    Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873

  5. Angle Closure Scoring System (ACSS)-A Scoring System for Stratification of Angle Closure Disease

    PubMed Central

    Rao, Aparna; Padhy, Debananda; Sarangi, Sarada; Das, Gopinath

    2016-01-01

    Purpose To evaluate the angle closure scoring system (ACSS) for stratifying primary angle course disease. Methods This observational cross sectional institutional study included patients with primary open angle glaucoma suspects (n = 21) and primary angle closure disease (primary angle closure, PAC, n = 63 and primary angle course glaucoma, PACG, n = 58 (defined by International society of Geographical and Epidemiological Ophthalmology, ISGEO). Two independent examiners blinded to clinical details, graded good quality pre-laser goniophotographs of the patients incorporating quadrants of peripheral anterior synechieae (PAS), non-visibility of posterior trabecular meshwork (PTM) and blotchy pigments (ranging from 1–4 quadrants), iris configuration, angle recess (sum of above depicting ACSSg) and lens thickness/axial length ratio (LT/AL), cup disc ratio and baseline intraocular pressure (IOP) to give total score (ACSSt). Result There were significant differences in ACSSg scores within the same ISGEO stage of PAC and PACG between eyes that required nil or >1medicines after laser iridotomy, p<0.001. The ACSSg was associated with need for >1 medicines in both PAC and PACG eyes, p<0.001. An ACSSg score>12 and 14 in PAC (odds ratio = 2.7(95% CI-1.7–5.9) and PACG (Odds ratio = 1.6(95%CI-1.19–2.2) predicted need for single medicines while ACSSg scores >14 and 19 predicted need for ≥2 medicines in PAC and PACG eyes, respectively. The LT/Al ratio, IOP score or cup disc score did not influence the need for medical treatment independently. Conclusion The ACSS can be a useful clinical adjunct to the ISGEO system to predict need for medicines and prognosticate each stage more accurately. PMID:27788183

  6. Scoring ligand similarity in structure-based virtual screening.

    PubMed

    Zavodszky, Maria I; Rohatgi, Anjali; Van Voorst, Jeffrey R; Yan, Honggao; Kuhn, Leslie A

    2009-01-01

    Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein-ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein-ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein-ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein-ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring

  7. The Machine Scoring of Writing

    ERIC Educational Resources Information Center

    McCurry, Doug

    2010-01-01

    This article provides an introduction to the kind of computer software that is used to score student writing in some high stakes testing programs, and that is being promoted as a teaching and learning tool to schools. It sketches the state of play with machines for the scoring of writing, and describes how these machines work and what they do.…

  8. Trends in Classroom Observation Scores

    ERIC Educational Resources Information Center

    Casabianca, Jodi M.; Lockwood, J. R.; McCaffrey, Daniel F.

    2015-01-01

    Observations and ratings of classroom teaching and interactions collected over time are susceptible to trends in both the quality of instruction and rater behavior. These trends have potential implications for inferences about teaching and for study design. We use scores on the Classroom Assessment Scoring System-Secondary (CLASS-S) protocol from…

  9. High Scores but Low Skills

    ERIC Educational Resources Information Center

    Liu, Liqun; Neilson, William S.

    2011-01-01

    In this paper college admissions are based on test scores and students can exert two types of effort: real learning and exam preparation. The former improves skills but the latter is more effective in raising test scores. In this setting the students with the lowest skills are no longer the ones with the lowest aptitude, but instead are the ones…

  10. Skyrocketing Scores: An Urban Legend

    ERIC Educational Resources Information Center

    Krashen, Stephen

    2005-01-01

    A new urban legend claims, "As a result of the state dropping bilingual education, test scores in California skyrocketed." Krashen disputes this theory, pointing out that other factors offer more logical explanations of California's recent improvements in SAT-9 scores. He discusses research on the effects of California's Proposition 227, which…

  11. Optimum Reliability of Gain Scores.

    ERIC Educational Resources Information Center

    Sharma, K. K.; Gupta, J. K.

    1986-01-01

    This paper gives a mathematical treatment to findings of Zimmerman and Williams and establishes a minimum reliability for gain scores when the pretest and posttest have equal reliabilities and equal standard deviations. It discusses the behavior of the reliability of gain scores in terms of variations in other test parameters. (Author/LMO)

  12. More than Just Test Scores

    ERIC Educational Resources Information Center

    Levin, Henry M.

    2012-01-01

    Around the world we hear considerable talk about creating world-class schools. Usually the term refers to schools whose students get very high scores on the international comparisons of student achievement such as PISA or TIMSS. The practice of restricting the meaning of exemplary schools to the narrow criterion of achievement scores is usually…

  13. Interpreting Linked Psychomotor Performance Scores

    ERIC Educational Resources Information Center

    Looney, Marilyn A.

    2013-01-01

    Given that equating/linking applications are now appearing in kinesiology literature, this article provides an overview of the different types of linked test scores: equated, concordant, and predicted. It also addresses the different types of evidence required to determine whether the scores from two different field tests (measuring the same…

  14. D-score: a search engine independent MD-score.

    PubMed

    Vaudel, Marc; Breiter, Daniela; Beck, Florian; Rahnenführer, Jörg; Martens, Lennart; Zahedi, René P

    2013-03-01

    While peptides carrying PTMs are routinely identified in gel-free MS, the localization of the PTMs onto the peptide sequences remains challenging. Search engine scores of secondary peptide matches have been used in different approaches in order to infer the quality of site inference, by penalizing the localization whenever the search engine similarly scored two candidate peptides with different site assignments. In the present work, we show how the estimation of posterior error probabilities for peptide candidates allows the estimation of a PTM score called the D-score, for multiple search engine studies. We demonstrate the applicability of this score to three popular search engines: Mascot, OMSSA, and X!Tandem, and evaluate its performance using an already published high resolution data set of synthetic phosphopeptides. For those peptides with phosphorylation site inference uncertainty, the number of spectrum matches with correctly localized phosphorylation increased by up to 25.7% when compared to using Mascot alone, although the actual increase depended on the fragmentation method used. Since this method relies only on search engine scores, it can be readily applied to the scoring of the localization of virtually any modification at no additional experimental or in silico cost.

  15. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.

    PubMed

    Landau, Meytal; Mayrose, Itay; Rosenberg, Yossi; Glaser, Fabian; Martz, Eric; Pupko, Tal; Ben-Tal, Nir

    2005-07-01

    Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf (http://consurf.tau.ac.il/) is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.

  16. Conceptual versus Monolingual Scoring: When Does It Make a Difference?

    ERIC Educational Resources Information Center

    Bedore, Lisa M.; Pena, Elizabeth D.; Garcia, Melissa; Cortez, Celina

    2005-01-01

    Purpose: This study evaluates the extent to which bilingual children produce the same or overlapping responses on tasks assessing semantic skills in each of their languages and whether classification analysis based on monolingual or conceptual scoring can accurately classify the semantic development of typically developing (TD) bilingual children.…

  17. Effort Analysis: Individual Score Validation of Achievement Test Data

    ERIC Educational Resources Information Center

    Wise, Steven L.

    2015-01-01

    Whenever the purpose of measurement is to inform an inference about a student's achievement level, it is important that we be able to trust that the student's test score accurately reflects what that student knows and can do. Such trust requires the assumption that a student's test event is not unduly influenced by construct-irrelevant factors…

  18. Two Language Screening Tests Compared with Developmental Sentence Scoring.

    ERIC Educational Resources Information Center

    Blaxley, Lynn; And Others

    1983-01-01

    The performance of 90 children between the ages of four and six years on two language screening tests was compared with their performance on Developmental Sentence Scoring (DSS) to determine the accuracy of these screening tests in identifying language impairments. The Bankson Language Screening Test was generally accurate in the identification of…

  19. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

    PubMed

    Bryce, Richard A

    2011-04-01

    The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

  20. Effectiveness of sequential automatic-manual home respiratory polygraphy scoring.

    PubMed

    Masa, Juan F; Corral, Jaime; Pereira, Ricardo; Duran-Cantolla, Joaquin; Cabello, Marta; Hernández-Blasco, Luis; Monasterio, Carmen; Alonso-Fernandez, Alberto; Chiner, Eusebi; Vázquez-Polo, Francisco-José; Montserrat, Jose M

    2013-04-01

    Automatic home respiratory polygraphy (HRP) scoring functions can potentially confirm the diagnosis of sleep apnoea-hypopnoea syndrome (SAHS) (obviating technician scoring) in a substantial number of patients. The result would have important management and cost implications. The aim of this study was to determine the diagnostic cost-effectiveness of a sequential HRP scoring protocol (automatic and then manual for residual cases) compared with manual HRP scoring, and with in-hospital polysomnography. We included suspected SAHS patients in a multicentre study and assigned them to home and hospital protocols at random. We constructed receiver operating characteristic (ROC) curves for manual and automatic scoring. Diagnostic agreement for several cut-off points was explored and costs for two equally effective alternatives were calculated. Of 366 randomised patients, 348 completed the protocol. Manual scoring produced better ROC curves than automatic scoring. There was no sensitive automatic or subsequent manual HRP apnoea-hypopnoea index (AHI) cut-off point. The specific cut-off points for automatic and subsequent manual HRP scorings (AHI >25 and >20, respectively) had a specificity of 93% for automatic and 94% for manual scorings. The costs of manual protocol were 9% higher than sequential HRP protocol; these were 69% and 64%, respectively, of the cost of the polysomnography. A sequential HRP scoring protocol is a cost-effective alternative to polysomnography, although with limited cost savings compared to HRP manual scoring.

  1. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  2. The ORBIT bleeding score: a simple bedside score to assess bleeding risk in atrial fibrillation

    PubMed Central

    O'Brien, Emily C.; Simon, DaJuanicia N.; Thomas, Laine E.; Hylek, Elaine M.; Gersh, Bernard J.; Ansell, Jack E.; Kowey, Peter R.; Mahaffey, Kenneth W.; Chang, Paul; Fonarow, Gregg C.; Pencina, Michael J.; Piccini, Jonathan P.; Peterson, Eric D.

    2015-01-01

    Background Therapeutic decisions in atrial fibrillation (AF) are often influenced by assessment of bleeding risk. However, existing bleeding risk scores have limitations. Objectives We sought to develop and validate a novel bleeding risk score using routinely available clinical information to predict major bleeding in a large, community-based AF population. Methods We analysed data from Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT-AF), a prospective registry that enrolled incident and prevalent AF patients at 176 US sites. Using Cox proportional hazards regression, we identified factors independently associated with major bleeding among patients taking oral anticoagulation (OAC) over a median follow-up of 2 years (interquartile range = 1.6–2.5). We also created a numerical bedside risk score that included the five most predictive risk factors weighted according to their strength of association with major bleeding. The predictive performance of the full model, the simple five-item score, and two existing risk scores (hypertension, abnormal renal/liver function, stroke, bleeding history or predisposition, labile INR, elderly, drugs/alcohol concomitantly, HAS-BLED, and anticoagulation and risk factors in atrial fibrillation, ATRIA) were then assessed in both the ORBIT-AF cohort and a separate clinical trial population, Rivaroxaban Once-daily oral direct factor Xa inhibition compared with vitamin K antagonism for prevention of stroke and embolism trial in atrial fibrillation (ROCKET-AF). Results Among 7411 ORBIT-AF patients taking OAC, the rate of major bleeding was 4.0/100 person-years. The full continuous model (12 variables) and five-factor ORBIT risk score (older age [75+ years], reduced haemoglobin/haematocrit/history of anaemia, bleeding history, insufficient kidney function, and treatment with antiplatelet) both had good ability to identify those who bled vs. not (C-index 0.69 and 0.67, respectively). These scores both had

  3. Speed Reading Scores in Perspective

    ERIC Educational Resources Information Center

    Smith, Brenda Golembesky

    1975-01-01

    Cites the factors that influence reading rates and comprehension scores on timed speed reading tests, concluding that the reading speed achieved for any particular test or timed reading is the speed for that situation only. (RB)

  4. Obstetrical disseminated intravascular coagulation score.

    PubMed

    Kobayashi, Takao

    2014-06-01

    Obstetrical disseminated intravascular coagulation (DIC) is usually a very acute, serious complication of pregnancy. The obstetrical DIC score helps with making a prompt diagnosis and starting treatment early. This DIC score, in which higher scores are given for clinical parameters rather than for laboratory parameters, has three components: (i) the underlying diseases; (ii) the clinical symptoms; and (iii) the laboratory findings (coagulation tests). It is justifiably appropriate to initiate therapy for DIC when the obstetrical DIC score reaches 8 points or more before obtaining the results of coagulation tests. Improvement of blood coagulation tests and clinical symptoms are essential to the efficacy evaluation for treatment after a diagnosis of obstetrical DIC. Therefore, the efficacy evaluation criteria for obstetrical DIC are also defined to enable follow-up of the clinical efficacy of DIC therapy.

  5. Formulas for Image Factor Scores

    ERIC Educational Resources Information Center

    Hakstian, A. Ralph

    1973-01-01

    Formulas are presented in this paper for computing scores associated with factors of G, the image covariance matrix, under three conditions. The subject of the paper is restricted to "pure" image analysis. (Author/NE)

  6. Accurate basis set truncation for wavefunction embedding

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  7. Accurate documentation and wound measurement.

    PubMed

    Hampton, Sylvie

    This article, part 4 in a series on wound management, addresses the sometimes routine yet crucial task of documentation. Clear and accurate records of a wound enable its progress to be determined so the appropriate treatment can be applied. Thorough records mean any practitioner picking up a patient's notes will know when the wound was last checked, how it looked and what dressing and/or treatment was applied, ensuring continuity of care. Documenting every assessment also has legal implications, demonstrating due consideration and care of the patient and the rationale for any treatment carried out. Part 5 in the series discusses wound dressing characteristics and selection.

  8. Beyond the SYNTAX score--advantages and limitations of other risk assessment systems in left main percutaneous coronary intervention.

    PubMed

    Capodanno, Davide

    2013-01-01

    Risk stratification is an emerging topic in the modern management of patients with left main disease referred for percutaneous coronary intervention (PCI). Recent years have witnessed an explosive multiplication of risk models for prognostic stratification in complex PCI. Many of this models deal with modification of the angiographic SYNTAX score, or seek to overcome its known pitfalls and limitations, including lack of clinical and functional information, inter- and intra-observer variabilities, and poor calibration. Risk scoring systems beyond the SYNTAX score may be classified into angiographic (residual SYNTAX score, coronary artery bypass grafting SYNTAX score), clinical (EuroSCORE I and II, ACEF score and modified ACEF scores), combined clinical and angiographic (Global Risk Classification, Clinical SYNTAX score, logistic Clinical SYNTAX score, SYNTAX score II) and functional (Functional SYNTAX score). This article reviews current concepts in risk modeling and explores the advantages and limitations of the alternatives to the SYNTAX score in patients undergoing left main PCI. 

  9. Scoring systems of severity in patients with multiple trauma.

    PubMed

    Rapsang, Amy Grace; Shyam, Devajit Chowlek

    2015-04-01

    Trauma is a major cause of morbidity and mortality; hence severity scales are important adjuncts to trauma care in order to characterize the nature and extent of injury. Trauma scoring models can assist with triage and help in evaluation and prediction of prognosis in order to organise and improve trauma systems. Given the wide variety of scoring instruments available to assess the injured patient, it is imperative that the choice of the severity score accurately match the application. Even though trauma scores are not the key elements of trauma treatment, they are however, an essential part of improvement in triage decisions and in identifying patients with unexpected outcomes. This article provides the reader with a compendium of trauma severity scales along with their predicted death rate calculation, which can be adopted in order to improve decision making, trauma care, research and in comparative analyses in quality assessment.

  10. Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.

    PubMed

    Koes, David Ryan; Baumgartner, Matthew P; Camacho, Carlos J

    2013-08-26

    We describe a general methodology for designing an empirical scoring function and provide smina, a version of AutoDock Vina specially optimized to support high-throughput scoring and user-specified custom scoring functions. Using our general method, the unique capabilities of smina, a set of default interaction terms from AutoDock Vina, and the CSAR (Community Structure-Activity Resource) 2010 data set, we created a custom scoring function and evaluated it in the context of the CSAR 2011 benchmarking exercise. We find that our custom scoring function does a better job sampling low RMSD poses when crossdocking compared to the default AutoDock Vina scoring function. The design and application of our method and scoring function reveal several insights into possible improvements and the remaining challenges when scoring and ranking putative ligands. PMID:23379370

  11. Complex versus Simple Modeling for Differential Item Functioning (DIF) Detection: When the Intraclass Correlation Coefficient (Rho) of the Studied Item Is Less than the Rho of the Total Score

    ERIC Educational Resources Information Center

    Jin, Ying

    2013-01-01

    Previous research has demonstrated that DIF methods that do not account for multilevel data structure could result in too frequent rejection of the null hypothesis (i.e., no DIF) when the intraclass correlation coefficient (?) of the studied item was the same as ? of the total score. The current study extended previous research by comparing the…

  12. [Coronary risk assessment in subjects with type 2 diabetes mellitus. General population-based scores or specific scores?].

    PubMed

    Hernáez, Rubén; Choque, Lucía; Giménez, Margarita; Costa, Angels; Márquez, Juan I; Conget, Ignacio

    2004-06-01

    Coronary risk in patients with type 2 diabetes mellitus can be calculated using population-based scores or diabetes-specific scores. Our objective was to compare the results with both scores in a group of patients with type 2 diabetes and no history of cardiovascular disease. We analyzed the results for 101 patients aged 40 to 65 years with type 2 diabetes and no prior cardiovascular disease. Two scales were used, one based on the general population (Framingham function adapted from the REGICOR study), and the other based on the population with type 2 diabetes mellitus (UKPDS risk engine). The average 10-year likelihood of coronary events was 5.8 (2.5)% and 15.7 (8.4)% for the REGICOR risk score and the UKPDS risk score, respectively (P<.001), with a Pearson correlation coefficient of 0.525 (P<.01). Risk was higher in men (19.2 [8.7]% based on the UKPDS score, and 5.6 [2.8]% based on the REGICOR score, P<.001). The figures for women were 11.3 [5.9]% and 5.9 [2.1]% with the UKPDS and REGICOR scores, respectively (P<.001). Our results suggest that substantially different findings are obtained when general population-based scores or specific scores are used to assess cardiovascular risk in subjects with type 2 diabetes.

  13. Accurately Mapping M31's Microlensing Population

    NASA Astrophysics Data System (ADS)

    Crotts, Arlin

    2004-07-01

    We propose to augment an existing microlensing survey of M31 with source identifications provided by a modest amount of ACS {and WFPC2 parallel} observations to yield an accurate measurement of the masses responsible for microlensing in M31, and presumably much of its dark matter. The main benefit of these data is the determination of the physical {or "einstein"} timescale of each microlensing event, rather than an effective {"FWHM"} timescale, allowing masses to be determined more than twice as accurately as without HST data. The einstein timescale is the ratio of the lensing cross-sectional radius and relative velocities. Velocities are known from kinematics, and the cross-section is directly proportional to the {unknown} lensing mass. We cannot easily measure these quantities without knowing the amplification, hence the baseline magnitude, which requires the resolution of HST to find the source star. This makes a crucial difference because M31 lens m ass determinations can be more accurate than those towards the Magellanic Clouds through our Galaxy's halo {for the same number of microlensing events} due to the better constrained geometry in the M31 microlensing situation. Furthermore, our larger survey, just completed, should yield at least 100 M31 microlensing events, more than any Magellanic survey. A small amount of ACS+WFPC2 imaging will deliver the potential of this large database {about 350 nights}. For the whole survey {and a delta-function mass distribution} the mass error should approach only about 15%, or about 6% error in slope for a power-law distribution. These results will better allow us to pinpoint the lens halo fraction, and the shape of the halo lens spatial distribution, and allow generalization/comparison of the nature of halo dark matter in spiral galaxies. In addition, we will be able to establish the baseline magnitude for about 50, 000 variable stars, as well as measure an unprecedentedly deta iled color-magnitude diagram and luminosity

  14. SPLASH: Accurate OH maser positions

    NASA Astrophysics Data System (ADS)

    Walsh, Andrew; Gomez, Jose F.; Jones, Paul; Cunningham, Maria; Green, James; Dawson, Joanne; Ellingsen, Simon; Breen, Shari; Imai, Hiroshi; Lowe, Vicki; Jones, Courtney

    2013-10-01

    The hydroxyl (OH) 18 cm lines are powerful and versatile probes of diffuse molecular gas, that may trace a largely unstudied component of the Galactic ISM. SPLASH (the Southern Parkes Large Area Survey in Hydroxyl) is a large, unbiased and fully-sampled survey of OH emission, absorption and masers in the Galactic Plane that will achieve sensitivities an order of magnitude better than previous work. In this proposal, we request ATCA time to follow up OH maser candidates. This will give us accurate (~10") positions of the masers, which can be compared to other maser positions from HOPS, MMB and MALT-45 and will provide full polarisation measurements towards a sample of OH masers that have not been observed in MAGMO.

  15. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  16. Accurate thickness measurement of graphene.

    PubMed

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  17. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2003-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  18. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2002-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  19. Interpreting Force Concept Inventory Scores: Normalized Gain and SAT Scores

    ERIC Educational Resources Information Center

    Coletta, Vincent P.; Phillips, Jeffrey A.; Steinert, Jeffrey J.

    2007-01-01

    Preinstruction SAT scores and normalized gains (G) on the force concept inventory (FCI) were examined for individual students in interactive engagement (IE) courses in introductory mechanics at one high school (N=335) and one university (N=292), and strong, positive correlations were found for both populations (r=0.57 and r=0.46, respectively).…

  20. Knee instability scores for ACL reconstruction.

    PubMed

    Rahnemai-Azar, Ata A; Naendrup, Jan-Hendrik; Soni, Ashish; Olsen, Adam; Zlotnicki, Jason; Musahl, Volker

    2016-06-01

    Despite abundant biological, biomechanical, and clinical research, return to sport after anterior cruciate ligament (ACL) injury remains a significant challenge. Residual rotatory knee laxity has been identified as one of the factors responsible for poor functional outcome. To improve and standardize the assessment of knee instability, a variety of instability scoring systems is available. Recently, devices to objectively quantify static and dynamic clinical exams have been developed to complement traditional subjective grading systems. These devices enable an improved evaluation of knee instability and possible associated injuries. This additional information may promote the development of new treatment algorithms and allow for individualized treatment. In this review, the different subjective laxity scores as well as complementary objective measuring systems are discussed, along with an introduction of injury to an individualized treatment algorithm. PMID:26980119

  1. EDUCATION AND PSYCHOLOGICAL TEST SCORES

    PubMed Central

    Pershad, Dwarka; Verma, S. K.

    1980-01-01

    Education, a long neglected variable affecting psychological test score, is in search of reemphasis. Some evidence for this has accumulated on the psychological tests constructed and standardized here at the department of Psychiatry, P.G.I., Chandigarh. Tentative norms prepared education wise on WAIS-Verbal section, PGI-Memory Scale, Proverb and Similarity Tests, Psychoticism Questionnaire, and PGI MQN 2, for adults, in the age range of 16-50, are reported. The results showed marked difference in the mean scores of different educational categories and thus stressed the need for reporting norms separately for different educational levels. PMID:22064617

  2. Education and psychological test scores.

    PubMed

    Pershad, D; Verma, S K

    1980-04-01

    Education, a long neglected variable affecting psychological test score, is in search of reemphasis. Some evidence for this has accumulated on the psychological tests constructed and standardized here at the department of Psychiatry, P.G.I., Chandigarh. Tentative norms prepared education wise on WAIS-Verbal section, PGI-Memory Scale, Proverb and Similarity Tests, Psychoticism Questionnaire, and PGI MQN 2, for adults, in the age range of 16-50, are reported. The results showed marked difference in the mean scores of different educational categories and thus stressed the need for reporting norms separately for different educational levels. PMID:22064617

  3. Estimating Decision Indices Based on Composite Scores

    ERIC Educational Resources Information Center

    Knupp, Tawnya Lee

    2009-01-01

    The purpose of this study was to develop an IRT model that would enable the estimation of decision indices based on composite scores. The composite scores, defined as a combination of unidimensional test scores, were either a total raw score or an average scale score. Additionally, estimation methods for the normal and compound multinomial models…

  4. A Bootstrap Procedure of Propensity Score Estimation

    ERIC Educational Resources Information Center

    Bai, Haiyan

    2013-01-01

    Propensity score estimation plays a fundamental role in propensity score matching for reducing group selection bias in observational data. To increase the accuracy of propensity score estimation, the author developed a bootstrap propensity score. The commonly used propensity score matching methods: nearest neighbor matching, caliper matching, and…

  5. Weighting Regressions by Propensity Scores

    ERIC Educational Resources Information Center

    Freedman, David A.; Berk, Richard A.

    2008-01-01

    Regressions can be weighted by propensity scores in order to reduce bias. However, weighting is likely to increase random error in the estimates, and to bias the estimated standard errors downward, even when selection mechanisms are well understood. Moreover, in some cases, weighting will increase the bias in estimated causal parameters. If…

  6. Seniors Increase Scores on NAEP

    ERIC Educational Resources Information Center

    Gewertz, Catherine

    2010-01-01

    The latest administration of the assessment provides state-by-state results for 12th graders for the first time. Twelfth graders' reading and mathematics scores on the National Assessment of Educational Progress have improved only modestly in the past four years, according to results from the latest administration, prompting renewed recognition…

  7. Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors.

    PubMed

    Fanfrlík, Jindřich; Brahmkshatriya, Pathik S; Řezáč, Jan; Jílková, Adéla; Horn, Martin; Mareš, Michael; Hobza, Pavel; Lepšík, Martin

    2013-12-01

    The quantum mechanics (QM)-based scoring function that we previously developed for the description of noncovalent binding in protein-ligand complexes has been modified and extended to treat covalent binding of inhibitory ligands. The enhancements are (i) the description of the covalent bond breakage and formation using hybrid QM/semiempirical QM (QM/SQM) restrained optimizations and (ii) the addition of the new ΔG(cov)' term to the noncovalent score, describing the "free" energy difference between the covalent and noncovalent complexes. This enhanced QM-based scoring function is applied to a series of 20 vinyl sulfone-based inhibitory compounds inactivating the cysteine peptidase cathepsin B1 of the Schistosoma mansoni parasite (SmCB1). The available X-ray structure of the SmCB1 in complex with a potent vinyl sulfone inhibitor K11017 is used as a template to build the other covalently bound complexes and to model the derived noncovalent complexes. We present the correlation of the covalent score and its constituents with the experimental binding data. Four outliers are identified. They contain bulky R1' substituents structurally divergent from the template, which might induce larger protein rearrangements than could be accurately modeled. In summary, we propose a new computational approach and an optimal protocol for the rapid evaluation and prospective design of covalent inhibitors with a conserved binding mode. PMID:24195769

  8. Accurate upwind methods for the Euler equations

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1993-01-01

    A new class of piecewise linear methods for the numerical solution of the one-dimensional Euler equations of gas dynamics is presented. These methods are uniformly second-order accurate, and can be considered as extensions of Godunov's scheme. With an appropriate definition of monotonicity preservation for the case of linear convection, it can be shown that they preserve monotonicity. Similar to Van Leer's MUSCL scheme, they consist of two key steps: a reconstruction step followed by an upwind step. For the reconstruction step, a monotonicity constraint that preserves uniform second-order accuracy is introduced. Computational efficiency is enhanced by devising a criterion that detects the 'smooth' part of the data where the constraint is redundant. The concept and coding of the constraint are simplified by the use of the median function. A slope steepening technique, which has no effect at smooth regions and can resolve a contact discontinuity in four cells, is described. As for the upwind step, existing and new methods are applied in a manner slightly different from those in the literature. These methods are derived by approximating the Euler equations via linearization and diagonalization. At a 'smooth' interface, Harten, Lax, and Van Leer's one intermediate state model is employed. A modification for this model that can resolve contact discontinuities is presented. Near a discontinuity, either this modified model or a more accurate one, namely, Roe's flux-difference splitting. is used. The current presentation of Roe's method, via the conceptually simple flux-vector splitting, not only establishes a connection between the two splittings, but also leads to an admissibility correction with no conditional statement, and an efficient approximation to Osher's approximate Riemann solver. These reconstruction and upwind steps result in schemes that are uniformly second-order accurate and economical at smooth regions, and yield high resolution at discontinuities.

  9. Linear score tests for variance components in linear mixed models and applications to genetic association studies.

    PubMed

    Qu, Long; Guennel, Tobias; Marshall, Scott L

    2013-12-01

    Following the rapid development of genome-scale genotyping technologies, genetic association mapping has become a popular tool to detect genomic regions responsible for certain (disease) phenotypes, especially in early-phase pharmacogenomic studies with limited sample size. In response to such applications, a good association test needs to be (1) applicable to a wide range of possible genetic models, including, but not limited to, the presence of gene-by-environment or gene-by-gene interactions and non-linearity of a group of marker effects, (2) accurate in small samples, fast to compute on the genomic scale, and amenable to large scale multiple testing corrections, and (3) reasonably powerful to locate causal genomic regions. The kernel machine method represented in linear mixed models provides a viable solution by transforming the problem into testing the nullity of variance components. In this study, we consider score-based tests by choosing a statistic linear in the score function. When the model under the null hypothesis has only one error variance parameter, our test is exact in finite samples. When the null model has more than one variance parameter, we develop a new moment-based approximation that performs well in simulations. Through simulations and analysis of real data, we demonstrate that the new test possesses most of the aforementioned characteristics, especially when compared to existing quadratic score tests or restricted likelihood ratio tests. PMID:24328714

  10. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

    PubMed

    González-Pérez, Abel; López-Bigas, Nuria

    2011-04-01

    Several large ongoing initiatives that profit from next-generation sequencing technologies have driven--and in coming years will continue to drive--the emergence of long catalogs of missense single-nucleotide variants (SNVs) in the human genome. As a consequence, researchers have developed various methods and their related computational tools to classify these missense SNVs as probably deleterious or probably neutral polymorphisms. The outputs produced by each of these computational tools are of different natures and thus difficult to compare and integrate. Taking advantage of the possible complementarity between different tools might allow more accurate classifications. Here we propose an effective approach to integrating the output of some of these tools into a unified classification; this approach is based on a weighted average of the normalized scores of the individual methods (WAS). (In this paper, the approach is illustrated for the integration of five tools.) We show that this WAS outperforms each individual method in the task of classifying missense SNVs as deleterious or neutral. Furthermore, we demonstrate that this WAS can be used not only for classification purposes (deleterious versus neutral mutation) but also as an indicator of the impact of the mutation on the functionality of the mutant protein. In other words, it may be used as a deleteriousness score of missense SNVs. Therefore, we recommend the use of this WAS as a consensus deleteriousness score of missense mutations (Condel). PMID:21457909

  11. Accurate Measurements of Dielectric and Optical Functions of Liquid Water and Liquid Benzene in the VUV Region (1-100 eV) Using Small-Angle Inelastic X-ray Scattering.

    PubMed

    Hayashi, Hisashi; Hiraoka, Nozomu

    2015-04-30

    Using a third-generation synchrotron source (the BL12XU beamline at SPring-8), inelastic X-ray scattering (IXS) spectra of liquid water and liquid benzene were measured at energy losses of 1-100 eV with 0.24 eV resolution for small momentum transfers (q) of 0.23 and 0.32 au with ±0.06 au uncertainty for q. For both liquids, the IXS profiles at these values of q converged well after we corrected for multiple scattering, and these results confirmed the dipole approximation for q ≤ ∼0.3 au. Several dielectric and optical functions [including the optical oscillator strength distribution (OOS), the optical energy-loss function (OLF), the complex dielectric function, the complex index of refraction, and the reflectance] in the vacuum ultraviolet region were derived and tabulated from these small-angle (small q) IXS spectra. These new data were compared with previously obtained results, and this comparison demonstrated the strong reproducibility and accuracy of IXS spectroscopy. For both water and benzene, there was a notable similarity between the OOSs of the liquids and amorphous solids, and there was no evidence of plasmon excitation in the OLF. The static structure factor [S(q)] for q ≤ ∼0.3 au was also deduced and suggests that molecular models that include electron correlation effects can serve as a good approximation for the liquid S(q) values over the full range of q.

  12. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  13. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  14. Can Contemporary Density Functional Theory Predict Energy Spans in Molecular Catalysis Accurately Enough To Be Applicable for in Silico Catalyst Design? A Computational/Experimental Case Study for the Ruthenium-Catalyzed Hydrogenation of Olefins.

    PubMed

    Rohmann, Kai; Hölscher, Markus; Leitner, Walter

    2016-01-13

    The catalytic hydrogenation of cyclohexene and 1-methylcyclohexene is investigated experimentally and by means of density functional theory (DFT) computations using novel ruthenium Xantphos(Ph) (4,5-bis(diphenylphosphino)-9,9-dimethylxanthene) and Xantphos(Cy) (4,5-bis(dicyclohexylphosphino)-9,9-dimethylxanthene) precatalysts [Ru(Xantphos(Ph))(PhCO2)(Cl)] (1) and [Ru(Xantphos(Cy))(PhCO2)(Cl)] (2), the synthesis, characterization, and crystal structures of which are reported. The intention of this work is to (i) understand the reaction mechanisms on the microscopic level and (ii) compare experimentally observed activation barriers with computed barriers. The Gibbs free activation energy ΔG(⧧) was obtained experimentally with precatalyst 1 from Eyring plots for the hydrogenation of cyclohexene (ΔG(⧧) = 17.2 ± 1.0 kcal/mol) and 1-methylcyclohexene (ΔG(⧧) = 18.8 ± 2.4 kcal/mol), while the Gibbs free activation energy ΔG(⧧) for the hydrogenation of cyclohexene with precatalyst 2 was determined to be 21.1 ± 2.3 kcal/mol. Plausible activation pathways and catalytic cycles were computed in the gas phase (M06-L/def2-SVP). A variety of popular density functionals (ωB97X-D, LC-ωPBE, CAM-B3LYP, B3LYP, B97-D3BJ, B3LYP-D3, BP86-D3, PBE0-D3, M06-L, MN12-L) were used to reoptimize the turnover determining states in the solvent phase (DF/def2-TZVP; IEF-PCM and/or SMD) to investigate how well the experimentally obtained activation barriers can be reproduced by the calculations. The density functionals B97-D3BJ, MN12-L, M06-L, B3LYP-D3, and CAM-B3LYP reproduce the experimentally observed activation barriers for both olefins very well with very small (0.1 kcal/mol) to moderate (3.0 kcal/mol) mean deviations from the experimental values indicating for the field of hydrogenation catalysis most of these functionals to be useful for in silico catalyst design prior to experimental work. PMID:26713773

  15. Do Examinees Understand Score Reports for Alternate Methods of Scoring Computer Based Tests?

    ERIC Educational Resources Information Center

    Whittaker, Tiffany A.; Williams, Natasha J.; Dodd, Barbara G.

    2011-01-01

    This study assessed the interpretability of scaled scores based on either number correct (NC) scoring for a paper-and-pencil test or one of two methods of scoring computer-based tests: an item pattern (IP) scoring method and a method based on equated NC scoring. The equated NC scoring method for computer-based tests was proposed as an alternative…

  16. Interpreting force concept inventory scores: Normalized gain and SAT scores

    NASA Astrophysics Data System (ADS)

    Coletta, Vincent P.; Phillips, Jeffrey A.; Steinert, Jeffrey J.

    2007-06-01

    Preinstruction SAT scores and normalized gains (G) on the force concept inventory (FCI) were examined for individual students in interactive engagement (IE) courses in introductory mechanics at one high school (N=335) and one university (N=292) , and strong, positive correlations were found for both populations ( r=0.57 and r=0.46 , respectively). These correlations are likely due to the importance of cognitive skills and abstract reasoning in learning physics. The larger correlation coefficient for the high school population may be a result of the much shorter time interval between taking the SAT and studying mechanics, because the SAT may provide a more current measure of abilities when high school students begin the study of mechanics than it does for college students, who begin mechanics years after the test is taken. In prior research a strong correlation between FCI G and scores on Lawson’s Classroom Test of Scientific Reasoning for students from the same two schools was observed. Our results suggest that, when interpreting class average normalized FCI gains and comparing different classes, it is important to take into account the variation of students’ cognitive skills, as measured either by the SAT or by Lawson’s test. While Lawson’s test is not commonly given to students in most introductory mechanics courses, SAT scores provide a readily available alternative means of taking account of students’ reasoning abilities. Knowing the students’ cognitive level before instruction also allows one to alter instruction or to use an intervention designed to improve students’ cognitive level.

  17. Dictyostelium possesses highly diverged presenilin/γ-secretase that regulates growth and cell-fate specification and can accurately process human APP: a system for functional studies of the presenilin/γ-secretase complex

    PubMed Central

    McMains, Vanessa C.; Myre, Michael; Kreppel, Lisa; Kimmel, Alan R.

    2010-01-01

    SUMMARY Presenilin (PS) is the catalytic moiety of the γ-secretase complex. PS and other γ-secretase components are well conserved among metazoa, but their presence and function in more-distant species are not resolved. Because inappropriate γ-secretase processing of amyloid precursor protein (APP) in humans is associated with familial Alzheimer’s disease, understanding essential elements within each γ-secretase component is crucial to functional studies. Diverged proteins have been identified in primitive plants but experiments have failed to demonstrate γ-secretase activity. We have identified highly diverged orthologs for each γ-secretase component in the ancient eukaryote Dictyostelium, which lacks equivalents of APP, Notch and other characterized PS/γ-secretase substrates. We show that wild-type (WT) Dictyostelium is capable of amyloidogenic processing of ectopically expressed human APP to generate amyloid-β peptides Aβ40 and Aβ42; strains deficient in γ-secretase cannot produce Aβ peptides but accumulate processed intermediates of APP that co-migrate with the C-terminal fragments α- and β-CTF of APP that are found in mammalian cells. We further demonstrate that Dictyostelium requires PS for phagocytosis and cell-fate specification in a cell-autonomous manner, and show that regulation of phagocytosis requires an active γ-secretase, a pathway suggested, but not proven, to occur in mammalian and Drosophila cells. Our results indicate that PS signaling is an ancient process that arose prior to metazoan radiation, perhaps independently of Notch. Dictyostelium might serve to identify novel PS/γ-secretase signaling targets and provide a unique system for high-throughput screening of small-molecule libraries to select new therapeutic targets for diseases associated with this pathway. PMID:20699477

  18. Dictyostelium possesses highly diverged presenilin/gamma-secretase that regulates growth and cell-fate specification and can accurately process human APP: a system for functional studies of the presenilin/gamma-secretase complex.

    PubMed

    McMains, Vanessa C; Myre, Michael; Kreppel, Lisa; Kimmel, Alan R

    2010-01-01

    Presenilin (PS) is the catalytic moiety of the gamma-secretase complex. PS and other gamma-secretase components are well conserved among metazoa, but their presence and function in more-distant species are not resolved. Because inappropriate gamma-secretase processing of amyloid precursor protein (APP) in humans is associated with familial Alzheimer's disease, understanding essential elements within each gamma-secretase component is crucial to functional studies. Diverged proteins have been identified in primitive plants but experiments have failed to demonstrate gamma-secretase activity. We have identified highly diverged orthologs for each gamma-secretase component in the ancient eukaryote Dictyostelium, which lacks equivalents of APP, Notch and other characterized PS/gamma-secretase substrates. We show that wild-type (WT) Dictyostelium is capable of amyloidogenic processing of ectopically expressed human APP to generate amyloid-beta peptides Abeta(40) and Abeta(42); strains deficient in gamma-secretase cannot produce Abeta peptides but accumulate processed intermediates of APP that co-migrate with the C-terminal fragments alpha- and beta-CTF of APP that are found in mammalian cells. We further demonstrate that Dictyostelium requires PS for phagocytosis and cell-fate specification in a cell-autonomous manner, and show that regulation of phagocytosis requires an active gamma-secretase, a pathway suggested, but not proven, to occur in mammalian and Drosophila cells. Our results indicate that PS signaling is an ancient process that arose prior to metazoan radiation, perhaps independently of Notch. Dictyostelium might serve to identify novel PS/gamma-secretase signaling targets and provide a unique system for high-throughput screening of small-molecule libraries to select new therapeutic targets for diseases associated with this pathway. PMID:20699477

  19. Scoring and Standard Setting with Standardized Patients.

    ERIC Educational Resources Information Center

    Norcini, John J.; And Others

    1993-01-01

    The continuous method of scoring a performance test composed of standardized patients was compared with a derivative method that assigned each of the 131 examinees (medical residents) a dichotomous score, and use of Angoff's method with these scoring methods was studied. Both methods produce reasonable means and distributions of scores. (SLD)

  20. Item Response Modeling with Sum Scores

    ERIC Educational Resources Information Center

    Johnson, Timothy R.

    2013-01-01

    One of the distinctions between classical test theory and item response theory is that the former focuses on sum scores and their relationship to true scores, whereas the latter concerns item responses and their relationship to latent scores. Although item response theory is often viewed as the richer of the two theories, sum scores are still…

  1. An Optimizing Weight For Wrong Scores.

    ERIC Educational Resources Information Center

    Donlon, Thomas F.

    This study empirically determined the optimizing weight to be applied to the Wrongs Total Score in scoring rubrics of the general form = R - kW, where S is the Score, R the Rights Total, k the weight and W the Wrongs Total, if reliability is to be maximized. As is well known, the traditional formula score rests on a theoretical framework which is…

  2. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  3. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  4. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  5. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  6. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  7. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    To understand different aspects of life at the molecular level, one would think that ideally all components of specific processes should be individually isolated and studied in details. Reductionist approaches, i.e., studying one biological event at a one-gene or one-protein-at-a-time basis, indeed have made significant contributions to our understanding of many basic facts of biology. However, these individual “building blocks” can not be visualized as a comprehensive “model” of the life of cells, tissues, and organisms, without using more integrative approaches.1,2 For example, the emerging field of “systems biology” aims to quantify all of the components of a biological system to assess their interactions and to integrate diverse types of information obtainable from this system into models that could explain and predict behaviors.3-6 Recent breakthroughs in genomics, proteomics, and bioinformatics are making this daunting task a reality.7-14 Proteomics, the systematic study of the entire complement of proteins expressed by an organism, tissue, or cell under a specific set of conditions at a specific time (i.e., the proteome), has become an essential enabling component of systems biology. While the genome of an organism may be considered static over short timescales, the expression of that genome as the actual gene products (i.e., mRNAs and proteins) is a dynamic event that is constantly changing due to the influence of environmental and physiological conditions. Exclusive monitoring of the transcriptomes can be carried out using high-throughput cDNA microarray analysis,15-17 however the measured mRNA levels do not necessarily correlate strongly with the corresponding abundances of proteins,18-20 The actual amount of functional proteins can be altered significantly and become independent of mRNA levels as a result of post-translational modifications (PTMs),21 alternative splicing,22,23 and protein turnover.24,25 Moreover, the functions of expressed

  8. Accurately measuring dynamic coefficient of friction in ultraform finishing

    NASA Astrophysics Data System (ADS)

    Briggs, Dennis; Echaves, Samantha; Pidgeon, Brendan; Travis, Nathan; Ellis, Jonathan D.

    2013-09-01

    UltraForm Finishing (UFF) is a deterministic sub-aperture computer numerically controlled grinding and polishing platform designed by OptiPro Systems. UFF is used to grind and polish a variety of optics from simple spherical to fully freeform, and numerous materials from glasses to optical ceramics. The UFF system consists of an abrasive belt around a compliant wheel that rotates and contacts the part to remove material. This work aims to accurately measure the dynamic coefficient of friction (μ), how it changes as a function of belt wear, and how this ultimately affects material removal rates. The coefficient of friction has been examined in terms of contact mechanics and Preston's equation to determine accurate material removal rates. By accurately predicting changes in μ, polishing iterations can be more accurately predicted, reducing the total number of iterations required to meet specifications. We have established an experimental apparatus that can accurately measure μ by measuring triaxial forces during translating loading conditions or while manufacturing the removal spots used to calculate material removal rates. Using this system, we will demonstrate μ measurements for UFF belts during different states of their lifecycle and assess the material removal function from spot diagrams as a function of wear. Ultimately, we will use this system for qualifying belt-wheel-material combinations to develop a spot-morphing model to better predict instantaneous material removal functions.

  9. The Thoracolumbar AOSpine Injury Score.

    PubMed

    Kepler, Christopher K; Vaccaro, Alexander R; Schroeder, Gregory D; Koerner, John D; Vialle, Luiz R; Aarabi, Bizhan; Rajasekaran, Shanmuganathan; Bellabarba, Carlo; Chapman, Jens R; Kandziora, Frank; Schnake, Klaus J; Dvorak, Marcel F; Reinhold, Max; Oner, F Cumhur

    2016-06-01

    Study Design Survey of 100 worldwide spine surgeons. Objective To develop a spine injury score for the AOSpine Thoracolumbar Spine Injury Classification System. Methods Each respondent was asked to numerically grade the severity of each variable of the AOSpine Thoracolumbar Spine Injury Classification System. Using the results, as well as limited input from the AOSpine Trauma Knowledge Forum, the Thoracolumbar AOSpine Injury Score was developed. Results Beginning with 1 point for A1, groups A, B, and C were consecutively awarded an additional point (A1, 1 point; A2, 2 points; A3, 3 points); however, because of a significant increase in the severity between A3 and A4 and because the severity of A4 and B1 was similar, both A4 and B1 were awarded 5 points. An uneven stepwise increase in severity moving from N0 to N4, with a substantial increase in severity between N2 (nerve root injury with radicular symptoms) and N3 (incomplete spinal cord injury) injuries, was identified. Hence, each grade of neurologic injury was progressively given an additional point starting with 0 points for N0, and the substantial difference in severity between N2 and N3 injuries was recognized by elevating N3 to 4 points. Finally, 1 point was awarded to the M1 modifier (indeterminate posterolateral ligamentous complex injury). Conclusion The Thoracolumbar AOSpine Injury Score is an easy-to-use, data-driven metric that will allow for the development of a surgical algorithm to accompany the AOSpine Thoracolumbar Spine Injury Classification System. PMID:27190734

  10. The Thoracolumbar AOSpine Injury Score

    PubMed Central

    Kepler, Christopher K.; Vaccaro, Alexander R.; Schroeder, Gregory D.; Koerner, John D.; Vialle, Luiz R.; Aarabi, Bizhan; Rajasekaran, Shanmuganathan; Bellabarba, Carlo; Chapman, Jens R.; Kandziora, Frank; Schnake, Klaus J.; Dvorak, Marcel F.; Reinhold, Max; Oner, F. Cumhur

    2015-01-01

    Study Design Survey of 100 worldwide spine surgeons. Objective To develop a spine injury score for the AOSpine Thoracolumbar Spine Injury Classification System. Methods Each respondent was asked to numerically grade the severity of each variable of the AOSpine Thoracolumbar Spine Injury Classification System. Using the results, as well as limited input from the AOSpine Trauma Knowledge Forum, the Thoracolumbar AOSpine Injury Score was developed. Results Beginning with 1 point for A1, groups A, B, and C were consecutively awarded an additional point (A1, 1 point; A2, 2 points; A3, 3 points); however, because of a significant increase in the severity between A3 and A4 and because the severity of A4 and B1 was similar, both A4 and B1 were awarded 5 points. An uneven stepwise increase in severity moving from N0 to N4, with a substantial increase in severity between N2 (nerve root injury with radicular symptoms) and N3 (incomplete spinal cord injury) injuries, was identified. Hence, each grade of neurologic injury was progressively given an additional point starting with 0 points for N0, and the substantial difference in severity between N2 and N3 injuries was recognized by elevating N3 to 4 points. Finally, 1 point was awarded to the M1 modifier (indeterminate posterolateral ligamentous complex injury). Conclusion The Thoracolumbar AOSpine Injury Score is an easy-to-use, data-driven metric that will allow for the development of a surgical algorithm to accompany the AOSpine Thoracolumbar Spine Injury Classification System. PMID:27190734

  11. Haemophilia Joint Health Score in healthy adults playing sports.

    PubMed

    Sluiter, D; Foppen, W; de Kleijn, P; Fischer, K

    2014-03-01

    To evaluate outcome of prophylactic clotting factor replacement in children with haemophilia, the Haemophilia Joint Health Score (HJHS) was developed aiming at scoring early joint changes in children aged 4-18. The HJHS has been used for adults on long-term prophylaxis but interpretation of small changes remains difficult. Some changes in these patients may be due to sports-related injuries. Evaluation of HJHS score in healthy adults playing sports could improve the interpretation of this score in haemophilic patients. The aim of this study was to evaluate the HJHS scores in a cohort of young, healthy men participating in sports. Concomitant with a project collecting MRI images of ankles and knees in normal young adults, HJHS scores were assessed in 30 healthy men aged 18-26, participating in sports one to three times per week. One physiotherapist assessed their clinical function using the HJHS 2.1. History of joint injuries was documented. MRI images were scored by a single radiologist, using the International Prophylaxis Study Group additive MRI score. Median age of the study group was 24.3 years (range 19.0-26.4) and median frequency of sports activities was three times per week (range 1-4). Six joints (five knees, one ankle) had a history of sports-related injury. The median overall HJHS score was 0 out of 124 (range 0-3), with 60% of subjects showing no abnormalities on HJHS. All joints were normal on MRI. These results suggest that frequent sports participation and related injuries are not related with abnormalities in HJHS scores.

  12. Accurate adiabatic correction in the hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-01

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10-12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10-7 cm-1, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  13. Accurate adiabatic correction in the hydrogen molecule

    SciTech Connect

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  14. Accurate adiabatic correction in the hydrogen molecule.

    PubMed

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10(-12) at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10(-7) cm(-1), which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels. PMID:25494728

  15. Accurate Weather Forecasting for Radio Astronomy

    NASA Astrophysics Data System (ADS)

    Maddalena, Ronald J.

    2010-01-01

    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; www.gb.nrao.edu/DSS) that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews (www.gb.nrao.edu/ rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  16. Scoring of precision spur gears

    SciTech Connect

    Budinski, K.G. )

    1994-09-01

    A group of manufacturing machines employed precision spur gears as the timing mechanism for machine operations. These machines had worked successfully for about ten years with little or no problems with gear wear or deterioration. When new machines were brought on line with recently made gears there were immediate problems with gear tooth scoring. A laboratory study was conducted to determine if metallurgical conditions were related to the gear scoring. Recent gears were made from a modification of the alloy used in early gears. The new alloy has been modified to make it more resistant to softening in coating operations. Reciprocating wear tests and galling tests were conducted to compare the tribological characteristics of the old and new gear steels. It was determined that the threshold galling stress of the gear steels was strongly dependent on the hardness. The reciprocating wear tests indicated that the wear resistance was affected by the volume fraction of hard phases in the steels. The recommended short-term solution was to alter the tempering procedure for the steel to keep Rockwell C hardness above 60; the long-term solution was to change the gear material and lubrication.

  17. Loop modeling: Sampling, filtering, and scoring

    PubMed Central

    Soto, Cinque S; Fasnacht, Marc; Zhu, Jiang; Forrest, Lucy; Honig, Barry

    2008-01-01

    We describe a fast and accurate protocol, LoopBuilder, for the prediction of loop conformations in proteins. The procedure includes extensive sampling of backbone conformations, side chain addition, the use of a statistical potential to select a subset of these conformations, and, finally, an energy minimization and ranking with an all-atom force field. We find that the Direct Tweak algorithm used in the previously developed LOOPY program is successful in generating an ensemble of conformations that on average are closer to the native conformation than those generated by other methods. An important feature of Direct Tweak is that it checks for interactions between the loop and the rest of the protein during the loop closure process. DFIRE is found to be a particularly effective statistical potential that can bias conformation space toward conformations that are close to the native structure. Its application as a filter prior to a full molecular mechanics energy minimization both improves prediction accuracy and offers a significant savings in computer time. Final scoring is based on the OPLS/SBG-NP force field implemented in the PLOP program. The approach is also shown to be quite successful in predicting loop conformations for cases where the native side chain conformations are assumed to be unknown, suggesting that it will prove effective in real homology modeling applications. Proteins 2008. © 2007 Wiley-Liss, Inc. PMID:17729286

  18. Docking and scoring protein interactions: CAPRI 2009.

    PubMed

    Lensink, Marc F; Wodak, Shoshana J

    2010-11-15

    Protein docking algorithms are assessed by evaluating blind predictions performed during 2007-2009 in Rounds 13-19 of the community-wide experiment on critical assessment of predicted interactions (CAPRI). We evaluated the ability of these algorithms to sample docking poses and to single out specific association modes in 14 targets, representing 11 distinct protein complexes. These complexes play important biological roles in RNA maturation, G-protein signal processing, and enzyme inhibition and function. One target involved protein-RNA interactions not previously considered in CAPRI, several others were hetero-oligomers, or featured multiple interfaces between the same protein pair. For most targets, predictions started from the experimentally determined structures of the free (unbound) components, or from models built from known structures of related or similar proteins. To succeed they therefore needed to account for conformational changes and model inaccuracies. In total, 64 groups and 12 web-servers submitted docking predictions of which 4420 were evaluated. Overall our assessment reveals that 67% of the groups, more than ever before, produced acceptable models or better for at least one target, with many groups submitting multiple high- and medium-accuracy models for two to six targets. Forty-one groups including four web-servers participated in the scoring experiment with 1296 evaluated models. Scoring predictions also show signs of progress evidenced from the large proportion of correct models submitted. But singling out the best models remains a challenge, which also adversely affects the ability to correctly rank docking models. With the increased interest in translating abstract protein interaction networks into realistic models of protein assemblies, the growing CAPRI community is actively developing more efficient and reliable docking and scoring methods for everyone to use.

  19. Individual Differences in Accurately Judging Personality From Text.

    PubMed

    Hall, Judith A; Goh, Jin X; Mast, Marianne Schmid; Hagedorn, Christian

    2016-08-01

    This research examines correlates of accuracy in judging Big Five traits from first-person text excerpts. Participants in six studies were recruited from psychology courses or online. In each study, participants performed a task of judging personality from text and performed other ability tasks and/or filled out questionnaires. Participants who were more accurate in judging personality from text were more likely to be female; had personalities that were more agreeable, conscientious, and feminine, and less neurotic and dominant (all controlling for participant gender); scored higher on empathic concern; self-reported more interest in, and attentiveness to, people's personalities in their daily lives; and reported reading more for pleasure, especially fiction. Accuracy was not associated with SAT scores but had a significant relation to vocabulary knowledge. Accuracy did not correlate with tests of judging personality and emotion based on audiovisual cues. This research is the first to address individual differences in accurate judgment of personality from text, thus adding to the literature on correlates of the good judge of personality.

  20. Scoring with the Computer: Alternative Procedures for Improving the Reliability of Holistic Essay Scoring

    ERIC Educational Resources Information Center

    Attali, Yigal; Lewis, Will; Steier, Michael

    2013-01-01

    Automated essay scoring can produce reliable scores that are highly correlated with human scores, but is limited in its evaluation of content and other higher-order aspects of writing. The increased use of automated essay scoring in high-stakes testing underscores the need for human scoring that is focused on higher-order aspects of writing. This…

  1. scoringRules - A software package for probabilistic model evaluation

    NASA Astrophysics Data System (ADS)

    Lerch, Sebastian; Jordan, Alexander; Krüger, Fabian

    2016-04-01

    Models in the geosciences are generally surrounded by uncertainty, and being able to quantify this uncertainty is key to good decision making. Accordingly, probabilistic forecasts in the form of predictive distributions have become popular over the last decades. With the proliferation of probabilistic models arises the need for decision theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way. Various scoring rules have been developed over the past decades to address this demand. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. As such, they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This poster presents the software package scoringRules for the statistical programming language R, which contains functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. Two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, Bayesian forecasts produced via Markov Chain Monte Carlo take this form. Thereby, the scoringRules package provides a framework for generalized model evaluation that both includes Bayesian as well as classical parametric models. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices.

  2. Field trials of the Baby Check score card in general practice.

    PubMed

    Morley, C J; Thornton, A J; Green, S J; Cole, T J

    1991-01-01

    Sixteen general practitioners (GPs) used the Baby Check score card to assess illness severity in 86 babies under 6 months old. Their reactions to Baby Check were positive: in 79 (92%) it gave an accurate assessment of the baby's illness and 16 (100%) said they would trust it. Fifteen (94%) found it useful, and most of those who did not said the baby was not ill or had an obvious diagnosis. Thirteen (81%) said they would use it and wanted their health visitors and midwives to use it and 15 (94%) wanted the mothers in their practice to use it. The majority (64%) of babies scored 0-7; 31% scored 8 to 19; and only 5% scored over 20. Well babies had low scores, while the two sickest babies, needing urgent hospital treatment, scored 29 and 33. The use of Baby Check by GPs would help them assess babies thoroughly and quantify illness severity objectively.

  3. Reliability and validity of scores from the Singer-Loomis Type Deployment Inventory.

    PubMed

    Arnau, R C; Rosen, D H; Thompson, B

    2000-07-01

    This paper focuses on the Singer-Loomis Type Deployment Inventory (SL-TDI), which is an alternative to the Myers-Briggs Type Indicator (MBTI). The SL-TDI utilizes a continuous, non-forced choice format and therefore is a more accurate representation of Jung's personality theory of psychological types. The purpose of the study reported here is to evaluate the reliability and validity of scores from the SL-TDI. Specifically, the goals were to (a) provide estimates of the internal consistency of SL-TDI scores; (b) evaluate the divergent validity of SL-TDI scores by examination of their relationships with the scores on a social desirability responding measure; and (c) examine the test-retest stability of scores from the SL-TDI. Strong support was found for both the reliability and validity of SL-TDI scores. PMID:10953511

  4. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    PubMed

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures. PMID:26846813

  5. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    PubMed

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.

  6. Accurate SHAPE-directed RNA structure determination

    PubMed Central

    Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.

    2009-01-01

    Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441

  7. The Scoring of Writing Portfolios: Phase 2

    ERIC Educational Resources Information Center

    White, Edward M.

    2005-01-01

    Although most portfolio evaluation currently uses some adaptation of holistic scoring, the problems with scoring portfolios holistically are many, much more than for essays, and the problems are not readily resolvable. Indeed, many aspects of holistic scoring work against the principles behind portfolio assessment. We have from the start needed a…

  8. Local Linear Observed-Score Equating

    ERIC Educational Resources Information Center

    Wiberg, Marie; van der Linden, Wim J.

    2011-01-01

    Two methods of local linear observed-score equating for use with anchor-test and single-group designs are introduced. In an empirical study, the two methods were compared with the current traditional linear methods for observed-score equating. As a criterion, the bias in the equated scores relative to true equating based on Lord's (1980)…

  9. Validation of Automated Scoring of Science Assessments

    ERIC Educational Resources Information Center

    Liu, Ou Lydia; Rios, Joseph A.; Heilman, Michael; Gerard, Libby; Linn, Marcia C.

    2016-01-01

    Constructed response items can both measure the coherence of student ideas and serve as reflective experiences to strengthen instruction. We report on new automated scoring technologies that can reduce the cost and complexity of scoring constructed-response items. This study explored the accuracy of c-rater-ML, an automated scoring engine…

  10. "Score Choice": A Tempest in a Teapot?

    ERIC Educational Resources Information Center

    Hoover, Eric

    2009-01-01

    A new option that allows students to choose which of their test scores to send to colleges has generated renewed criticism of the College Board. College Board officials tout the option, called Score Choice, as a way to ease test taker anxiety. Some prominent admissions officials have publicly described Score Choice as a sales tactic that will…

  11. Smoothing Methods for Estimating Test Score Distributions.

    ERIC Educational Resources Information Center

    Kolen, Michael J.

    1991-01-01

    Estimation/smoothing methods that are flexible enough to fit a wide variety of test score distributions are reviewed: kernel method, strong true-score model-based method, and method that uses polynomial log-linear models. Applications of these methods include describing/comparing test score distributions, estimating norms, and estimating…

  12. Developing Score Reports for Cognitive Diagnostic Assessments

    ERIC Educational Resources Information Center

    Roberts, Mary Roduta; Gierl, Mark J.

    2010-01-01

    This paper presents a framework to provide a structured approach for developing score reports for cognitive diagnostic assessments ("CDAs"). Guidelines for reporting and presenting diagnostic scores are based on a review of current educational test score reporting practices and literature from the area of information design. A sample diagnostic…

  13. Credit Scores, Race, and Residential Sorting

    ERIC Educational Resources Information Center

    Nelson, Ashlyn Aiko

    2010-01-01

    Credit scores have a profound impact on home purchasing power and mortgage pricing, yet little is known about how credit scores influence households' residential location decisions. This study estimates the effects of credit scores on residential sorting behavior using a novel mortgage industry data set combining household demographic, credit, and…

  14. Developmental Sentence Scoring for Japanese (DSSJ)

    PubMed Central

    Miyata, Susanne; MacWhinney, Brian; Otomo, Kiyoshi; Sirai, Hidetosi; Oshima-Takane, Yuriko; Hirakawa, Makiko; Shirai, Yasuhiro; Sugiura, Masatoshi; Itoh, Keiko

    2014-01-01

    This paper reports on the development and use of the Developmental Sentence Scoring for Japanese (DSSJ), a new morpho-syntactical measure for Japanese constructed after the model of the English Developmental Sentence Scoring model (Lee, 1974). Using this measure, we calculated DSSJ scores for 84 children divided into six age groups between 2;8 and 5;2 on the basis of 100-sentence samples collected from free-play child-adult conversations. The analysis showed a high correlation of the DSSJ overall score with the Mean Length of Utterance. The analysis of the DSSJ subarea scores revealed large variations between these subarea scores for children with similar overall DSSJ scores. When investigating the high-scoring children (over 1 SD over group average), most children scored high in three to five subareas, but the combination of scores for these subareas varied from child to child. It is concluded that DSSJ is a valuable tool especially for the language acquisition research. The overall DSSJ score reliably reflects the overall morpho-syntactic development of Japanese children, and the subarea scores provide specific information on individual acquisition patterns. PMID:25414535

  15. Dental maturity in Belgian children using Demirjian's method and polynomial functions: new standard curves for forensic and clinical use.

    PubMed

    Chaillet, N; Willems, G; Demirjian, A

    2004-12-01

    Dental maturity was studied from dental panoramic radiographs of 2523 Belgian children (1255 girls and 1268 boys) aged 2 to 18 years. The aim was to compare the efficiency of two methods of age prediction: Demirjian's method, using differently weighted scores, and polynomial functions. The two methods present some differences: Demirjian is used to determine the maturity score as a function of age and polynomial functions are used to determine age as a function of the maturity score. We present, for each method, gender-specific dental maturity tables and curves for Belgian children. Girls always present advanced dental maturity compared with boys. The polynomial functions are highly reliable (0.21% of incorrect classifications) and the percentile method, using Belgian weighted scores, is very accurate (+/- 2.08 years on average, between 2 and 16 years of age).

  16. Automatic recognition and scoring of olympic rhythmic gymnastic movements.

    PubMed

    Díaz-Pereira, M Pino; Gómez-Conde, Iván; Escalona, Merly; Olivieri, David N

    2014-04-01

    We describe a conceptually simple algorithm for assigning judgement scores to rhythmic gymnastic movements, which could improve scoring objectivity and reduce judgemental bias during competitions. Our method, implemented as a real-time computer vision software, takes a video shot or a live performance video stream as input and extracts detailed velocity field information from body movements, transforming them into specialized spatio-temporal image templates. The collection of such images over time, when projected into a velocity covariance eigenspace, trace out unique but similar trajectories for a particular gymnastic movement type. By comparing separate executions of the same atomic gymnastic routine, our method assigns a quality judgement score that is related to the distance between the respective spatio-temporal trajectories. For several standard gymnastic movements, the method accurately assigns scores that are comparable to those assigned by expert judges. We also describe our rhythmic gymnastic video shot database, which we have made freely available to the human movement research community. The database can be obtained at http://www.milegroup.net/apps/gymdb/. PMID:24502991

  17. Committee Opinion No. 644: The Apgar Score.

    PubMed

    2015-10-01

    The Apgar score provides an accepted and convenient method for reporting the status of the newborn infant immediately after birth and the response to resuscitation if needed. The Apgar score alone cannot be considered to be evidence of or a consequence of asphyxia, does not predict individual neonatal mortality or neurologic outcome, and should not be used for that purpose. An Apgar score assigned during a resuscitation is not equivalent to a score assigned to a spontaneously breathing infant. The American Academy of Pediatrics and the American College of Obstetricians and Gynecologists encourage use of an expanded Apgar score reporting form that accounts for concurrent resuscitative interventions.

  18. Mapping Inundation Uncertainty with a Standard Score (Z-Score) Technique

    NASA Astrophysics Data System (ADS)

    Hadley, B. C.; Schmid, K. A.; Waters, K. J.; Marcy, D. C.

    2010-12-01

    Vertical error in the topographic data is the most important factor affecting the accuracy of single value surface model inundation maps (NRC, 2009). A single value surface model, often referred to as a ‘bathtub’ model, requires two primary topographic input variables: (1) the water surface (i.e. tidal datum + inundation level), and (2) the ground elevation. Unfortunately, both variables include spatially varying vertical error that introduces uncertainty into the resultant map for a given inundation scenario. More sophisticated hydraulic and geomorphic models have their own error budgets, which can be quite complex depending on model assumptions. Standard scores, or z-scores, measure the number of standard deviations an observation falls above or below the mean. This investigation employs z-scores to map the uncertainty introduced by the propagated error associated with the topographic variables. The technique permits greater flexibility than existing uncertainty methods which map the horizontal extension of the elevation data at the 95% confidence level. The vertical error in the water surface variable is due to uncertainties and spatial variability in the hydrodynamic models which drive the tidal datum conversions. The National Geodetic Survey’s (NGS) Vertical Datum Transformation Tool (VDatum) software can be used to convert between tidally referenced and orthometric elevations, but depending on location, results in errors on the order of 5-20 cm. An additional source of uncertainty is the elevation data itself. Most inundation mapping applications employ Digital Elevation Models (DEM) derived from topographic lidar data. Although lidar is among the most accurate large area elevation collection techniques, it has limitations in certain land cover types (e.g. forest or estuarine marsh), and its vertical accuracy can vary both within and between collections. To quantify this variability, accuracy assessments are performed to determine the vertical root mean

  19. Must Kohn-Sham oscillator strengths be accurate at threshold?

    SciTech Connect

    Yang Zenghui; Burke, Kieron; Faassen, Meta van

    2009-09-21

    The exact ground-state Kohn-Sham (KS) potential for the helium atom is known from accurate wave function calculations of the ground-state density. The threshold for photoabsorption from this potential matches the physical system exactly. By carefully studying its absorption spectrum, we show the answer to the title question is no. To address this problem in detail, we generate a highly accurate simple fit of a two-electron spectrum near the threshold, and apply the method to both the experimental spectrum and that of the exact ground-state Kohn-Sham potential.

  20. Inter-Rater Reliability of Total Body Score-A Scale for Quantification of Corpse Decomposition.

    PubMed

    Nawrocka, Marta; Frątczak, Katarzyna; Matuszewski, Szymon

    2016-05-01

    The degree of body decomposition can be quantified using Total Body Score (TBS), a scale frequently used in taphonomic or entomological studies of decomposition. Here, the inter-rater reliability of the scale is analyzed. The study was made on 120 laymen, which were trained in the use of the scale. Participants scored decomposition of pig carcasses from photographs. It was found that the scale, when used by different people, gives homogeneous results irrespective of the user qualifications (the Krippendorff's alfa for all participants was 0.818). The study also indicated that carcasses in advanced decomposition receive significantly less accurate scores. Moreover, it was found that scores for cadavers in mosaic decomposition (i.e., representing signs of at least two stages of decomposition) are less accurate. These results demonstrate that the scale may be regarded as inter-rater reliable. Some propositions for refinement of the scale were also discussed. PMID:27093214

  1. Inter-Rater Reliability of Total Body Score-A Scale for Quantification of Corpse Decomposition.

    PubMed

    Nawrocka, Marta; Frątczak, Katarzyna; Matuszewski, Szymon

    2016-05-01

    The degree of body decomposition can be quantified using Total Body Score (TBS), a scale frequently used in taphonomic or entomological studies of decomposition. Here, the inter-rater reliability of the scale is analyzed. The study was made on 120 laymen, which were trained in the use of the scale. Participants scored decomposition of pig carcasses from photographs. It was found that the scale, when used by different people, gives homogeneous results irrespective of the user qualifications (the Krippendorff's alfa for all participants was 0.818). The study also indicated that carcasses in advanced decomposition receive significantly less accurate scores. Moreover, it was found that scores for cadavers in mosaic decomposition (i.e., representing signs of at least two stages of decomposition) are less accurate. These results demonstrate that the scale may be regarded as inter-rater reliable. Some propositions for refinement of the scale were also discussed.

  2. Improving iris recognition performance using segmentation, quality enhancement, match score fusion, and indexing.

    PubMed

    Vatsa, Mayank; Singh, Richa; Noore, Afzel

    2008-08-01

    This paper proposes algorithms for iris segmentation, quality enhancement, match score fusion, and indexing to improve both the accuracy and the speed of iris recognition. A curve evolution approach is proposed to effectively segment a nonideal iris image using the modified Mumford-Shah functional. Different enhancement algorithms are concurrently applied on the segmented iris image to produce multiple enhanced versions of the iris image. A support-vector-machine-based learning algorithm selects locally enhanced regions from each globally enhanced image and combines these good-quality regions to create a single high-quality iris image. Two distinct features are extracted from the high-quality iris image. The global textural feature is extracted using the 1-D log polar Gabor transform, and the local topological feature is extracted using Euler numbers. An intelligent fusion algorithm combines the textural and topological matching scores to further improve the iris recognition performance and reduce the false rejection rate, whereas an indexing algorithm enables fast and accurate iris identification. The verification and identification performance of the proposed algorithms is validated and compared with other algorithms using the CASIA Version 3, ICE 2005, and UBIRIS iris databases.

  3. Automated scoring of regional lung perfusion in children from contrast enhanced 3D MRI

    NASA Astrophysics Data System (ADS)

    Heimann, Tobias; Eichinger, Monika; Bauman, Grzegorz; Bischoff, Arved; Puderbach, Michael; Meinzer, Hans-Peter

    2012-03-01

    MRI perfusion images give information about regional lung function and can be used to detect pulmonary pathologies in cystic fibrosis (CF) children. However, manual assessment of the percentage of pathologic tissue in defined lung subvolumes features large inter- and intra-observer variation, making it difficult to determine disease progression consistently. We present an automated method to calculate a regional score for this purpose. First, lungs are located based on thresholding and morphological operations. Second, statistical shape models of left and right children's lungs are initialized at the determined locations and used to precisely segment morphological images. Segmentation results are transferred to perfusion maps and employed as masks to calculate perfusion statistics. An automated threshold to determine pathologic tissue is calculated and used to determine accurate regional scores. We evaluated the method on 10 MRI images and achieved an average surface distance of less than 1.5 mm compared to manual reference segmentations. Pathologic tissue was detected correctly in 9 cases. The approach seems suitable for detecting early signs of CF and monitoring response to therapy.

  4. Clinical Importance of the Heel Drop Test and a New Clinical Score for Adult Appendicitis

    PubMed Central

    Ahn, Shin; Lee, Hyeji; Choi, Wookjin; Ahn, Ryeok; Hong, Jung-Suk; Sohn, Chang Hwan; Seo, Dong Woo; Lee, Yoon-Seon; Lim, Kyung Soo; Kim, Won Young

    2016-01-01

    Objective We tried to evaluate the accuracy of the heel drop test in patients with suspected appendicitis and tried to develop a new clinical score, which incorporates the heel drop test and other parameters, for the diagnosis of this condition. Methods We performed a prospective observational study on adult patients with suspected appendicitis at two academic urban emergency departments between January and August 2015. The predictive characteristics of each parameter, along with heel drop test results were calculated. A composite score was generated by logistic regression analysis. The performance of the generated score was compared to that of the Alvarado score. Results Of the 292 enrolled patients, 165 (56.5%) had acute appendicitis. The heel drop test had a higher predictive value than rebound tenderness. Variables and their points included in the new (MESH) score were pain migration (2), elevated white blood cell (WBC) >10,000/μL (3), shift to left (2), and positive heel drop test (3). The MESH score had a higher AUC than the Alvarado score (0.805 vs. 0.701). Scores of 5 and 11 were chosen as cut-off values; a MESH score ≥5 compared to an Alvarado score ≥5, and a MESH score ≥8 compared to an Alvarado score ≥7 showed better performance in diagnosing appendicitis. Conclusion MESH (migration, elevated WBC, shift to left, and heel drop test) is a simple clinical scoring system for assessing patients with suspected appendicitis and is more accurate than the Alvarado score. Further validation studies are needed. PMID:27723842

  5. Dental maturity curves in Finnish children: Demirjian's method revisited and polynomial functions for age estimation.

    PubMed

    Chaillet, Nils; Nyström, Marjatta; Kataja, Matti; Demirjian, Arto

    2004-11-01

    Dental maturity was studied from 2213 dental panoramic radiographs of healthy ethnic Finns from southern Finland, aged between 2 and 19 years. The aim was to provide new Finnish maturity tables and curves and to compare the efficiency of Demirjian's method when differently weighted scores and polynomial regressions are used. The inter-ethnic variations lead us to calculate specific Finnish weighted scores. Demirjian's method gives maturity score as a function of age and seems better adapted for clinicians because, in their case, the maturity score is unknown. Polynomial functions give age as a function of maturity score and are statically adapted for age estimation studies. Finnish dental maturity tables and development curves are given for Demirjian's method and for polynomial functions. Sexual dimorphism is established for the same weighted score for girls and boys, and girls present a greater maturity than boys for all of age groups. Polynomial functions are highly reliable (0.19% of misclassifies) and the percentile method, using Finnish weighted scores, is very accurate (+/- 1.95 years on average, between 2 and 18 years of age). This suggests that polynomial functions are most useful in forensic sciences, while Demirjian's method is most useful for dental health clinicians.

  6. Proposal of a Mediterranean Diet Serving Score

    PubMed Central

    Monteagudo, Celia; Mariscal-Arcas, Miguel; Rivas, Ana; Lorenzo-Tovar, María Luisa; Tur, Josep A.; Olea-Serrano, Fátima

    2015-01-01

    Background and Aims Numerous studies have demonstrated a relationship between Mediterranean Diet (MD) adherence and the prevention of cardiovascular diseases, cancer, and diabetes, etc. The study aim was to validate a novel instrument to measure MD adherence based on the consumption of food servings and food groups, and apply it in a female population from southern Spain and determining influential factors. Methods and Results The study included 1,155 women aged 12-83 yrs, classified as adolescents, adults, and over-60-yr-olds. All completed a validated semi-quantitative food frequency questionnaire (FFQ). The Mediterranean Dietary Serving Score (MDSS) is based on the latest update of the Mediterranean Diet Pyramid, using the recommended consumption frequency of foods and food groups; the MDSS ranges from 0 to 24. The discriminative power or correct subject classification capacity of the MDSS was analyzed with the Receiver Operating Characteristic (ROC) curve, using the MDS as reference method. Predictive factors for higher MDSS adherence were determined with a logistic regression model, adjusting for age. According to ROC curve analysis, MDSS evidenced a significant discriminative capacity between adherents and non-adherents to the MD pattern (optimal cutoff point=13.50; sensitivity=74%; specificity=48%). The mean MDSS was 12.45 (2.69) and was significantly higher with older age (p<0.001). Logistic regression analysis showed highest MD adherence by over 60-year-olds with low BMI and no habit of eating between meals. Conclusions The MDSS is an updated, easy, valid, and accurate instrument to assess MD adherence based on the consumption of foods and food groups per meal, day, and week. It may be useful in future nutritional education programs to prevent the early onset of chronic non-transmittable diseases in younger populations. PMID:26035442

  7. Some Results on Mean Square Error for Factor Score Prediction

    ERIC Educational Resources Information Center

    Krijnen, Wim P.

    2006-01-01

    For the confirmatory factor model a series of inequalities is given with respect to the mean square error (MSE) of three main factor score predictors. The eigenvalues of these MSE matrices are a monotonic function of the eigenvalues of the matrix gamma[subscript rho] = theta[superscript 1/2] lambda[subscript rho] 'psi[subscript rho] [superscript…

  8. Building a User-Oriented Statewide Score Reporting System.

    ERIC Educational Resources Information Center

    Bunch, Michael B.

    In 1983 the Maryland State Department of Public Education (MSDE) issued a request for proposals for "The Development of the Score Reporting System for the Maryland Functional Testing Program." The MSDE called for a literature review, a national survey, a statewide survey of user needs and capabilities, an assessment of the state's report producing…

  9. Developmental Sentence Scoring: Still Useful after All These Years.

    ERIC Educational Resources Information Center

    Hughes, Diana L.; And Others

    1992-01-01

    Developmental Sentence Scoring (DSS) is a measure of spoken syntax that provides a numeric variable, provides some developmental data, and serves an organizing function for asking and answering clinical questions. DSS is useful in making diagnostic judgments, selecting goals and planning treatment, and measuring intervention efficacy. Difficulties…

  10. The highly accurate anteriolateral portal for injecting the knee

    PubMed Central

    2011-01-01

    Background The extended knee lateral midpatellar portal for intraarticular injection of the knee is accurate but is not practical for all patients. We hypothesized that a modified anteriolateral portal where the synovial membrane of the medial femoral condyle is the target would be highly accurate and effective for intraarticular injection of the knee. Methods 83 subjects with non-effusive osteoarthritis of the knee were randomized to intraarticular injection using the modified anteriolateral bent knee versus the standard lateral midpatellar portal. After hydrodissection of the synovial membrane with lidocaine using a mechanical syringe (reciprocating procedure device), 80 mg of triamcinolone acetonide were injected into the knee with a 2.0-in (5.1-cm) 21-gauge needle. Baseline pain, procedural pain, and pain at outcome (2 weeks and 6 months) were determined with the 10 cm Visual Analogue Pain Score (VAS). The accuracy of needle placement was determined by sonographic imaging. Results The lateral midpatellar and anteriolateral portals resulted in equivalent clinical outcomes including procedural pain (VAS midpatellar: 4.6 ± 3.1 cm; anteriolateral: 4.8 ± 3.2 cm; p = 0.77), pain at outcome (VAS midpatellar: 2.6 ± 2.8 cm; anteriolateral: 1.7 ± 2.3 cm; p = 0.11), responders (midpatellar: 45%; anteriolateral: 56%; p = 0.33), duration of therapeutic effect (midpatellar: 3.9 ± 2.4 months; anteriolateral: 4.1 ± 2.2 months; p = 0.69), and time to next procedure (midpatellar: 7.3 ± 3.3 months; anteriolateral: 7.7 ± 3.7 months; p = 0.71). The anteriolateral portal was 97% accurate by real-time ultrasound imaging. Conclusion The modified anteriolateral bent knee portal is an effective, accurate, and equivalent alternative to the standard lateral midpatellar portal for intraarticular injection of the knee. Trial Registration ClinicalTrials.gov: NCT00651625 PMID:21447197

  11. Accurate Thermal Conductivities from First Principles

    NASA Astrophysics Data System (ADS)

    Carbogno, Christian

    2015-03-01

    In spite of significant research efforts, a first-principles determination of the thermal conductivity at high temperatures has remained elusive. On the one hand, Boltzmann transport techniques that include anharmonic effects in the nuclear dynamics only perturbatively become inaccurate or inapplicable under such conditions. On the other hand, non-equilibrium molecular dynamics (MD) methods suffer from enormous finite-size artifacts in the computationally feasible supercells, which prevent an accurate extrapolation to the bulk limit of the thermal conductivity. In this work, we overcome this limitation by performing ab initio MD simulations in thermodynamic equilibrium that account for all orders of anharmonicity. The thermal conductivity is then assessed from the auto-correlation function of the heat flux using the Green-Kubo formalism. Foremost, we discuss the fundamental theory underlying a first-principles definition of the heat flux using the virial theorem. We validate our approach and in particular the techniques developed to overcome finite time and size effects, e.g., by inspecting silicon, the thermal conductivity of which is particularly challenging to converge. Furthermore, we use this framework to investigate the thermal conductivity of ZrO2, which is known for its high degree of anharmonicity. Our calculations shed light on the heat resistance mechanism active in this material, which eventually allows us to discuss how the thermal conductivity can be controlled by doping and co-doping. This work has been performed in collaboration with R. Ramprasad (University of Connecticut), C. G. Levi and C. G. Van de Walle (University of California Santa Barbara).

  12. The Validity of Law School Admission Test Scores for Repeaters: A Replication. LSAT Technical Report. LSAC Research Report Series.

    ERIC Educational Resources Information Center

    Dalessandro, Susan P.; McLeod, Lori D.

    The fair and accurate treatment of multiple test scores for law school applicants who take the Law School Admission Test (LSAT) more than one time is the focus of this study. The study reexamines the differential validity and predictive accuracy of the different test scores that are presented by repeat test takers. The study includes U.S. law…

  13. Are the Best Scores the Best Scores for Predicting College Success?

    ERIC Educational Resources Information Center

    Patterson, Brian F.; Mattern, Krista D.; Swerdzewski, Peter

    2012-01-01

    The College Board's SAT[R] Score Choice[TM] policy allows students to choose which set(s) of scores to send to colleges and universities to which they plan to apply. Based on data gathered before the implementation of that policy, the following study evaluated the predictive validity of the various sets of SAT scores. The value of five score sets…

  14. Relationship between Praxis 1 Scores and SAT/ACT Scores: A Correlational Study

    ERIC Educational Resources Information Center

    Saravanabhavan, Sheila; Jones, Enid B.; Wilson, Carolyn H.

    2005-01-01

    The purpose of this paper is to test the premise that there is a significant correlation between Praxis1 scores and SAT scores among African American students who are applying for admission into the teacher education program. Data for the study included the Praxis 1 (reading, writing and math) scores and SAT (reading, writing and math) scores of…

  15. The Influence of an NCLB Accountability Plan on the Distribution of Student Test Score Gains

    ERIC Educational Resources Information Center

    Springer, Matthew G.

    2008-01-01

    Previous research on the effect of accountability programs on the distribution of student test score gains is decidedly mixed. This study examines the issue by estimating an educational production function in which test score gains are a function of the incentives schools have to focus instruction on below-proficient students. NCLB's threat of…

  16. Development of dengue infection severity score.

    PubMed

    Pongpan, Surangrat; Wisitwong, Apichart; Tawichasri, Chamaiporn; Patumanond, Jayanton; Namwongprom, Sirianong

    2013-01-01

    Objectives. To develop a simple scoring system to predict dengue infection severity based on patient characteristics and routine clinical profiles. Methods. Retrospective data of children with dengue infection from 3 general hospitals in Thailand were reviewed. Dengue infection was categorized into 3 severity levels: dengue infection (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS). Coefficients of significant predictors of disease severity under ordinal regression analysis were transformed into item scores. Total scores were used to classify patients into 3 severity levels. Results. Significant clinical predictors of dengue infection severity were age >6 years, hepatomegaly, hematocrit ≥40%, systolic pressure <90 mmHg, white cell count >5000 / μ L, and platelet ≤50000 / μ L. The derived total scores, which ranged from 0 to 18, classified patients into 3 severity levels: DF (scores <2.5, n = 451, 58.1%), DHF (scores 2.5-11.5, n = 276, 35.5%), and DSS (scores >11.5, n = 50, 6.4%). The derived score correctly classified patients into their original severity levels in 60.7%. An under-estimation of 25.7% and an over-estimation of 13.5% were clinically acceptable. Conclusions. The derived dengue infection severity score classified patients into DF, DHF, or DSS, correctly into their original severity levels. Validation of the score should be reconfirmed before application of routine practice.

  17. Prospective validation of the CLIP score: a new prognostic system for patients with cirrhosis and hepatocellular carcinoma. The Cancer of the Liver Italian Program (CLIP) Investigators.

    PubMed

    2000-04-01

    Prognosis of patients with cirrhosis and hepatocellular carcinoma (HCC) depends on both residual liver function and tumor extension. The CLIP score includes Child-Pugh stage, tumor morphology and extension, serum alfa-fetoprotein (AFP) levels, and portal vein thrombosis. We externally validated the CLIP score and compared its discriminatory ability and predictive power with that of the Okuda staging system in 196 patients with cirrhosis and HCC prospectively enrolled in a randomized trial. No significant associations were found between the CLIP score and the age, sex, and pattern of viral infection. There was a strong correlation between the CLIP score and the Okuda stage. As of June 1999, 150 patients (76.5%) had died. Median survival time was 11 months, overall, and it was 36, 22, 9, 7, and 3 months for CLIP categories 0, 1, 2, 3, and 4 to 6, respectively. In multivariate analysis, the CLIP score had additional explanatory power above that of the Okuda stage. This was true for both patients treated with locoregional therapy or not. A quantitative estimation of 2-year survival predictive power showed that the CLIP score explained 37% of survival variability, compared with 21% explained by Okuda stage. In conclusion, the CLIP score, compared with the Okuda staging system, gives more accurate prognostic information, is statistically more efficient, and has a greater survival predictive power. It could be useful in treatment planning by improving baseline prognostic evaluation of patients with HCC, and could be used in prospective therapeutic trials as a stratification variable, reducing the variability of results owing to patient selection.

  18. Mill profiler machines soft materials accurately

    NASA Technical Reports Server (NTRS)

    Rauschl, J. A.

    1966-01-01

    Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

  19. Accurate theoretical chemistry with coupled pair models.

    PubMed

    Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan

    2009-05-19

    Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now

  20. Regional myocardial contractile function: multiparametric strain mapping.

    PubMed

    Cupps, Brian P; Taggar, Ajay K; Reynolds, Lina M; Lawton, Jennifer S; Pasque, Michael K

    2010-06-01

    Magnetic resonance imaging (MRI) with tissue tagging enables the quantification of multiple strain indices that can be combined through normalization into a single multiparametric index of regional myocardial contractile function. The aim of this study was to test the ability of multiparametric strain analysis to quantify regional differences in contractile function in an ovine model of myocardial injury. Regional variance in myocardial contractile function was induced in eight sheep by the ligation of the blood supply to the anterior and apical left ventricular (LV) myocardial walls. LV systolic strain was obtained from tissue tagged MRI images. A normal strain database (n=50) defines all parameters of systolic strain and allows normalization of regional function at 15,300 LV points by calculation of a z-score. Multiparametric systolic strain z-scores were therefore determined for 15,300 points in each injured sheep left ventricle. Multiparametric z-scores were found to vary significantly by region (P<0.001). z-Scores in regions remote to the infarct were found to be significantly smaller than those in the regions most likely to include infarcted myocardium. In this pre-clinical evaluation of MRI-based multiparametric strain analysis, it accurately quantified and visually defined regional differences in myocardial contractile function.

  1. Value of the "TAVI2-SCORe" versus surgical risk scores for prediction of one year mortality in 511 patients who underwent transcatheter aortic valve implantation.

    PubMed

    Debonnaire, Philippe; Fusini, Laura; Wolterbeek, Ron; Kamperidis, Vasileios; van Rosendael, Philippe; van der Kley, Frank; Katsanos, Spyridon; Joyce, Emer; Tamborini, Gloria; Muratori, Manuela; Gripari, Paola; Bax, Jeroen J; Marsan, Nina Ajmone; Pepi, Mauro; Delgado, Victoria

    2015-01-15

    A bedside-available transcatheter aortic valve implantation (TAVI)-dedicated prognostic risk score is an unmet clinical need. We aimed to develop such a risk score predicting 1-year mortality post-TAVI and to compare it with the performance of the logistic EuroSCORE (LES) I and LES-II and the Society of Thoracic Surgeons' (STS) score. Baseline variables of 511 consecutive patients who underwent TAVI that were independently associated with 1-year mortality post-TAVI were included in the "TAVI2-SCORe." Discrimination and calibration abilities of the novel score were assessed and compared with surgical risk scores. One-year mortality was 17.0% (n = 80 of 471). Porcelain thoracic aorta (hazard ratio [HR] 2.56), anemia (HR 2.03), left ventricular dysfunction (HR 1.98), recent myocardial infarction (HR 3.78), male sex (HR 1.81), critical aortic valve stenosis (HR 2.46), old age (HR 1.68), and renal dysfunction (HR 1.76) formed the TAVI2-SCORe (all p <0.05). According to the number of points assigned (1 for each variable and 2 for infarction), patients were stratified into 5 risk categories: 0, 1 (HR 2.6), 2 (HR 3.6), 3 (HR 10.5), and ≥4 (HR 17.6). TAVI2-SCORe showed better discrimination ability (Harrells' C statistic 0.715) compared with LES-I, LES-II, and STS score (0.609, 0.633, and 0.50, respectively). Cumulative 1-year survival rate was 54% versus 88% for patients with TAVI2-SCORE ≥3 versus <3 points, respectively (p <0.001). Contrary to surgical risk scores, there was no significant difference between observed and expected 1-year mortality for all TAVI2-SCORe risk strata (all p >0.05, Hosmer-Lemeshow statistic 0.304), suggesting superior calibration performance. In conclusion, the TAVI2-SCORe is an accurate, simple, and bedside-available score predicting 1-year mortality post-TAVI, outperforming conventional surgical risk scores for this end point. PMID:25432413

  2. Development of the Knowledge-based & Empirical Combined Scoring Algorithm (KECSA) to Score Protein-Ligand Interactions

    PubMed Central

    Zheng, Zheng

    2013-01-01

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the PDB. Forty-nine types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training-set and enthalpy/entropy of KECSA The second validation benchmark suite included two large-scale and five small-scale test sets to compare the reproducibility of KECSA with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods especially in its ability to minimize the RMSE. LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed which would KECSA more sensitive to subtle changes in ligand structure. PMID:23560465

  3. Fast and accurate determination of modularity and its effect size

    NASA Astrophysics Data System (ADS)

    Treviño, Santiago, III; Nyberg, Amy; Del Genio, Charo I.; Bassler, Kevin E.

    2015-02-01

    We present a fast spectral algorithm for community detection in complex networks. Our method searches for the partition with the maximum value of the modularity via the interplay of several refinement steps that include both agglomeration and division. We validate the accuracy of the algorithm by applying it to several real-world benchmark networks. On all these, our algorithm performs as well or better than any other known polynomial scheme. This allows us to extensively study the modularity distribution in ensembles of Erdős-Rényi networks, producing theoretical predictions for means and variances inclusive of finite-size corrections. Our work provides a way to accurately estimate the effect size of modularity, providing a z-score measure of it and enabling a more informative comparison of networks with different numbers of nodes and links.

  4. A general formula for computing maximum proportion correct scores in various psychophysical paradigms with arbitrary probability distributions of stimulus observations.

    PubMed

    Dai, Huanping; Micheyl, Christophe

    2015-05-01

    Proportion correct (Pc) is a fundamental measure of task performance in psychophysics. The maximum Pc score that can be achieved by an optimal (maximum-likelihood) observer in a given task is of both theoretical and practical importance, because it sets an upper limit on human performance. Within the framework of signal detection theory, analytical solutions for computing the maximum Pc score have been established for several common experimental paradigms under the assumption of Gaussian additive internal noise. However, as the scope of applications of psychophysical signal detection theory expands, the need is growing for psychophysicists to compute maximum Pc scores for situations involving non-Gaussian (internal or stimulus-induced) noise. In this article, we provide a general formula for computing the maximum Pc in various psychophysical experimental paradigms for arbitrary probability distributions of sensory activity. Moreover, easy-to-use MATLAB code implementing the formula is provided. Practical applications of the formula are illustrated, and its accuracy is evaluated, for two paradigms and two types of probability distributions (uniform and Gaussian). The results demonstrate that Pc scores computed using the formula remain accurate even for continuous probability distributions, as long as the conversion from continuous probability density functions to discrete probability mass functions is supported by a sufficiently high sampling resolution. We hope that the exposition in this article, and the freely available MATLAB code, facilitates calculations of maximum performance for a wider range of experimental situations, as well as explorations of the impact of different assumptions concerning internal-noise distributions on maximum performance in psychophysical experiments.

  5. Correlation between the different pH-metry scores in gastroesophageal reflux disease in children

    PubMed Central

    Lupu, Vasile Valeriu; Ignat, Ancuţa; Paduraru, Gabriela; Ciubara, Anamaria; Moscalu, Mihaela; Marginean, Cristina Oana; Burlea, Marin

    2016-01-01

    Abstract The 24-hour esophageal pH-metry is the most widely used method to diagnose the gastroesophageal reflux disease (GERD). The study compares the different scores obtained during the 24-hour esophageal pH-metry. A retrospective study over 5 years including 234 children (1 month and 18 years old) admitted in a pediatric gastroenterology regional center in Northeast Romania, with suspicion of GERD. They underwent 24- hour esophageal pH-metry, and the scores obtained (Boix-Ochoa, DeMeester, Johnson-DeMeester) were compared. Out of the 234 children, 172 (73.50%) had positive Boix-Ochoa score and 62 (26.50%) had normal Boix-Ochoa score (<11.99). Based on the DeMeester score, 149 children (63.68%) were positive and 85 (36.32%) were negative. The correlation of the Demeester score with the Boix-Ochoa score was very high (r = 0.978, P <  < 0.01, 95% confidence interval). Considering the Johnson-DeMeester score, 120 cases (51.28%) had GERD and 114 (48.72%) did not. The correlation of the Johnson-DeMeester score with the Boix-Ochoa score was still high (r = 0.94, P <  < 0.01, 95% 95% confidence interval). As considered until now, the Boix-Ochoa score is the most accurate score to be used in pediatrics for the diagnosis of GERD. The use of the different scores—Boix-Ochoa, DeMeester, Johnson-DeMeester—showed a high sensitivity and specificity of the pH-metry measurements applied to the study lot, but the last score has a higher risk of false-negative results. PMID:27367982

  6. Analytic Monte Carlo score distributions for future statistical confidence interval studies

    SciTech Connect

    Booth, T.E. )

    1992-10-01

    The interpretation of the statistical error estimates produced by Monte Carlo transport codes is still somewhat of an art. Empirically, there are variance reduction techniques whose error estimates are almost always reliable, and there are variance reduction techniques whose error estimates are often unreliable. Unreliable error estimates usually result from inadequate large score sampling from the score distribution's tail. Statisticians believe that more accurate confidence interval statements are possible if the general nature of the score distribution can be characterized. The analytic score distribution for geometry splitting/Russian roulette applied to a simple Monte Carlo problem and the analytic score distribution for the exponential transform applied to the same Monte Carlo problem are provided in this paper.

  7. [The cardiovascular surgeon and the Syntax score].

    PubMed

    Gómez-Sánchez, Mario; Soulé-Egea, Mauricio; Herrera-Alarcón, Valentín; Barragán-García, Rodolfo

    2015-01-01

    The Syntax score has been established as a tool to determine the complexity of coronary artery disease and as a guide for decision-making among coronary artery bypass surgery and percutaneous coronary intervention. The purpose of this review is to systematically examine what the Syntax score is, and how the surgeon should integrate the information in the selection and treatment of patients. We reviewed the results of the SYNTAX Trial, the clinical practice guidelines, as well as the benefits and limitations of the score. Finally we discuss the future directions of the Syntax score. PMID:25595855

  8. [The cardiovascular surgeon and the Syntax score].

    PubMed

    Gómez-Sánchez, Mario; Soulé-Egea, Mauricio; Herrera-Alarcón, Valentín; Barragán-García, Rodolfo

    2015-01-01

    The Syntax score has been established as a tool to determine the complexity of coronary artery disease and as a guide for decision-making among coronary artery bypass surgery and percutaneous coronary intervention. The purpose of this review is to systematically examine what the Syntax score is, and how the surgeon should integrate the information in the selection and treatment of patients. We reviewed the results of the SYNTAX Trial, the clinical practice guidelines, as well as the benefits and limitations of the score. Finally we discuss the future directions of the Syntax score.

  9. Reliability Assessment of an Innovative Wound Score.

    PubMed

    Strauss, Michael B; Moon, Hojin; Busch, Jeremy A; Jones, Christopher K; Nhan, Lisa; Miller, Stuart; Le, Phi-Nga Jeannie

    2016-06-01

    The authors describe an innovative wound score and demonstrate its versatility for scoring a variety of wound types in addition to diabetic foot ulcers (DFUs). To further test its merits, they determined its interobserver reliability in a prospective series of patients. The Wound Score system the authors created integrates the most important features of 4 predominantly used wound scoring systems. It utilizes a logical 0 to 10 format based on 5 assessments each graded from 2 (best) to 0 (worst). The versatility and reliability of the Wound Score were studied in a prospective series of 94 patients with lower extremity wounds. The Wound Score was quick to determine, applicable to a variety of wound types and locations, and highly objective for grading the severity of each of the 5 assessments. The Wound Score categorized wound types as "healthy," "problem," or "futile" for evaluation and management. Diabetes was present in 75.9%, with 70% of the DFUs scoring in the "problem" wound range. Interobserver reli- ability was high (r = 0.81). The objectivity, versatility, and reliability of the Wound Score system facilitates making decisions about the management of wounds, whether DFUs or not, and provides quantification for compara- tive effectiveness research for wound management. PMID:27377611

  10. Development and Validation of a Disease Severity Scoring Model for Pediatric Sepsis

    PubMed Central

    HU, Li; ZHU, Yimin; CHEN, Mengshi; LI, Xun; LU, Xiulan; LIANG, Ying; TAN, Hongzhuan

    2016-01-01

    Background: Multiple severity scoring systems have been devised and evaluated in adult sepsis, but a simplified scoring model for pediatric sepsis has not yet been developed. This study aimed to develop and validate a new scoring model to stratify the severity of pediatric sepsis, thus assisting the treatment of sepsis in children. Methods: Data from 634 consecutive patients who presented with sepsis at Children’s hospital of Hunan province in China in 2011–2013 were analyzed, with 476 patients placed in training group and 158 patients in validation group. Stepwise discriminant analysis was used to develop the accurate discriminate model. A simplified scoring model was generated using weightings defined by the discriminate coefficients. The discriminant ability of the model was tested by receiver operating characteristic curves (ROC). Results: The discriminant analysis showed that prothrombin time, D-dimer, total bilirubin, serum total protein, uric acid, PaO2/FiO2 ratio, myoglobin were associated with severity of sepsis. These seven variables were assigned with values of 4, 3, 3, 4, 3, 3, 3 respectively based on the standardized discriminant coefficients. Patients with higher scores had higher risk of severe sepsis. The areas under ROC (AROC) were 0.836 for accurate discriminate model, and 0.825 for simplified scoring model in validation group. Conclusions: The proposed disease severity scoring model for pediatric sepsis showed adequate discriminatory capacity and sufficient accuracy, which has important clinical significance in evaluating the severity of pediatric sepsis and predicting its progress. PMID:27516993

  11. Longitudinal clinical score prediction in Alzheimer's disease with soft-split sparse regression based random forest.

    PubMed

    Huang, Lei; Jin, Yan; Gao, Yaozong; Thung, Kim-Han; Shen, Dinggang

    2016-10-01

    Alzheimer's disease (AD) is an irreversible neurodegenerative disease and affects a large population in the world. Cognitive scores at multiple time points can be reliably used to evaluate the progression of the disease clinically. In recent studies, machine learning techniques have shown promising results on the prediction of AD clinical scores. However, there are multiple limitations in the current models such as linearity assumption and missing data exclusion. Here, we present a nonlinear supervised sparse regression-based random forest (RF) framework to predict a variety of longitudinal AD clinical scores. Furthermore, we propose a soft-split technique to assign probabilistic paths to a test sample in RF for more accurate predictions. In order to benefit from the longitudinal scores in the study, unlike the previous studies that often removed the subjects with missing scores, we first estimate those missing scores with our proposed soft-split sparse regression-based RF and then utilize those estimated longitudinal scores at all the previous time points to predict the scores at the next time point. The experiment results demonstrate that our proposed method is superior to the traditional RF and outperforms other state-of-art regression models. Our method can also be extended to be a general regression framework to predict other disease scores. PMID:27500865

  12. Discrepancy Between Clinician and Research Assistant in TIMI Score Calculation (TRIAGED CPU)

    PubMed Central

    Taylor, Brian T.; Mancini, Michelino

    2015-01-01

    Introduction Several studies have attempted to demonstrate that the Thrombolysis in Myocardial Infarction (TIMI) risk score has the ability to risk stratify emergency department (ED) patients with potential acute coronary syndromes (ACS). Most of the studies we reviewed relied on trained research investigators to determine TIMI risk scores rather than ED providers functioning in their normal work capacity. We assessed whether TIMI risk scores obtained by ED providers in the setting of a busy ED differed from those obtained by trained research investigators. Methods This was an ED-based prospective observational cohort study comparing TIMI scores obtained by 49 ED providers admitting patients to an ED chest pain unit (CPU) to scores generated by a team of trained research investigators. We examined provider type, patient gender, and TIMI elements for their effects on TIMI risk score discrepancy. Results Of the 501 adult patients enrolled in the study, 29.3% of TIMI risk scores determined by ED providers and trained research investigators were generated using identical TIMI risk score variables. In our low-risk population the majority of TIMI risk score differences were small; however, 12% of TIMI risk scores differed by two or more points. Conclusion TIMI risk scores determined by ED providers in the setting of a busy ED frequently differ from scores generated by trained research investigators who complete them while not under the same pressure of an ED provider. PMID:25671004

  13. PISA and TIMSS Science Score, Which Clock Is More Accurate to Indicate National Science and Technology Competitiveness?

    ERIC Educational Resources Information Center

    Shi, Wei-Zhao; He, Xiqin; Wang, Yan; Fan, Zeng-Guang; Guo, Liangdong

    2016-01-01

    In 2015, PISA and TIMSS are coming up to us together. In this study, the data from PISA and TIMSS are used to investigate that which one is a better indicator of national science and technology (S&T) competitiveness? Number of S & T journal articles (per million people) is used as a measure to represent the national S&T…

  14. Influence of accurate and inaccurate 'split-time' feedback upon 10-mile time trial cycling performance.

    PubMed

    Wilson, Mathew G; Lane, Andy M; Beedie, Chris J; Farooq, Abdulaziz

    2012-01-01

    The objective of the study is to examine the impact of accurate and inaccurate 'split-time' feedback upon a 10-mile time trial (TT) performance and to quantify power output into a practically meaningful unit of variation. Seven well-trained cyclists completed four randomised bouts of a 10-mile TT on a SRM™ cycle ergometer. TTs were performed with (1) accurate performance feedback, (2) without performance feedback, (3) and (4) false negative and false positive 'split-time' feedback showing performance 5% slower or 5% faster than actual performance. There were no significant differences in completion time, average power output, heart rate or blood lactate between the four feedback conditions. There were significantly lower (p < 0.001) average [Formula: see text] (ml min(-1)) and [Formula: see text] (l min(-1)) scores in the false positive (3,485 ± 596; 119 ± 33) and accurate (3,471 ± 513; 117 ± 22) feedback conditions compared to the false negative (3,753 ± 410; 127 ± 27) and blind (3,772 ± 378; 124 ± 21) feedback conditions. Cyclists spent a greater amount of time in a '20 watt zone' 10 W either side of average power in the negative feedback condition (fastest) than the accurate feedback (slowest) condition (39.3 vs. 32.2%, p < 0.05). There were no significant differences in the 10-mile TT performance time between accurate and inaccurate feedback conditions, despite significantly lower average [Formula: see text] and [Formula: see text] scores in the false positive and accurate feedback conditions. Additionally, cycling with a small variation in power output (10 W either side of average power) produced the fastest TT. Further psycho-physiological research should examine the mechanism(s) why lower [Formula: see text] and [Formula: see text] scores are observed when cycling in a false positive or accurate feedback condition compared to a false negative or blind feedback condition.

  15. Scoring Dawg Core Breakoff and Retention Mechanism

    NASA Technical Reports Server (NTRS)

    Badescu, Mircea; Sherrit, Stewart; Bar-Cohen, Yoseph; Bao, Xiaoqi; Backes, Paul G.

    2011-01-01

    This novel core break-off and retention mechanism consists of a scoring dawg controlled by a set of two tubes (a drill tube and an inner tube). The drill tube and the inner tube have longitudinal concentric holes. The solution can be implemented in an eccentric tube configuration as well where the tubes have eccentric longitudinal holes. The inner tube presents at the bottom two control surfaces for controlling the orientation of the scoring dawg. The drill tube presents a sunk-in profile on the inside of the wall for housing the scoring dawg. The inner tube rotation relative to the drill tube actively controls the orientation of the scoring dawg and hence its penetration and retrieval from the core. The scoring dawg presents a shaft, two axially spaced arms, and a tooth. The two arms slide on the control surfaces of the inner tube. The tooth, when rotated, can penetrate or be extracted from the core. During drilling, the two tubes move together maintaining the scoring dawg completely outside the core. After the desired drilling depth has been reached the inner tube is rotated relative to the drill tube such that the tooth of the scoring dawg moves toward the central axis. By rotating the drill tube, the scoring dawg can score the core and so reduce its cross sectional area. The scoring dawg can also act as a stress concentrator for breaking the core in torsion or tension. After breaking the core, the scoring dawg can act as a core retention mechanism. For scoring, it requires the core to be attached to the rock. If the core is broken, the dawg can be used as a retention mechanism. The scoring dawg requires a hard-tip insert like tungsten carbide for scoring hard rocks. The relative rotation of the two tubes can be controlled manually or by an additional actuator. In the implemented design solution the bit rotation for scoring was in the same direction as the drilling. The device was tested for limestone cores and basalt cores. The torque required for breaking the

  16. An audit of the current U.S. Department of Agriculture frame size scoring system.

    PubMed

    Reinhardt, C D; Busby, W D

    2014-06-01

    Feedlot and carcass data from steers (n = 16,700) and heifers (n = 6,357) originating from 16 different states and fed in 17 feedlots located in southwest Iowa were used to evaluate the accuracy of the USDA frame score for predicting final BW of fed cattle. Frame score was recorded by USDA or state personnel for cattle either before leaving the state of origin or on arrival at the terminal feedlot. Mixed model procedures were used to investigate relationships between USDA frame score and measures of live performance and carcass traits. Other fixed effects included in the model included USDA muscle score, sex, age classification on feedlot entry (calf: ≤270 d of age, yearling: 271-365 d of age, and long yearling: >365 d of age), BCS on feedlot arrival, number of treatments for respiratory disease, hide color, and site of frame or muscle scoring; the interactions of sex × frame score and hide color × frame score were also included; fat thickness was included as a fixed effect (covariate) in the analysis of ADG, final BW, days on feed, LM area, marbling score, and quality grade. Random effects included in the model were year of feedlot arrival and feedlot in which cattle were fed. The system accurately projects the minimum target final BW for large frame steers and heifers; however, the final BW of the smallest medium frame steers and heifers exceeds the target minimum final BW by 35 and 40 kg, respectively. When frame score was assigned post facto based on actual final BW (adjusted to 1.27 cm fat thickness), it was determined that large frame was over-assigned by graders (62 vs. 35% for steers and 54 vs. 32% for heifers, actual score vs. postharvest score, respectively), medium frame was underassigned (37 vs. 51% and 46 vs. 58% for steers and heifers), and small frame was underassigned (0.7 vs. 15% and 0.6 vs. 10% for steers and heifers; K = 0.01, P < 0.01). Across sexes, of the cattle assigned to small, medium, or large frame score, 40, 59, and 43% actually had

  17. A robust and accurate formulation of molecular and colloidal electrostatics

    NASA Astrophysics Data System (ADS)

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y. C.

    2016-08-01

    This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics.

  18. A robust and accurate formulation of molecular and colloidal electrostatics.

    PubMed

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y C

    2016-08-01

    This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics. PMID:27497538

  19. Ultra-accurate collaborative information filtering via directed user similarity

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  20. Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

    PubMed

    Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

    2015-09-01

    Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need to

  1. Validation of Automated Scoring of Oral Reading

    ERIC Educational Resources Information Center

    Balogh, Jennifer; Bernstein, Jared; Cheng, Jian; Van Moere, Alistair; Townshend, Brent; Suzuki, Masanori

    2012-01-01

    A two-part experiment is presented that validates a new measurement tool for scoring oral reading ability. Data collected by the U.S. government in a large-scale literacy assessment of adults were analyzed by a system called VersaReader that uses automatic speech recognition and speech processing technologies to score oral reading fluency. In the…

  2. Predictors of MCAT Scores for Black Americans

    PubMed Central

    Carmichael, J. W.; Bauer, Joanne; Hunter, Jacqueline R.; Labat, Deidre D.; Sevenair, John P.

    1987-01-01

    If minority students likely to score low on the Medical College Admissions Test (MCAT) can be identified in advance, they can be advised to take existing preparatory programs, or programs can be developed to meet their needs. Correlation coefficients for a number of available independent variables with MCAT scores were determined for a population of premedical students at Xavier University of Louisiana. American College Testing (ACT) and Scholastic Aptitude Test (SAT) scores were found to have similar ability to predict MCAT scores, with a correlation coefficient of 0.64 between ACT composite and MCAT total scores. Correlations of sophomore year grade point average (GPA) with MCAT scores were only slightly weaker. Use of subtest scores for the ACT and SAT, grades in science courses, and Nelson-Denny Reading Test scores did not improve prediction to any real extent, either when used alone or in multiple linear regression analysis. In contrast to some previous studies, predictions for black men were as good as those for black women. Use of only ACT composite and sophomore year GPA together gave correlations only slightly weaker than predictions using a full range of variables; data from ACT composite and sophomore year GPA can be used for calculating predictive equations on many available micro-computers. These procedures may not be applicable to minority students at majority institutions. PMID:3612830

  3. 7 CFR 1776.9 - Scoring applications.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 12 2010-01-01 2010-01-01 false Scoring applications. 1776.9 Section 1776.9 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE (CONTINUED) HOUSEHOLD WATER WELL SYSTEM GRANT PROGRAM HWWS Grants § 1776.9 Scoring...

  4. 7 CFR 1776.9 - Scoring applications.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 12 2013-01-01 2013-01-01 false Scoring applications. 1776.9 Section 1776.9 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE (CONTINUED) HOUSEHOLD WATER WELL SYSTEM GRANT PROGRAM HWWS Grants § 1776.9 Scoring...

  5. 7 CFR 1776.9 - Scoring applications.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 12 2012-01-01 2012-01-01 false Scoring applications. 1776.9 Section 1776.9 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE (CONTINUED) HOUSEHOLD WATER WELL SYSTEM GRANT PROGRAM HWWS Grants § 1776.9 Scoring...

  6. 7 CFR 1776.9 - Scoring applications.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 12 2011-01-01 2011-01-01 false Scoring applications. 1776.9 Section 1776.9 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE (CONTINUED) HOUSEHOLD WATER WELL SYSTEM GRANT PROGRAM HWWS Grants § 1776.9 Scoring...

  7. 7 CFR 1776.9 - Scoring applications.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 12 2014-01-01 2013-01-01 true Scoring applications. 1776.9 Section 1776.9 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE (CONTINUED) HOUSEHOLD WATER WELL SYSTEM GRANT PROGRAM HWWS Grants § 1776.9 Scoring...

  8. 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…

  9. Predicting Latent Class Scores for Subsequent Analysis

    ERIC Educational Resources Information Center

    Petersen, Janne; Bandeen-Roche, Karen; Budtz-Jorgensen, Esben; Larsen, Klaus Groes

    2012-01-01

    Latent class regression models relate covariates and latent constructs such as psychiatric disorders. Though full maximum likelihood estimation is available, estimation is often in three steps: (i) a latent class model is fitted without covariates; (ii) latent class scores are predicted; and (iii) the scores are regressed on covariates. We propose…

  10. Methodological Approaches to Online Scoring of Essays.

    ERIC Educational Resources Information Center

    Chung, Gregory K. W. K.; O'Neil, Harold F., Jr.

    This report examines the feasibility of scoring essays using computer-based techniques. Essays have been incorporated into many of the standardized testing programs. Issues of validity and reliability must be addressed to deploy automated approaches to scoring fully. Two approaches that have been used to classify documents, surface- and word-based…

  11. Causal Moderation Analysis Using Propensity Score Methods

    ERIC Educational Resources Information Center

    Dong, Nianbo

    2012-01-01

    This paper is based on previous studies in applying propensity score methods to study multiple treatment variables to examine the causal moderator effect. The propensity score methods will be demonstrated in a case study to examine the causal moderator effect, where the moderators are categorical and continuous variables. Moderation analysis is an…

  12. Bayesian Model Averaging for Propensity Score Analysis

    ERIC Educational Resources Information Center

    Kaplan, David; Chen, Jianshen

    2013-01-01

    The purpose of this study is to explore Bayesian model averaging in the propensity score context. Previous research on Bayesian propensity score analysis does not take into account model uncertainty. In this regard, an internally consistent Bayesian framework for model building and estimation must also account for model uncertainty. The…

  13. An Overview of Automated Scoring of Essays

    ERIC Educational Resources Information Center

    Dikli, Semire

    2006-01-01

    Automated Essay Scoring (AES) is defined as the computer technology that evaluates and scores the written prose (Shermis & Barrera, 2002; Shermis & Burstein, 2003; Shermis, Raymat, & Barrera, 2003). AES systems are mainly used to overcome time, cost, reliability, and generalizability issues in writing assessment (Bereiter, 2003; Burstein,…

  14. Observed Score Linear Equating with Covariates

    ERIC Educational Resources Information Center

    Branberg, Kenny; Wiberg, Marie

    2011-01-01

    This paper examined observed score linear equating in two different data collection designs, the equivalent groups design and the nonequivalent groups design, when information from covariates (i.e., background variables correlated with the test scores) was included. The main purpose of the study was to examine the effect (i.e., bias, variance, and…

  15. Understanding Scoring Rubrics: A Guide for Teachers.

    ERIC Educational Resources Information Center

    Boston, Carol, Ed.

    This compilation provides an introduction to using scoring rubrics in the classroom. When good rubrics are used well, teachers and students receive extensive feedback on the quality and quantity of student learning. When scoring rubrics are used in large-scale assessment, technical questions related to interrater reliability tend to dominate the…

  16. Coefficient Alpha and Reliability of Scale Scores

    ERIC Educational Resources Information Center

    Almehrizi, Rashid S.

    2013-01-01

    The majority of large-scale assessments develop various score scales that are either linear or nonlinear transformations of raw scores for better interpretations and uses of assessment results. The current formula for coefficient alpha (a; the commonly used reliability coefficient) only provides internal consistency reliability estimates of raw…

  17. 10 Tips for Higher Test Scores.

    ERIC Educational Resources Information Center

    Priestley, Michael

    2000-01-01

    Ten suggestions to help students increase standardized test scores include: read directions carefully; peek at the questions before reading stories or articles; note key words; use parts of questions to help plan answers; look back at the text; think before writing; write clearly and legibly; pay attention to how the test is scored; manage time…

  18. Selecting the Right Similarity-Scoring Matrix.

    PubMed

    Pearson, William R

    2013-01-01

    Protein sequence similarity searching programs like BLASTP, SSEARCH (UNIT 3.10), and FASTA use scoring matrices that are designed to identify distant evolutionary relationships (BLOSUM62 for BLAST, BLOSUM50 for SEARCH and FASTA). Different similarity scoring matrices are most effective at different evolutionary distances. "Deep" scoring matrices like BLOSUM62 and BLOSUM50 target alignments with 20 - 30% identity, while "shallow" scoring matrices (e.g. VTML10 - VTML80), target alignments that share 90 - 50% identity, reflecting much less evolutionary change. While "deep" matrices provide very sensitive similarity searches, they also require longer sequence alignments and can sometimes produce alignment overextension into non-homologous regions. Shallower scoring matrices are more effective when searching for short protein domains, or when the goal is to limit the scope of the search to sequences that are likely to be orthologous between recently diverged organisms. Likewise, in DNA searches, the match and mismatch parameters set evolutionary look-back times and domain boundaries. In this unit, we will discuss the theoretical foundations that drive practical choices of protein and DNA similarity scoring matrices and gap penalties. Deep scoring matrices (BLOSUM62 and BLOSUM50) should be used for sensitive searches with full-length protein sequences, but short domains or restricted evolutionary look-back require shallower scoring matrices.

  19. Model feedback in Bayesian propensity score estimation.

    PubMed

    Zigler, Corwin M; Watts, Krista; Yeh, Robert W; Wang, Yun; Coull, Brent A; Dominici, Francesca

    2013-03-01

    Methods based on the propensity score comprise one set of valuable tools for comparative effectiveness research and for estimating causal effects more generally. These methods typically consist of two distinct stages: (1) a propensity score stage where a model is fit to predict the propensity to receive treatment (the propensity score), and (2) an outcome stage where responses are compared in treated and untreated units having similar values of the estimated propensity score. Traditional techniques conduct estimation in these two stages separately; estimates from the first stage are treated as fixed and known for use in the second stage. Bayesian methods have natural appeal in these settings because separate likelihoods for the two stages can be combined into a single joint likelihood, with estimation of the two stages carried out simultaneously. One key feature of joint estimation in this context is "feedback" between the outcome stage and the propensity score stage, meaning that quantities in a model for the outcome contribute information to posterior distributions of quantities in the model for the propensity score. We provide a rigorous assessment of Bayesian propensity score estimation to show that model feedback can produce poor estimates of causal effects absent strategies that augment propensity score adjustment with adjustment for individual covariates. We illustrate this phenomenon with a simulation study and with a comparative effectiveness investigation of carotid artery stenting versus carotid endarterectomy among 123,286 Medicare beneficiaries hospitlized for stroke in 2006 and 2007. PMID:23379793

  20. Factor Score Reliabilities and Domain Validities.

    ERIC Educational Resources Information Center

    Gorsuch, Richard L.

    1980-01-01

    Kaiser and Michael reported a formula for factor scores giving an internal consistency reliability and its square root, the domain validity. Using this formula is inappropriate if variables are included which have trival weights rather than salient weights for the factor for which the score is being computed. (Author/RL)