Science.gov

Sample records for accurate scoring functions

  1. An unexpected way forward: towards a more accurate and rigorous protein-protein binding affinity scoring function by eliminating terms from an already simple scoring function.

    PubMed

    Swanson, Jon; Audie, Joseph

    2017-01-16

    A fundamental and unsolved problem in biophysical chemistry is the development of a computationally simple, physically intuitive, and generally applicable method for accurately predicting and physically explaining protein-protein binding affinities from protein-protein interaction (PPI) complex coordinates. Here, we propose that the simplification of a previously described six-term PPI scoring function to a four term function results in a simple expression of all physically and statistically meaningful terms that can be used to accurately predict and explain binding affinities for a well-defined subset of PPIs that are characterized by (1) crystallographic coordinates, (2) rigid-body association, (3) normal interface size, and hydrophobicity and hydrophilicity, and (4) high quality experimental binding affinity measurements. We further propose that the four-term scoring function could be regarded as a core expression for future development into a more general PPI scoring function. Our work has clear implications for PPI modeling and structure-based drug design.

  2. AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.

    PubMed

    Uehara, Shota; Tanaka, Shigenori

    2016-11-23

    Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.

  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.

  4. Customizing scoring functions for docking.

    PubMed

    Pham, Tuan A; Jain, Ajay N

    2008-05-01

    Empirical scoring functions used in protein-ligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function's training towards a particular application, such as screening enrichment. The approach combines multiple instance learning, positive data in the form of ligands of protein binding sites of known and unknown affinity and binding geometry, and negative (decoy) data of ligands thought not to bind particular protein binding sites or known not to bind in particular geometries. Performance of the method for the Surflex-Dock scoring function is shown in cross-validation studies and in eight blind test cases. Tuned functions optimized with a sufficient amount of data exhibited either improved or undiminished screening performance relative to the original function across all eight complexes. Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility.

  5. Customizing scoring functions for docking

    NASA Astrophysics Data System (ADS)

    Pham, Tuan A.; Jain, Ajay N.

    2008-05-01

    Empirical scoring functions used in protein-ligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function's training towards a particular application, such as screening enrichment. The approach combines multiple instance learning, positive data in the form of ligands of protein binding sites of known and unknown affinity and binding geometry, and negative (decoy) data of ligands thought not to bind particular protein binding sites or known not to bind in particular geometries. Performance of the method for the Surflex-Dock scoring function is shown in cross-validation studies and in eight blind test cases. Tuned functions optimized with a sufficient amount of data exhibited either improved or undiminished screening performance relative to the original function across all eight complexes. Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility.

  6. Assessing scoring functions for protein-ligand interactions.

    PubMed

    Ferrara, Philippe; Gohlke, Holger; Price, Daniel J; Klebe, Gerhard; Brooks, Charles L

    2004-06-03

    of 116 complexes that does not contain any of the complexes used to calibrate this scoring function. Neither a more accurate treatment of solvation nor a more sophisticated charge model for zinc improves the quality of the results. Improved modeling of the protonation states, however, leads to a better prediction of binding affinities in the case of the generalized Born and the Poisson continuum models used in conjunction with the CHARMm force field.

  7. Does a pneumotach accurately characterize voice function?

    NASA Astrophysics Data System (ADS)

    Walters, Gage; Krane, Michael

    2016-11-01

    A study is presented which addresses how a pneumotach might adversely affect clinical measurements of voice function. A pneumotach is a device, typically a mask, worn over the mouth, in order to measure time-varying glottal volume flow. By measuring the time-varying difference in pressure across a known aerodynamic resistance element in the mask, the glottal volume flow waveform is estimated. Because it adds aerodynamic resistance to the vocal system, there is some concern that using a pneumotach may not accurately portray the behavior of the voice. To test this hypothesis, experiments were performed in a simplified airway model with the principal dimensions of an adult human upper airway. A compliant constriction, fabricated from silicone rubber, modeled the vocal folds. Variations of transglottal pressure, time-averaged volume flow, model vocal fold vibration amplitude, and radiated sound with subglottal pressure were performed, with and without the pneumotach in place, and differences noted. Acknowledge support of NIH Grant 2R01DC005642-10A1.

  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. Mangled extremity severity score: an accurate guide to treatment of the severely injured upper extremity.

    PubMed

    Slauterbeck, J R; Britton, C; Moneim, M S; Clevenger, F W

    1994-08-01

    The mangled extremity severity score (MESS) is a scoring system that can be applied to mangled extremities and help one determine which mangled limbs will eventually come to amputation. The MESS is a graduated grading system based on skeletal and soft tissue injury, shock, ischemia, and age. The records of 37 patients having sustained 43 open fractures or mangled upper extremity injuries, seen and treated at the University of New Mexico's Regional Trauma Center between April 1987 and September 1990, have been reviewed. All nine extremity injuries with a MESS of greater than or equal to seven were amputated, and 34 of 34 with a MESS of less than seven were salvaged. Nine Grade IIIC and six mangled extremities were identified in our study. Five of these Grade IIIC and four of the mangled extremities with a MESS of greater than or equal to seven were amputated. All Grade IIIC or mangled extremities with a MESS of less than seven were salvaged. In conclusion, the MESS is an early and accurate predictor for identifying the extremities that may be best treated by amputation.

  10. Accurate sperm morphology assessment predicts sperm function.

    PubMed

    Abu Hassan Abu, D; Franken, D R; Hoffman, B; Henkel, R

    2012-05-01

    Sperm morphology has been associated with in vitro as well as in vivo fertilisation. The study aimed to evaluate the possible relation between the percentage of spermatozoa with normal morphology and the following sperm functional assays: (i) zona-induced acrosome reaction (ZIAR); (ii) DNA integrity; (iii) chromatin condensation; (iv) sperm apoptosis; and (v) fertilisation rates. Regression analysis was employed to calculate the association between morphology and different functional tests. Normal sperm morphology correlated significantly with the percentages of live acrosome-reacted spermatozoa in the ZIAR (r = 0.518; P < 0.0001; n = 92), DNA integrity (r = -0.515; P = 0.0018; n = 34), CMA(3) -positive spermatozoa (r = -0.745; P < 0.0001; n = 92), sperm apoptosis (r = -0.395; P = 0.0206; n = 34) and necrosis (r = -0.545; P = 0.0009; n = 34). Negative correlations existed between for the acrosome reaction, and DNA integrity, while negative associations were recorded with the percentages of CMA(3) -positive spermatozoa, apoptotic and necrotic spermatozoa. Sperm morphology is related to sperm dysfunction such as poor chromatin condensation, acrosome reaction and DNA integrity. Negative and significant correlations existed between normal sperm morphology and chromatin condensation, the percentage of spermatozoa with abnormal DNA and spermatozoa with apoptotic activity. The authors do not regard sperm morphology as the only test for the diagnosis of male fertility, but sperm morphology can serve as a valuable indicator of underlying dysfunction.

  11. DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach

    PubMed Central

    Wang, Zhiheng; Yang, Qianqian; Li, Tonghua; Cong, Peisheng

    2015-01-01

    The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database. Availability The DisoMCS is available at http://cal.tongji.edu.cn/disorder/. PMID:26090958

  12. 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

  13. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets. PMID:28358834

  14. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.

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

    PubMed

    Quiroga, Rodrigo; 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.

  16. 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

  17. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.

    PubMed

    Halgren, Thomas A; Murphy, Robert B; Friesner, Richard A; Beard, Hege S; Frye, Leah L; Pollard, W Thomas; Banks, Jay L

    2004-03-25

    Glide's ability to identify active compounds in a database screen is characterized by applying Glide to a diverse set of nine protein receptors. In many cases, two, or even three, protein sites are employed to probe the sensitivity of the results to the site geometry. To make the database screens as realistic as possible, the screens use sets of "druglike" decoy ligands that have been selected to be representative of what we believe is likely to be found in the compound collection of a pharmaceutical or biotechnology company. Results are presented for releases 1.8, 2.0, and 2.5 of Glide. The comparisons show that average measures for both "early" and "global" enrichment for Glide 2.5 are 3 times higher than for Glide 1.8 and more than 2 times higher than for Glide 2.0 because of better results for the least well-handled screens. This improvement in enrichment stems largely from the better balance of the more widely parametrized GlideScore 2.5 function and the inclusion of terms that penalize ligand-protein interactions that violate established principles of physical chemistry, particularly as it concerns the exposure to solvent of charged protein and ligand groups. Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.

  18. Nonsymmetric Two-Body Score Function for Protein Fold Recognition:

    NASA Astrophysics Data System (ADS)

    Heo, Muyoung; Cheon, Mookyung; Chang, Iksoo

    The usual two-body score (energy) function to recognize native folds of proteins is Miyazawa-Jernigan (MJ) pairwise-contact function. The pairwise-contact parameters between two amino acids in MJ function are symmetric in a sense that a directional order of amino acids sequence along the backbone of a protein is ignored in constructing score parameters. Here we report that we succeeded in constructing a nonsymmetric two-body score function, capturing a directional order of amino acids sequence, by a perceptron learning and a protein threading. We considered pairs of two adjacent amino acids that are separated by two consecutive peptide bonds with the backbone directionality from the N-terminus to the C-terminus of a protein. We also considered the local environmental character, such as the secondary structures and the hydrophobicity (solvation), of amino acids in protein structures. The score is a corresponding propensity for a directional alignment of these two adjacent amino acids with their local environments. The resulting score function simultaneously recognized native folds of 1006 proteins covering all representative proteins with a homology less than 30% among them. The quality of this score function was validated by a threading test of new distinct 382 proteins with a homology less than 90% among them, and it entailed a high success ratio for recognizing native folds of 364 (95.3%) proteins. It showed a good feasibility of designing protein score functions for protein fold recognition by a perceptron learning and a protein threading.

  19. A combinatorial scoring function for protein-RNA docking.

    PubMed

    Zhang, Zhao; Lu, Lin; Zhang, Yue; Hua Li, Chun; Wang, Cun Xin; Zhang, Xiao Yi; Tan, Jian Jun

    2017-04-01

    Protein-RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near-native structures from the incorrect ones. To solve the problem, we have constructed a knowledge-based residue-nucleotide pairwise potential with secondary structure information considered for nonribosomal protein-RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics-based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics-based method derived potential ITScore-PR, and the united atom-based statistical potentials QUASI-RNP and DARS-RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near-native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long-range electrostatic attractive energy plays an important role in distinguishing near-native structures from the incorrect ones. This work can be helpful for the development of protein-RNA docking methods and for the understanding of protein-RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741-752. © 2016 Wiley Periodicals, Inc.

  20. Simplified risk score models accurately predict the risk of major in-hospital complications following percutaneous coronary intervention.

    PubMed

    Resnic, F S; Ohno-Machado, L; Selwyn, A; Simon, D I; Popma, J J

    2001-07-01

    The objectives of this analysis were to develop and validate simplified risk score models for predicting the risk of major in-hospital complications after percutaneous coronary intervention (PCI) in the era of widespread stenting and use of glycoprotein IIb/IIIa antagonists. We then sought to compare the performance of these simplified models with those of full logistic regression and neural network models. From January 1, 1997 to December 31, 1999, data were collected on 4,264 consecutive interventional procedures at a single center. Risk score models were derived from multiple logistic regression models using the first 2,804 cases and then validated on the final 1,460 cases. The area under the receiver operating characteristic (ROC) curve for the risk score model that predicted death was 0.86 compared with 0.85 for the multiple logistic model and 0.83 for the neural network model (validation set). For the combined end points of death, myocardial infarction, or bypass surgery, the corresponding areas under the ROC curves were 0.74, 0.78, and 0.81, respectively. Previously identified risk factors were confirmed in this analysis. The use of stents was associated with a decreased risk of in-hospital complications. Thus, risk score models can accurately predict the risk of major in-hospital complications after PCI. Their discriminatory power is comparable to those of logistic models and neural network models. Accurate bedside risk stratification may be achieved with these simple models.

  1. Efficient and accurate computation of the incomplete Airy functions

    NASA Technical Reports Server (NTRS)

    Constantinides, E. D.; Marhefka, R. J.

    1993-01-01

    The incomplete Airy integrals serve as canonical functions for the uniform ray optical solutions to several high-frequency scattering and diffraction problems that involve a class of integrals characterized by two stationary points that are arbitrarily close to one another or to an integration endpoint. Integrals with such analytical properties describe transition region phenomena associated with composite shadow boundaries. An efficient and accurate method for computing the incomplete Airy functions would make the solutions to such problems useful for engineering purposes. In this paper a convergent series solution for the incomplete Airy functions is derived. Asymptotic expansions involving several terms are also developed and serve as large argument approximations. The combination of the series solution with the asymptotic formulae provides for an efficient and accurate computation of the incomplete Airy functions. Validation of accuracy is accomplished using direct numerical integration data.

  2. 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…

  3. Accurate perception of negative emotions predicts functional capacity in schizophrenia.

    PubMed

    Abram, Samantha V; Karpouzian, Tatiana M; Reilly, James L; Derntl, Birgit; Habel, Ute; Smith, Matthew J

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration.

  4. 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…

  5. Beware of machine learning-based scoring functions-on the danger of developing black boxes.

    PubMed

    Gabel, Joffrey; Desaphy, Jérémy; Rognan, Didier

    2014-10-27

    Training machine learning algorithms with protein-ligand descriptors has recently gained considerable attention to predict binding constants from atomic coordinates. Starting from a series of recent reports stating the advantages of this approach over empirical scoring functions, we could indeed reproduce the claimed superiority of Random Forest and Support Vector Machine-based scoring functions to predict experimental binding constants from protein-ligand X-ray structures of the PDBBind dataset. Strikingly, these scoring functions, trained on simple protein-ligand element-element distance counts, were almost unable to enrich virtual screening hit lists in true actives upon docking experiments of 10 reference DUD-E datasets; this is a a feature that, however, has been verified for an a priori less-accurate empirical scoring function (Surflex-Dock). By systematically varying ligand poses from true X-ray coordinates, we show that the Surflex-Dock scoring function is logically sensitive to the quality of docking poses. Conversely, our machine-learning based scoring functions are totally insensitive to docking poses (up to 10 Å root-mean square deviations) and just describe atomic element counts. This report does not disqualify using machine learning algorithms to design scoring functions. Protein-ligand element-element distance counts should however be used with extreme caution and only applied in a meaningful way. To avoid developing novel but meaningless scoring functions, we propose that two additional benchmarking tests must be systematically done when developing novel scoring functions: (i) sensitivity to docking pose accuracy, and (ii) ability to enrich hit lists in true actives upon structure-based (docking, receptor-ligand pharmacophore) virtual screening of reference datasets.

  6. Accurate Computation of Divided Differences of the Exponential Function,

    DTIC Science & Technology

    1983-06-01

    differences are not for arbitrary smooth functions f but for well known analytic functions such as exp. sin and cos. Thus we can exploit their properties in...have a bad name in practice. However in a number of applications the functional form of f is known (e.g. exp) and can be exploited to obtain accurate...n do X =s(1) s(1)=d(i) For j=2.....-1 do11=t, (j) z=Y next j next i SS7 . (Shift back and stop.] ,-tt+77. d(i).-e"d(i), s(i-1)’e~ s(i-i) for i=2

  7. 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.

  8. Empirical evaluation of scoring functions for Bayesian network model selection.

    PubMed

    Liu, Zhifa; Malone, Brandon; Yuan, Changhe

    2012-01-01

    In this work, we empirically evaluate the capability of various scoring functions of Bayesian networks for recovering true underlying structures. Similar investigations have been carried out before, but they typically relied on approximate learning algorithms to learn the network structures. The suboptimal structures found by the approximation methods have unknown quality and may affect the reliability of their conclusions. Our study uses an optimal algorithm to learn Bayesian network structures from datasets generated from a set of gold standard Bayesian networks. Because all optimal algorithms always learn equivalent networks, this ensures that only the choice of scoring function affects the learned networks. Another shortcoming of the previous studies stems from their use of random synthetic networks as test cases. There is no guarantee that these networks reflect real-world data. We use real-world data to generate our gold-standard structures, so our experimental design more closely approximates real-world situations. A major finding of our study suggests that, in contrast to results reported by several prior works, the Minimum Description Length (MDL) (or equivalently, Bayesian information criterion (BIC)) consistently outperforms other scoring functions such as Akaike's information criterion (AIC), Bayesian Dirichlet equivalence score (BDeu), and factorized normalized maximum likelihood (fNML) in recovering the underlying Bayesian network structures. We believe this finding is a result of using both datasets generated from real-world applications rather than from random processes used in previous studies and learning algorithms to select high-scoring structures rather than selecting random models. Other findings of our study support existing work, e.g., large sample sizes result in learning structures closer to the true underlying structure; the BDeu score is sensitive to the parameter settings; and the fNML performs pretty well on small datasets. We also

  9. Empirical evaluation of scoring functions for Bayesian network model selection

    PubMed Central

    2012-01-01

    In this work, we empirically evaluate the capability of various scoring functions of Bayesian networks for recovering true underlying structures. Similar investigations have been carried out before, but they typically relied on approximate learning algorithms to learn the network structures. The suboptimal structures found by the approximation methods have unknown quality and may affect the reliability of their conclusions. Our study uses an optimal algorithm to learn Bayesian network structures from datasets generated from a set of gold standard Bayesian networks. Because all optimal algorithms always learn equivalent networks, this ensures that only the choice of scoring function affects the learned networks. Another shortcoming of the previous studies stems from their use of random synthetic networks as test cases. There is no guarantee that these networks reflect real-world data. We use real-world data to generate our gold-standard structures, so our experimental design more closely approximates real-world situations. A major finding of our study suggests that, in contrast to results reported by several prior works, the Minimum Description Length (MDL) (or equivalently, Bayesian information criterion (BIC)) consistently outperforms other scoring functions such as Akaike's information criterion (AIC), Bayesian Dirichlet equivalence score (BDeu), and factorized normalized maximum likelihood (fNML) in recovering the underlying Bayesian network structures. We believe this finding is a result of using both datasets generated from real-world applications rather than from random processes used in previous studies and learning algorithms to select high-scoring structures rather than selecting random models. Other findings of our study support existing work, e.g., large sample sizes result in learning structures closer to the true underlying structure; the BDeu score is sensitive to the parameter settings; and the fNML performs pretty well on small datasets. We also

  10. Combining heterogeneous data sources for accurate functional annotation of proteins

    PubMed Central

    2013-01-01

    Combining heterogeneous sources of data is essential for accurate prediction of protein function. The task is complicated by the fact that while sequence-based features can be readily compared across species, most other data are species-specific. In this paper, we present a multi-view extension to GOstruct, a structured-output framework for function annotation of proteins. The extended framework can learn from disparate data sources, with each data source provided to the framework in the form of a kernel. Our empirical results demonstrate that the multi-view framework is able to utilize all available information, yielding better performance than sequence-based models trained across species and models trained from collections of data within a given species. This version of GOstruct participated in the recent Critical Assessment of Functional Annotations (CAFA) challenge; since then we have significantly improved the natural language processing component of the method, which now provides performance that is on par with that provided by sequence information. The GOstruct framework is available for download at http://strut.sourceforge.net. PMID:23514123

  11. 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

  12. 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.

  13. 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.

  14. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function.

    PubMed

    Huang, Sheng-You; Zou, Xiaoqin

    2006-11-30

    We have developed an iterative knowledge-based scoring function (ITScore) to describe protein-ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein-ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 2287), and compared with 14 other scoring functions. The results show that ITScore yielded a high success rate of 82% on identifying native-like binding modes under the criterion of rmsd < or = 2 A for each top-ranked ligand conformation. The success rate increased to 98% if the top five conformations were considered for each ligand. In the case of binding affinity prediction, ITScore also obtained a good correlation for this test set (R = 0.65). Next, ITScore was used to predict binding affinities of a second diverse test set of 77 protein-ligand complexes prepared by Muegge and Martin (J Med Chem 1999, 42, 791), and compared with four other widely used knowledge-based scoring functions. ITScore yielded a high correlation of R2 = 0.65 (or R = 0.81) in the affinity prediction. Finally, enrichment tests were performed with ITScore against four target proteins using the compound databases constructed by Jacobsson et al. (J Med Chem 2003, 46, 5781). The results were compared with those of eight other scoring functions. ITScore yielded high enrichments in all four database screening tests. ITScore can be easily combined with the existing docking programs for the use of structure-based drug design.

  15. 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.

  16. Accurate van der Waals coefficients from density functional theory

    PubMed Central

    Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

    2012-01-01

    The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

  17. 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.

  18. Prognostic Value of Gai's Plaque Score and Agatston Coronary Artery Calcium Score for Functionally Significant Coronary Artery Stenosis

    PubMed Central

    Zhang, Chuang; Yang, Shuang; Gai, Lu-Yue; Han, Zhi-Qi; Xin, Qian; Yang, Xiao-Bo; Yang, Jun-Jie; Jin, Qin-Hua

    2016-01-01

    Background: The prognostic values of the coronary computed tomography angiography (CCTA) score for predicting future cardiovascular events have been previously demonstrated in numerous studies. However, few studies have used the rich information available from CCTA to detect functionally significant coronary lesions. We sought to compare the prognostic values of Gai's plaque score and the coronary artery calcium score (CACS) of CCTA for predicting functionally significant coronary lesions, using fractional flow reserve (FFR) as the gold standard. Methods: We retrospectively analyzed 107 visually assessed significant coronary lesions in 88 patients (mean age, 59.6 ± 10.2 years; 76.14% of males) who underwent CCTA, invasive coronary angiography, and invasive FFR measurement. An FFR <0.80 indicated hemodynamically significant coronary stenosis. Lesions were divided into two groups using an FFR cutoff value of 0.80. We compared Gai's plaque scores and CACS between the two groups and evaluated the correlations of these scores with FFR. The statistical methods included unpaired t-test, Mann-Whitney U-test, and Spearman's correlation coefficients. Results: Coronary lesions with FFR <0.80 had higher Gai's scores than those with FFR ≥0.80. Gai's score had the strongest correlation with FFR (r = −0.48, P < 0.01) and had a greater area under the curve = 0.72 (95% confidence interval: 0.61–0.82; P < 0.01) than the CACS of whole arteries and a single artery. Conclusions: Both CACS in a single artery and Gai's plaque score demonstrated a good capacity to assess functionally significant coronary artery stenosis when compared to the gold standard FFR. However, Gai's plaque score was more predictive of FFR <0.80. Gai's score can be easily calculated in daily clinical practice and could be used when considering revascularization. PMID:27900990

  19. Towards a more accurate van der Waals density functional

    NASA Astrophysics Data System (ADS)

    Hamada, Ikutaro

    2014-03-01

    The van der Waals density functional (vdW-DF) of Dion et al. [1] has attracted considerable attention, because the functional is able to describe intra- and intermolecular bondings with different natures, e.g., covalent and van der Waals bondings in a seamless fashion within the framework of density functional theory. However, the accuracy of the functional is yet to be improved for the applications to various systems. Here I propose an exchange functional for the second version of vdW-DF [2], which improves the accuracy of vdW-DF. The keys in the improved exchange are the matching to the gradient expansion approximation in the slowly varying limit and the large density gradient behavior set in Becke's exchange (B86b)[3]. Systematic study on gas phase molecules, solids, and molecular adsorption demonstrates the applicability of the proposed functional to a wide variety of materials.

  20. 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.

  1. A correction to a highly accurate voight function algorithm

    NASA Technical Reports Server (NTRS)

    Shippony, Z.; Read, W. G.

    2002-01-01

    An algorithm for rapidly computing the complex Voigt function was published by Shippony and Read. Its claimed accuracy was 1 part in 10^8. It was brought to our attention by Wells that Shippony and Read was not meeting its claimed accuracy for extremely small but non zero y values. Although true, the fix to the code is so trivial to warrant this note for those who use this algorithm.

  2. Determination of accurate, mean bond lengths from radial distribution functions

    NASA Astrophysics Data System (ADS)

    Sukhomlinov, Sergey V.; Müser, Martin H.

    2017-01-01

    The mean bond length d between a central atom and its nearest neighbors can be estimated from the position of the first peak in the radial distribution function g(r). However, as we demonstrate here, this estimate does not allow one to deduce temperature-induced changes in d. Instead, skewness has to be included into the analysis, which can be achieved, for example, via the skew normal distribution (SND). Fits to the first peak using the SND give bond length in good agreement with direct measurements of nearest-neighbor distribution functions in crystals as well as with a Voronoi-tessellation based detection of nearest-neighbors in liquids. While the location of the first peak in g(r) may shift to smaller values with increasing temperature for three studied liquids—argon, copper, and the bulk-metallic-glass (BMG) forming alloy Zr60Cu30Al10—we find our improved estimates of d to systematically increase with temperature in all cases. Recent conclusions on temperature-induced bond contractions in simple metallic or BMG-forming liquids may therefore have arisen from the neglect of skewness effects.

  3. Race-specific genetic risk score is more accurate than nonrace-specific genetic risk score for predicting prostate cancer and high-grade diseases.

    PubMed

    Na, Rong; Ye, Dingwei; Qi, Jun; Liu, Fang; Lin, Xiaoling; Helfand, Brian T; Brendler, Charles B; Conran, Carly; Gong, Jian; Wu, Yishuo; Gao, Xu; Chen, Yaqing; Zheng, S Lilly; Mo, Zengnan; Ding, Qiang; Sun, Yinghao; Xu, Jianfeng

    2016-01-01

    Genetic risk score (GRS) based on disease risk-associated single nucleotide polymorphisms (SNPs) is an informative tool that can be used to provide inherited information for specific diseases in addition to family history. However, it is still unknown whether only SNPs that are implicated in a specific racial group should be used when calculating GRSs. The objective of this study is to compare the performance of race-specific GRS and nonrace-specific GRS for predicting prostate cancer (PCa) among 1338 patients underwent prostate biopsy in Shanghai, China. A race-specific GRS was calculated with seven PCa risk-associated SNPs implicated in East Asians (GRS7), and a nonrace-specific GRS was calculated based on 76 PCa risk-associated SNPs implicated in at least one racial group (GRS76). The means of GRS7 and GRS76 were 1.19 and 1.85, respectively, in the study population. Higher GRS7 and GRS76 were independent predictors for PCa and high-grade PCa in univariate and multivariate analyses. GRS7 had a better area under the receiver-operating curve (AUC) than GRS76 for discriminating PCa (0.602 vs 0.573) and high-grade PCa (0.603 vs 0.575) but did not reach statistical significance. GRS7 had a better (up to 13% at different cutoffs) positive predictive value (PPV) than GRS76. In conclusion, a race-specific GRS is more robust and has a better performance when predicting PCa in East Asian men than a GRS calculated using SNPs that are not shown to be associated with East Asians.

  4. The Norberg angle is not an accurate predictor of canine hip conformation based on the distraction index and the dorsolateral subluxation score.

    PubMed

    Gaspar, Ana R; Hayes, Galina; Ginja, Catarina; Ginja, Mário M; Todhunter, Rory J

    2016-12-01

    Canine hip dysplasia (CHD) is a common complex trait characterized by abnormal hip joint development. Hip joint laxity, an early characteristic of CHD, results in degeneration of the joint due to mechanical trauma, which is a clinical problem mostly in medium to large breed dogs. Clinical signs include pain, decreased activity and lameness. A retrospective, multi-center, cross sectional study of 437 dogs was performed to determine if a Norberg angle (NA) ≥105° accurately predicts a non-dysplastic hip based on a distraction index (DI) cut-off of ≤0.3 or a dorsolateral subluxation (DLS) score cut-off of ≥55%. The predictive capacity of the NA against a DI ≤0.3 or a DLS score ≥55% was assessed using area under the receiver operator characteristic (ROC) curve analysis. The ROC curve of NA for the prediction of a DI ≤0.3 was 0.59 (95% CI=0.50-0.69) and for the prediction of DLS score ≥55% was 0.69 (95% CI=0.63-0.75). Optimizing the specificity of the NA to ≥80% for prediction of a DI ≤0.3 and a DLS score ≥55% gave a cut-point for the NA of ≥112° and 108.7°, respectively. In conclusion, at the cut-point of 105°, the NA is not an accurate measurement to score normal or abnormal hips, based on the DI or DLS score. Application of screening methods for CHD based on hip laxity, such as the DI or the DLS score, would help to remove additional dysplastic dogs from the breeding pool or the NA criterion should be higher when selecting unaffected dogs for breeding.

  5. Age-Related Differences and Heterogeneity in Executive Functions: Analysis of NAB Executive Functions Module Scores.

    PubMed

    Buczylowska, Dorota; Petermann, Franz

    2016-05-01

    Normative data from the German adaptation of the Neuropsychological Assessment Battery were used to examine age-related differences in 6 executive function tasks. A multivariate analysis of variance was employed to investigate the differences in performance in 484 participants aged 18-99 years. The coefficient of variation was calculated to compare the heterogeneity of scores between 10 age groups. Analyses showed an increase in the dispersion of scores with age, varying from 7% to 289%, in all subtests. Furthermore, age-dependent heterogeneity appeared to be associated with age-dependent decline because the subtests with the greatest increase in dispersion (i.e., Mazes, Planning, and Categories) also exhibited the greatest decrease in mean scores. In contrast, scores for the subtests Letter Fluency, Word Generation, and Judgment had the lowest increase in dispersion with the lowest decrease in mean scores. Consequently, the results presented here show a pattern of age-related differences in executive functioning that is consistent with the concept of crystallized and fluid intelligence.

  6. Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results.

    PubMed

    Li, Yan; Han, Li; Liu, Zhihai; Wang, Renxiao

    2014-06-23

    Our comparative assessment of scoring functions (CASF) benchmark is created to provide an objective evaluation of current scoring functions. The key idea of CASF is to compare the general performance of scoring functions on a diverse set of protein-ligand complexes. In order to avoid testing scoring functions in the context of molecular docking, the scoring process is separated from the docking (or sampling) process by using ensembles of ligand binding poses that are generated in prior. Here, we describe the technical methods and evaluation results of the latest CASF-2013 study. The PDBbind core set (version 2013) was employed as the primary test set in this study, which consists of 195 protein-ligand complexes with high-quality three-dimensional structures and reliable binding constants. A panel of 20 scoring functions, most of which are implemented in main-stream commercial software, were evaluated in terms of "scoring power" (binding affinity prediction), "ranking power" (relative ranking prediction), "docking power" (binding pose prediction), and "screening power" (discrimination of true binders from random molecules). Our results reveal that the performance of these scoring functions is generally more promising in the docking/screening power tests than in the scoring/ranking power tests. Top-ranked scoring functions in the scoring power test, such as X-Score(HM), ChemScore@SYBYL, ChemPLP@GOLD, and PLP@DS, are also top-ranked in the ranking power test. Top-ranked scoring functions in the docking power test, such as ChemPLP@GOLD, Chemscore@GOLD, GlidScore-SP, LigScore@DS, and PLP@DS, are also top-ranked in the screening power test. Our results obtained on the entire test set and its subsets suggest that the real challenge in protein-ligand binding affinity prediction lies in polar interactions and associated desolvation effect. Nonadditive features observed among high-affinity protein-ligand complexes also need attention.

  7. Sampling multiple scoring functions can improve protein loop structure prediction accuracy.

    PubMed

    Li, Yaohang; Rata, Ionel; Jakobsson, Eric

    2011-07-25

    Accurately predicting loop structures is important for understanding functions of many proteins. In order to obtain loop models with high accuracy, efficiently sampling the loop conformation space to discover reasonable structures is a critical step. In loop conformation sampling, coarse-grain energy (scoring) functions coupling with reduced protein representations are often used to reduce the number of degrees of freedom as well as sampling computational time. However, due to implicitly considering many factors by reduced representations, the coarse-grain scoring functions may have potential insensitivity and inaccuracy, which can mislead the sampling process and consequently ignore important loop conformations. In this paper, we present a new computational sampling approach to obtain reasonable loop backbone models, so-called the Pareto optimal sampling (POS) method. The rationale of the POS method is to sample the function space of multiple, carefully selected scoring functions to discover an ensemble of diversified structures yielding Pareto optimality to all sampled conformations. The POS method can efficiently tolerate insensitivity and inaccuracy in individual scoring functions and thereby lead to significant accuracy improvement in loop structure prediction. We apply the POS method to a set of 4-12-residue loop targets using a function space composed of backbone-only Rosetta and distance-scale finite ideal-gas reference (DFIRE) and a triplet backbone dihedral potential developed in our lab. Our computational results show that in 501 out of 502 targets, the model sets generated by POS contain structure models are within subangstrom resolution. Moreover, the top-ranked models have a root mean square deviation (rmsd) less than 1 A in 96.8, 84.1, and 72.2% of the short (4-6 residues), medium (7-9 residues), and long (10-12 residues) targets, respectively, when the all-atom models are generated by local optimization from the backbone models and are ranked by our

  8. Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015

    NASA Astrophysics Data System (ADS)

    Santos-Martins, Diogo

    2016-09-01

    Here is reported the development of a novel scoring function that performs remarkably well at identifying the native binding pose of a subset of HSP90 inhibitors containing aminopyrimidine or resorcinol based scaffolds. This scoring function is called PocketScore, and consists of the interaction energy between a ligand and three residues in the binding pocket: Asp93, Thr184 and a water molecule. We integrated PocketScore into a molecular docking workflow, and used it to participate in the Drug Design Data Resource (D3R) Grand Challenge 2015 (GC2015). PocketScore was able to rank 180 molecules of the GC2015 according to their binding affinity with satisfactory performance. These results indicate that the specific residues considered by PocketScore are determinant to properly model the interaction between HSP90 and its subset of inhibitors containing aminopyrimidine or resorcinol based scaffolds. Moreover, the development of PocketScore aimed at improving docking power while neglecting the prediction of binding affinities, suggesting that accurate identification of native binding poses is a determinant factor for the performance of virtual screens.

  9. The Effect of Clinical, Radiographic and Functional Scores on the Total Score in the Evaluation of Congenital Clubfoot

    PubMed Central

    Rakonjac, Zoran; Brdar, Radivoj; Popovic, Miroslav

    2014-01-01

    Introduction: The use of radical surgical treatments in treating congenital clubfoot is decreasing. Minimally invasive surgical treatment (MIST) is a way of treating congenital clubfoot, which is a kind of compromise between a radical surgical treatment and non-operational one. A few protocols of different authors McKay, Macnicol, Stevens, Meyer, G.W.Simons and Laaveg-Ponseti were used in the evaluation of the results. SCIENTIFIC OBJECTIVE: To determine the importance and role of groups of parameters (clinical, radiographic and functional) in the evaluation of the results in patients treated with the two methods (radical operation and MIST). Subjects and methods: This paper covers children who were treated for structural (idiopathic) form of PEVC. The testing is a prospective study and was conducted in two groups of patients. Group A (radical surgical treatment) – control group, where the total number of subjects was 50, out of which 35 male (70%) and 15 female (30%). The number of feet tested was 88. Group B (minimally invasive surgical treatment–MIST)–experimental group. The total number of subjects was 48, out of which 35 male (73%) and 13 female (27%). The number of feet tested was 84. For the analysis of the results, we used a questionnaire. The total number of parameters was fifteen, clinical, radiographic and functional, five parameters of each. Normal findings or measured value was determined by 0 points. The range of the total score (TS-a- total score range) 0-27 points, and the results were sorted out into the folowing categories: good result (0-5) satisfactory (6-11), poor (12-19) and deformity recrudescence (20-27) points. Results: The proportion of good results at 88 feet in group A was 0,477 as at 84 feet in group B it was significantly higher and came to 0,893. The difference between these proportions is statistically highly significant (t = 5.84, p <0.001). Chi-square test (χ2 = 30.083 df = 1 N = 172, p <0.001) indicated that there is a

  10. The Geriatric Functional Score Scale: A Preliminary Report on a Useful Tool for Assessing the Elderly.

    ERIC Educational Resources Information Center

    Lowe, Shari; Durrell, Kelly

    1988-01-01

    The Geriatric Function Score Scale was developed for the elderly. It is an objective tool that examines physical, cognitive, and motivational components of functioning. Results of a preliminary study revealed that the score patients received was able to discriminate the level of placement they would need upon hospital discharge. (Author/CH)

  11. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

    PubMed

    Tang, Yat T; Marshall, Garland R

    2011-02-28

    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 (r(pred)2) 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 (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). 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

  12. Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks.

    PubMed

    Yan, Chengfei; Grinter, Sam Z; Merideth, Benjamin Ryan; Ma, Zhiwei; Zou, Xiaoqin

    2016-06-27

    In this study, we developed two iterative knowledge-based scoring functions, ITScore_pdbbind(rigid) and ITScore_pdbbind(flex), using rigid decoy structures and flexible decoy structures, respectively, that were generated from the protein-ligand complexes in the refined set of PDBbind 2012. These two scoring functions were evaluated using the 2013 and 2014 CSAR benchmarks. The results were compared with the results of two other scoring functions, the Vina scoring function and ITScore, the scoring function that we previously developed from rigid decoy structures for a smaller set of protein-ligand complexes. A graph-based method was developed to evaluate the root-mean-square deviation between two conformations of the same ligand with different atom names and orders due to different file preparations, and the program is freely available. Our study showed that the two new scoring functions developed from the larger training set yielded significantly improved performance in binding mode predictions. For binding affinity predictions, all four scoring functions showed protein-dependent performance. We suggest the development of protein-family-dependent scoring functions for accurate binding affinity prediction.

  13. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.

    PubMed

    Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao

    2017-02-21

    In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole spectrum of protein-ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous. Scoring functions are often tested in molecular docking or even virtual screening trials, which do not directly reflect the genuine quality of scoring functions. Collectively, these underlying obstacles have impeded the invention of more advanced scoring functions. In this Account, we describe our long-lasting efforts to overcome these obstacles, which involve two related projects. On the first project, we have created the PDBbind database. It is the first database that systematically annotates the protein-ligand complexes in the Protein Data Bank (PDB) with experimental binding data. This database has been updated annually since its first public release in 2004. The latest release (version 2016) provides binding data for 16 179 biomolecular complexes in PDB. Data sets provided by PDBbind have been applied to many computational and statistical studies on protein-ligand interaction and various subjects. In particular, it has become a major data resource for scoring function development. On the second project, we have established the Comparative Assessment of Scoring Functions (CASF) benchmark for scoring function evaluation. Our key idea is to decouple the "scoring" process from the "sampling" process, so scoring functions can be tested in a relatively pure context to reflect their quality. In our

  14. Correlating observed odds ratios from lung cancer case-control studies to SNP functional scores predicted by bioinformatic tools

    PubMed Central

    Zhu, Yong; Hoffman, Aaron; Wu, Xifeng; Zhang, Heping; Zhang, Yawei; Leaderer, Derek; Zheng, Tongzhang

    2008-01-01

    Bioinformatic tools are widely utilized to predict functional single nucleotide polymorphisms (SNPs) for genotyping in molecular epidemiological studies. However, the extent to which these approaches are mirrored by epidemiological findings has not been fully explored. In this study, we first surveyed SNPs examined in case-control studies of lung cancer, the most extensively-studied cancer type. We then computed SNP functional scores using four popular bioinformatics tools: SIFT, PolyPhen, SNPs3D, and PMut, and determined their predictive potential using the odds ratios (ORs) reported. Spearman’s correlation coefficient (r) for the association with SNP score from SIFT, PolyPhen, SNPs3D, and PMut, and the summary ORs were r = −0.36 (p = 0.007), r = 0.25 (p = 0.068), r = −0.20 (p = 0.205), and r = −0.12 (p = 0.370) respectively. By creating a combined score using information from all four tools we were able to achieve a correlation coefficient of r = 0.51 (p < 0.001). These results indicate that scores of predicted functionality could explain a certain fraction of the lung cancer risk detected in genetic association studies and more accurate predictions may be obtained by combining information from a variety of tools. Our findings suggest that bioinformatic tools are useful in predicting SNP functionality and may facilitate future genetic epidemiological studies. PMID:18191955

  15. Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

    NASA Astrophysics Data System (ADS)

    Korb, Oliver; ten Brink, Tim; Victor Paul Raj, Fredrick Robin Devadoss; Keil, Matthias; Exner, Thomas E.

    2012-02-01

    Due to the large number of different docking programs and scoring functions available, researchers are faced with the problem of selecting the most suitable one when starting a structure-based drug discovery project. To guide the decision process, several studies comparing different docking and scoring approaches have been published. In the context of comparing scoring function performance, it is common practice to use a predefined, computer-generated set of ligand poses (decoys) and to reevaluate their score using the set of scoring functions to be compared. But are predefined decoy sets able to unambiguously evaluate and rank different scoring functions with respect to pose prediction performance? This question arose when the pose prediction performance of our piecewise linear potential derived scoring functions (Korb et al. in J Chem Inf Model 49:84-96, 2009) was assessed on a standard decoy set (Cheng et al. in J Chem Inf Model 49:1079-1093, 2009). While they showed excellent pose identification performance when they were used for rescoring of the predefined decoy conformations, a pronounced degradation in performance could be observed when they were directly applied in docking calculations using the same test set. This implies that on a discrete set of ligand poses only the rescoring performance can be evaluated. For comparing the pose prediction performance in a more rigorous manner, the search space of each scoring function has to be sampled extensively as done in the docking calculations performed here. We were able to identify relative strengths and weaknesses of three scoring functions (ChemPLP, GoldScore, and Astex Statistical Potential) by analyzing the performance for subsets of the complexes grouped by different properties of the active site. However, reasons for the overall poor performance of all three functions on this test set compared to other test sets of similar size could not be identified.

  16. 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.

  17. 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.

  18. Accurate calculation of Green functions on the d-dimensional hypercubic lattice

    NASA Astrophysics Data System (ADS)

    Loh, Yen Lee

    2011-07-01

    We write the Green function of the d-dimensional hypercubic lattice in a piecewise form covering the entire real frequency axis. Each piece is a single integral involving modified Bessel functions of the first and second kinds. The smoothness of the integrand allows both real and imaginary parts of the Green function to be computed quickly and accurately for any dimension d and any real frequency, and the computational time scales only linearly with d.

  19. 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

  20. 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.

  1. Accurate measurement method of Fabry-Perot cavity parameters via optical transfer function

    SciTech Connect

    Bondu, Francois; Debieu, Olivier

    2007-05-10

    It is shown how the transfer function from frequency noise to a Pound-Drever-Hall signal for a Fabry-Perot cavity can be used to accurately measure cavity length, cavity linewidth, mirror curvature, misalignments, laser beam shape mismatching with resonant beam shape, and cavity impedance mismatching with respect to vacuum.

  2. Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions

    NASA Astrophysics Data System (ADS)

    Heim, Andrew J.; Li, Zhijun

    2012-03-01

    Membrane proteins are of particular biological and pharmaceutical importance, and computational modeling and structure prediction approaches play an important role in studies of membrane proteins. Developing an accurate model quality assessment program is of significance to the structure prediction of membrane proteins. Few such programs are proposed that can be applied to a broad range of membrane protein classes and perform with high accuracy. We developed a new model scoring function Interaction-based Quality assessment (IQ), based on the analysis of four types of inter-residue interactions within the transmembrane domains of helical membrane proteins. This function was tested using three high-quality model sets: all 206 models of GPCR Dock 2008, all 284 models of GPCR Dock 2010, and all 92 helical membrane protein models of the HOMEP set. For all three sets, the scoring function can select the native structures among all of the models with the success rates of 93, 85, and 100% respectively. For comparison, these three model sets were also adopted for a recently published model assessment program for membrane protein structures, ProQM, which gave the success rates of 85, 79, and 92% separately. These results suggested that IQ outperforms ProQM when only the transmembrane regions of the models are considered. This scoring function should be useful for the computational modeling of membrane proteins.

  3. Correlation between musculoskeletal function and radiological joint scores in haemophilia A adolescents.

    PubMed

    Hassan, T H; Badr, M A; El-Gerby, K M

    2011-11-01

    The functional independence score in haemophilia (FISH) is a performance-based instrument used to assess musculoskeletal function in patients with haemophilia. We aimed to evaluate the functional independence of haemophilia A adolescents and its correlation to radiological joint scores. A cross-sectional study was carried out on 50 adolescent haemophilia A patients. Musculoskeletal function was assessed using the FISH and individual joints were assessed radiologically using the Pettersson score and MRI scale. The mean age of our patients was 16 ± 1.1 with a mean FISH of 23.32 ± 4.69 (range 13-28) and a mean Pettersson score of 2.32 ± 3.09 (range 0-13) for the knees, 1.86 ± 2.67 (range 0-11) for ankles and 1.42 ± 2.17 (range 0-10) for elbows. The mean MRI score for the knees was 3.92 ± 2.74 (range 0-10) while that for ankles was 3.16 ± 2.64 (range 0-10) and for elbows was 2.34 ± 2.63 (range 0-10). There was highly significant correlation between both radiological joint scores and FISH and between degree of factor VIII deficiency and each of FISH, Pettersson score and MRI score. MRI was superior to conventional radiography in detection of subchondral cyst formation and erosions at joint margins. Given the highly significant correlation with both radiological joint scores, FISH appears to be a reliable tool for assessment of functional independence in adolescents with haemophilia A. MRI is more sensitive than conventional radiography in detection of early joint abnormalities.

  4. The Ulcerative Colitis Endoscopic Index of Severity More Accurately Reflects Clinical Outcomes and Long-term Prognosis than the Mayo Endoscopic Score

    PubMed Central

    Ikeya, Kentaro; Sugimoto, Ken; Osawa, Satoshi; Kawasaki, Shinsuke; Iida, Takayuki; Maruyama, Yasuhiko; Watanabe, Fumitoshi

    2016-01-01

    Background and Aims: The Ulcerative Colitis Endoscopic Index of Severity (UCEIS) and the Mayo endoscopic score (Mayo ES) are used to evaluate ulcerative colitis (UC) severity. This study compared UCEIS and the Mayo ES for evaluating UC severity and outcomes in patients undergoing remission induction during routine clinical practice with the aim of predicting medium- to long-term prognosis. Methods: Forty-one UC patients who received colonoscopy before and after tacrolimus remission induction therapy were included. An index of clinical activity and endoscopic findings scored by both the UCEIS and the Mayo ES were determined. Changes in UCEIS and Mayo ES before and after induction therapy were compared. Results: The mean UCEIS improved from 6.2±0.9 to 3.4±2.1 (p < 0.001). Based on the UCEIS, a significant reduction was reached in both the response and the remission groups. In contrast, the Mayo ES did not reflect a significant change in the response group. The discrepancy appeared to be due to ulcers becoming smaller and shallower during the early stages of mucosal healing; the Mayo ES seems to miss these early changes. In other words, whereas the UCEIS indicates improvements when ulcers shrink, the Mayo ES does not distinguish deep ulcers from shallow ulcers and is 3 (severe UC) for both deep and shallow ulcers. Additionally, better UCEIS strata after induction therapy were associated with lower incidences of colectomy (p = 0.0001) or relapse (p = 0.0008). Conclusions: The UCEIS accurately reflects clinical outcomes and predicts the medium- to long-term prognosis in UC patients undergoing induction therapy. These findings should support decision-making in clinical practice settings. PMID:26581895

  5. A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

    PubMed Central

    2014-01-01

    We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616

  6. GFscore: a general nonlinear consensus scoring function for high-throughput docking.

    PubMed

    Betzi, Stéphane; Suhre, Karsten; Chétrit, Bernard; Guerlesquin, Françoise; Morelli, Xavier

    2006-01-01

    Most of the recent published works in the field of docking and scoring protein/ligand complexes have focused on ranking true positives resulting from a Virtual Library Screening (VLS) through the use of a specified or consensus linear scoring function. In this work, we present a methodology to speed up the High Throughput Screening (HTS) process, by allowing focused screens or for hitlist triaging when a prohibitively large number of hits is identified in the primary screen, where we have extended the principle of consensus scoring in a nonlinear neural network manner. This led us to introduce a nonlinear Generalist scoring Function, GFscore, which was trained to discriminate true positives from false positives in a data set of diverse chemical compounds. This original Generalist scoring Function is a combination of the five scoring functions found in the CScore package from Tripos Inc. GFscore eliminates up to 75% of molecules, with a confidence rate of 90%. The final result is a Hit Enrichment in the list of molecules to investigate during a research campaign for biological active compounds where the remaining 25% of molecules would be sent to in vitro screening experiments. GFscore is therefore a powerful tool for the biologist, saving both time and money.

  7. Measuring Knowledge of Mathematical Functions: Validity of Scores and Profiles of Participants

    ERIC Educational Resources Information Center

    Higley, Kelli

    2009-01-01

    Knowledge of mathematical functions is expected of university students. This knowledge was measured in this dissertation using two previously untested instruments. The aim of this dissertation was to validate the scores from these measures. The first instrument measured function knowledge in its declarative, procedural, or conditional form. The…

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Relationships between functional movement screen scores, maturation and physical performance in young soccer players.

    PubMed

    Lloyd, Rhodri S; Oliver, Jon L; Radnor, John M; Rhodes, Benjamin C; Faigenbaum, Avery D; Myer, Gregory D

    2015-01-01

    The purpose of this study was to examine relationships between functional movement screen scores, maturation and physical performance in young soccer players. Thirty males (11-16 years) were assessed for maturation, functional movement screen scores and a range of physical performance tests (squat jump, reactive strength index protocol and reactive agility cut). Older players significantly outperformed younger participants in all tests (P < 0.05; effect sizes = 1.25-3.40). Deep overhead squat, in-line lunge, active straight leg raise and rotary stability test were significantly correlated to all performance tests. In-line lunge performance explained the greatest variance in reactive strength index (adjusted R(2) = 47%) and reactive agility cut (adjusted R(2) = 38%) performance, whilst maturation was the strongest predictor of squat jump performance (adjusted R(2) = 46%). This study demonstrated that variation of physical performance in youth soccer players could be explained by a combination of both functional movement screen scores and maturation.

  10. Ability of Lower-Extremity Injury Severity Scores to Predict Functional Outcome After Limb Salvage

    PubMed Central

    Ly, Thuan V.; Travison, Thomas G.; Castillo, Renan C.; Bosse, Michael J.; MacKenzie, Ellen J.

    2008-01-01

    Background: Lower-extremity injury severity scoring systems were developed to assist surgeons in decision-making regarding whether to amputate or perform limb salvage after high-energy trauma to the lower extremity. These scoring systems have been shown to not be good predictors of limb amputation or salvage. This study was performed to evaluate the clinical utility of the five commonly used lower-extremity injury severity scoring systems as predictors of final functional outcome. Methods: We analyzed data from a cohort of patients who participated in a multicenter prospective study of clinical and functional outcomes after high-energy lower-extremity trauma. Injury severity was assessed with use of the Mangled Extremity Severity Score; the Limb Salvage Index; the Predictive Salvage Index; the Nerve Injury, Ischemia, Soft-Tissue Injury, Skeletal Injury, Shock, and Age of Patient Score; and the Hannover Fracture Scale-98. Functional outcomes were measured with use of the physical and psychosocial domains of the Sickness Impact Profile at both six months and two years following hospital discharge. Four hundred and seven subjects for whom the reconstruction regimen was considered successful at six months were included in the analysis. We used partial correlation statistics and multiple linear regression models to quantify the association between injury severity scores and Sickness Impact Profile outcomes with the subjects' ages held constant. Results: The mean age of the patients was thirty-six years (interquartile range, twenty-six to forty-four years); 75.2% were male and 24.8% were female. The median Sickness Impact Profile scores were 15.2 and 6.0 points at six and twenty-four months, respectively. The analysis showed that none of the scoring systems were predictive of the Sickness Impact Profile outcomes at six or twenty-four months to any reasonable degree. Likewise, none were predictive of patient recovery between six and twenty-four months postoperatively as

  11. 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

  12. AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes.

    PubMed

    Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M

    2008-07-01

    In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.

  13. NNScore 2.0: a neural-network receptor-ligand scoring function.

    PubMed

    Durrant, Jacob D; McCammon, J Andrew

    2011-11-28

    NNScore is a neural-network-based scoring function designed to aid the computational identification of small-molecule ligands. While the test cases included in the original NNScore article demonstrated the utility of the program, the application examples were limited. The purpose of the current work is to further confirm that neural-network scoring functions are effective, even when compared to the scoring functions of state-of-the-art docking programs, such as AutoDock, the most commonly cited program, and AutoDock Vina, thought to be two orders of magnitude faster. Aside from providing additional validation of the original NNScore function, we here present a second neural-network scoring function, NNScore 2.0. NNScore 2.0 considers many more binding characteristics when predicting affinity than does the original NNScore. The network output of NNScore 2.0 also differs from that of NNScore 1.0; rather than a binary classification of ligand potency, NNScore 2.0 provides a single estimate of the pK(d). To facilitate use, NNScore 2.0 has been implemented as an open-source python script. A copy can be obtained from http://www.nbcr.net/software/nnscore/ .

  14. Propensity Scores

    ERIC Educational Resources Information Center

    Luellen, Jason K.; Shadish, William R.; Clark, M. H.

    2005-01-01

    Propensity score analysis is a relatively recent statistical innovation that is useful in the analysis of data from quasi-experiments. The goal of propensity score analysis is to balance two non-equivalent groups on observed covariates to get more accurate estimates of the effects of a treatment on which the two groups differ. This article…

  15. 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.

  16. The Performance of the Upper Limb scores correlate with pulmonary function test measures and Egen Klassifikation scores in Duchenne muscular dystrophy.

    PubMed

    Lee, Ha Neul; Sawnani, Hemant; Horn, Paul S; Rybalsky, Irina; Relucio, Lani; Wong, Brenda L

    2016-01-01

    The Performance of the Upper Limb scale was developed as an outcome measure specifically for ambulant and non-ambulant patients with Duchenne muscular dystrophy and is implemented in clinical trials needing longitudinal data. The aim of this study is to determine whether this novel tool correlates with functional ability using pulmonary function test, cardiac function test and Egen Klassifikation scale scores as clinical measures. In this cross-sectional study, 43 non-ambulatory Duchenne males from ages 10 to 30 years and on long-term glucocorticoid treatment were enrolled. Cardiac and pulmonary function test results were analyzed to assess cardiopulmonary function, and Egen Klassifikation scores were analyzed to assess functional ability. The Performance of the Upper Limb scores correlated with pulmonary function measures and had inverse correlation with Egen Klassifikation scores. There was no correlation with left ventricular ejection fraction and left ventricular dysfunction. Body mass index and decreased joint range of motion affected total Performance of the Upper Limb scores and should be considered in clinical trial designs.

  17. An accurate solution of elastodynamic problems by numerical local Green's functions

    NASA Astrophysics Data System (ADS)

    Loureiro, F. S.; Silva, J. E. A.; Mansur, W. J.

    2015-09-01

    Green's function based methodologies for elastodynamics in both time and frequency domains, which can be either numerical or analytical, appear in many branches of physics and engineering. Thus, the development of exact expressions for Green's functions is of great importance. Unfortunately, such expressions are known only for relatively few kinds of geometry, medium and boundary conditions. In this way, due to the difficulty in finding exact Green's functions, specially in the time domain, the present paper presents a solution of the transient elastodynamic equations by a time-stepping technique based on the Explicit Green's Approach method written in terms of the Green's and Step response functions, both being computed numerically by the finite element method. The major feature is the computation of these functions separately by the central difference time integration scheme and locally owing to the principle of causality. More precisely, Green's functions are computed only at t = Δt adopting two time substeps while Step response functions are computed directly without substeps. The proposed time-stepping method shows to be quite accurate with distinct numerical properties not presented in the standard central difference scheme as addressed in the numerical example.

  18. 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.

  19. The MATPHOT Algorithm for Accurate and Precise Stellar Photometry and Astrometry Using Discrete Point Spread Functions

    NASA Astrophysics Data System (ADS)

    Mighell, K. J.

    2004-12-01

    I describe the key features of my MATPHOT algorithm for accurate and precise stellar photometry and astrometry using discrete Point Spread Functions. A discrete Point Spread Function (PSF) is a sampled version of a continuous two-dimensional PSF. The shape information about the photon scattering pattern of a discrete PSF is typically encoded using a numerical table (matrix) or a FITS image file. The MATPHOT algorithm shifts discrete PSFs within an observational model using a 21-pixel-wide damped sinc function and position partial derivatives are computed using a five-point numerical differentiation formula. The MATPHOT algorithm achieves accurate and precise stellar photometry and astrometry of undersampled CCD observations by using supersampled discrete PSFs that are sampled 2, 3, or more times more finely than the observational data. I have written a C-language computer program called MPD which is based on the current implementation of the MATPHOT algorithm; all source code and documentation for MPD and support software is freely available at the following website: http://www.noao.edu/staff/mighell/matphot . I demonstrate the use of MPD and present a detailed MATPHOT analysis of simulated James Webb Space Telescope observations which demonstrates that millipixel relative astrometry and millimag photometric accuracy is achievable with very complicated space-based discrete PSFs. This work was supported by a grant from the National Aeronautics and Space Administration (NASA), Interagency Order No. S-13811-G, which was awarded by the Applied Information Systems Research (AISR) Program of NASA's Science Mission Directorate.

  20. 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.

  1. Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

    PubMed

    Wang, Jui-Chih; Lin, Jung-Hsin; Chen, Chung-Ming; Perryman, Alex L; Olson, Arthur J

    2011-10-24

    Ordinary least-squares (OLS) regression has been used widely for constructing the scoring functions for protein-ligand interactions. However, OLS is very sensitive to the existence of outliers, and models constructed using it are easily affected by the outliers or even the choice of the data set. On the other hand, determination of atomic charges is regarded as of central importance, because the electrostatic interaction is known to be a key contributing factor for biomolecular association. In the development of the AutoDock4 scoring function, only OLS was conducted, and the simple Gasteiger method was adopted. It is therefore of considerable interest to see whether more rigorous charge models could improve the statistical performance of the AutoDock4 scoring function. In this study, we have employed two well-established quantum chemical approaches, namely the restrained electrostatic potential (RESP) and the Austin-model 1-bond charge correction (AM1-BCC) methods, to obtain atomic partial charges, and we have compared how different charge models affect the performance of AutoDock4 scoring functions. In combination with robust regression analysis and outlier exclusion, our new protein-ligand free energy regression model with AM1-BCC charges for ligands and Amber99SB charges for proteins achieve lowest root-mean-squared error of 1.637 kcal/mol for the training set of 147 complexes and 2.176 kcal/mol for the external test set of 1427 complexes. The assessment for binding pose prediction with the 100 external decoy sets indicates very high success rate of 87% with the criteria of predicted root-mean-squared deviation of less than 2 Å. The success rates and statistical performance of our robust scoring functions are only weakly class-dependent (hydrophobic, hydrophilic, or mixed).

  2. 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.

  3. Accurate alkynyl radical structures from density functional calculations without Hartree-Fock exchange

    NASA Astrophysics Data System (ADS)

    Janesko, Benjamin G.; Proynov, Emil

    2017-02-01

    Density functional approximations (DFAs) often suffer from self-repulsion and delocalization errors which are reduced by exact (Hartree-Fock-like) exchange admixture. Oyeyemi and co-workers recently showed that several DFAs with little exact exchange incorrectly predict bent alkynyl radical geometries, giving errors in ab initio composite methods using density functional theory geometries [V. B. Oyeyemi et al., J. Phys. Chem. Lett. 3, 289 (2012)]. We show that the simple Hartree-Fock-Slater and Xα DFAs, which have substantial delocalization error, predict linear alkynyl radical geometries without incorporating exact exchange. Our Rung 3.5 DFAs, and rescaled generalized gradient approximations, can give either linear σ, bent σ -π , or nearly linear π radicals, all without incorporating exact exchange. This highlights the complexity of delocalization error, the utility of accurate empirical DFA geometries for ab initio composite methods, and the insights to be gained from Rung 3.5 DFAs.

  4. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB).

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-06-05

    The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

  5. Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

    NASA Astrophysics Data System (ADS)

    Buda, I. G.; Lane, C.; Barbiellini, B.; Ruzsinszky, A.; Sun, J.; Bansil, A.

    2017-03-01

    We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functional for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.

  6. Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

    PubMed Central

    Buda, I. G.; Lane, C.; Barbiellini, B.; Ruzsinszky, A.; Sun, J.; Bansil, A.

    2017-01-01

    We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functional for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally. PMID:28333131

  7. 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.

  8. 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.

  9. The female sexual function index (FSFI): cross-validation and development of clinical cutoff scores.

    PubMed

    Wiegel, Markus; Meston, Cindy; Rosen, Raymond

    2005-01-01

    The Female Sexual Function Index (FSFI) is a brief multidimensional scale for assessing sexual function in women. The scale has received initial psychometric evaluation, including studies of reliability, convergent validity, and discriminant validity (Meston, 2003; Rosen et al., 2000). The present study was designed to crossvalidate the FSFI in several samples of women with mixed sexual dysfunctions (N = 568) and to develop diagnostic cut-off scores for potential classification of women's sexual dysfunction. Some of these samples were drawn from our previous validation studies (N = 414), and some were added for purposes of the present study (N = 154). The combined data set consisted of multiple samples of women with sexual dysfunction diagnoses (N = 307), including female sexual arousal disorder (FSAD), hypoactive sexual desire disorder (HSDD), female sexual orgasm disorder (FSOD), dyspareunia/vaginismus (pain), and multiple sexual dysfunctions, in addition to a large sample of nondysfunctional controls (n = 261). We conducted analyses on the individual and combined samples, including replicating the original factor structure using principal components analysis with varimax rotation. We assessed Cronbach's alpha (internal reliability) and interdomain correlations and tested discriminant validity by means of a MANOVA (multivariate analysis of variance; dysfunction diagnosis x FSFI domain), with Bonferroni-corrected post hoc comparisons. We developed diagnostic cut off scores by means of standard receiver operating characteristics-curves and the CART (Classification and Regression Trees) procedure. Principal components analysis replicated the original five-factor structure, including desire/arousal, lubrication, orgasm, pain, and satisfaction. We found the internal reliability for the total FSFI and six domain scores to be good to excellent, with Cronbach alpha's >0.9 for the combined sample and above 0.8 for the sexually dysfunctional and nondysfunctional samples

  10. Increasing the utility of the Functional Assessment for Burns Score: Not just for major burns.

    PubMed

    Smailes, Sarah T; Engelsman, Kayleen; Rodgers, Louise; Upson, Clara

    2016-02-01

    The Functional Assessment for Burns (FAB) score is established as an objective measure of physical function that predicts discharge outcome in adult patients with major burn. However, its validity in patients with minor and moderate burn is unknown. This is a multi-centre evaluation of the predictive validity of the FAB score for discharge outcome in adult inpatients with minor and moderate burns. FAB assessments were undertaken within 48 h of admission to (FAB 1), and within 48 h of discharge (FAB 2) from burn wards in 115 patients. Median age was 45 years and median burn size 4%. There were significant improvements in the patients' FAB scores (p<0.0001), 98 patients were discharged home (no social care) and 17 patients discharged to further inpatient rehabilitation or home with social care. FAB 1 score (≤ 14) is strongly associated with discharge to inpatient rehabilitation or home with social care (p=0.0001) and as such can be used to facilitate early discharge planning. FAB 2 (≤ 30) independently predicts discharge outcome to inpatient rehabilitation or home with social care (p<0.0001), increasing its utility to patients with minor and moderate burns.

  11. Painfree and accurate Bayesian estimation of psychometric functions for (potentially) overdispersed data.

    PubMed

    Schütt, Heiko H; Harmeling, Stefan; Macke, Jakob H; Wichmann, Felix A

    2016-05-01

    The psychometric function describes how an experimental variable, such as stimulus strength, influences the behaviour of an observer. Estimation of psychometric functions from experimental data plays a central role in fields such as psychophysics, experimental psychology and in the behavioural neurosciences. Experimental data may exhibit substantial overdispersion, which may result from non-stationarity in the behaviour of observers. Here we extend the standard binomial model which is typically used for psychometric function estimation to a beta-binomial model. We show that the use of the beta-binomial model makes it possible to determine accurate credible intervals even in data which exhibit substantial overdispersion. This goes beyond classical measures for overdispersion-goodness-of-fit-which can detect overdispersion but provide no method to do correct inference for overdispersed data. We use Bayesian inference methods for estimating the posterior distribution of the parameters of the psychometric function. Unlike previous Bayesian psychometric inference methods our software implementation-psignifit 4-performs numerical integration of the posterior within automatically determined bounds. This avoids the use of Markov chain Monte Carlo (MCMC) methods typically requiring expert knowledge. Extensive numerical tests show the validity of the approach and we discuss implications of overdispersion for experimental design. A comprehensive MATLAB toolbox implementing the method is freely available; a python implementation providing the basic capabilities is also available.

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

    PubMed Central

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

    2015-01-01

    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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Approximate but accurate quantum dynamics from the Mori formalism. II. Equilibrium time correlation functions.

    PubMed

    Montoya-Castillo, Andrés; Reichman, David R

    2017-02-28

    The ability to efficiently and accurately calculate equilibrium time correlation functions of many-body condensed phase quantum systems is one of the outstanding problems in theoretical chemistry. The Nakajima-Zwanzig-Mori formalism coupled to the self-consistent solution of the memory kernel has recently proven to be highly successful for the computation of nonequilibrium dynamical averages. Here, we extend this formalism to treat symmetrized equilibrium time correlation functions for the spin-boson model. Following the first paper in this series [A. Montoya-Castillo and D. R. Reichman, J. Chem. Phys. 144, 184104 (2016)], we use a Dyson-type expansion of the projected propagator to obtain a self-consistent solution for the memory kernel that requires only the calculation of normally evolved auxiliary kernels. We employ the approximate mean-field Ehrenfest method to demonstrate the feasibility of this approach. Via comparison with numerically exact results for the correlation function Czz(t)=Re⟨σz(0)σz(t)⟩, we show that the current scheme affords remarkable boosts in accuracy and efficiency over bare Ehrenfest dynamics. We further explore the sensitivity of the resulting dynamics to the choice of kernel closures and the accuracy of the initial canonical density operator.

  18. MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences

    PubMed Central

    2012-01-01

    Background Computational approaches for finding DNA regulatory motifs in promoter sequences are useful to biologists in terms of reducing the experimental costs and speeding up the discovery process of de novo binding sites. It is important for rule-based or clustering-based motif searching schemes to effectively and efficiently evaluate the similarity between a k-mer (a k-length subsequence) and a motif model, without assuming the independence of nucleotides in motif models or without employing computationally expensive Markov chain models to estimate the background probabilities of k-mers. Also, it is interesting and beneficial to use a priori knowledge in developing advanced searching tools. Results This paper presents a new scoring function, termed as MISCORE, for functional motif characterization and evaluation. Our MISCORE is free from: (i) any assumption on model dependency; and (ii) the use of Markov chain model for background modeling. It integrates the compositional complexity of motif instances into the function. Performance evaluations with comparison to the well-known Maximum a Posteriori (MAP) score and Information Content (IC) have shown that MISCORE has promising capabilities to separate and recognize functional DNA motifs and its instances from non-functional ones. Conclusions MISCORE is a fast computational tool for candidate motif characterization, evaluation and selection. It enables to embed priori known motif models for computing motif-to-motif similarity, which is more advantageous than IC and MAP score. In addition to these merits mentioned above, MISCORE can automatically filter out some repetitive k-mers from a motif model due to the introduction of the compositional complexity in the function. Consequently, the merits of our proposed MISCORE in terms of both motif signal modeling power and computational efficiency will make it more applicable in the development of computational motif discovery tools. PMID:23282090

  19. 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.

  20. 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.

  1. Cluster abundance in chameleon f(R) gravity I: toward an accurate halo mass function prediction

    NASA Astrophysics Data System (ADS)

    Cataneo, Matteo; Rapetti, David; Lombriser, Lucas; Li, Baojiu

    2016-12-01

    We refine the mass and environment dependent spherical collapse model of chameleon f(R) gravity by calibrating a phenomenological correction inspired by the parameterized post-Friedmann framework against high-resolution N-body simulations. We employ our method to predict the corresponding modified halo mass function, and provide fitting formulas to calculate the enhancement of the f(R) halo abundance with respect to that of General Relativity (GR) within a precision of lesssim 5% from the results obtained in the simulations. Similar accuracy can be achieved for the full f(R) mass function on the condition that the modeling of the reference GR abundance of halos is accurate at the percent level. We use our fits to forecast constraints on the additional scalar degree of freedom of the theory, finding that upper bounds competitive with current Solar System tests are within reach of cluster number count analyses from ongoing and upcoming surveys at much larger scales. Importantly, the flexibility of our method allows also for this to be applied to other scalar-tensor theories characterized by a mass and environment dependent spherical collapse.

  2. Negative emotions affect postoperative scores for evaluating functional knee recovery and quality of life after total knee replacement.

    PubMed

    Qi, A; Lin, C; Zhou, A; Du, J; Jia, X; Sun, L; Zhang, G; Zhang, L; Liu, M

    2016-01-01

    This study aimed to determine whether psychological factors affect health-related quality of life (HRQL) and recovery of knee function in total knee replacement (TKR) patients. A total of 119 TKR patients (male: 38; female: 81) completed the Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI), State Trait Anxiety Inventory (STAI), Eysenck Personality Questionnaire-revised (EPQR-S), Knee Society Score (KSS), and HRQL (SF-36). At 1 and 6 months after surgery, anxiety, depression, and KSS scores in TKR patients were significantly better compared with those preoperatively (P<0.05). SF-36 scores at the sixth month after surgery were significantly improved compared with preoperative scores (P<0.001). Preoperative Physical Component Summary Scale (PCS) and Mental Component Summary Scale (MCS) scores were negatively associated with extraversion (E score) (B=-0.986 and -0.967, respectively, both P<0.05). Postoperative PCS and State Anxiety Inventory (SAI) scores were negatively associated with neuroticism (N score; B=-0.137 and -0.991, respectively, both P<0.05). Postoperative MCS, SAI, Trait Anxiety Inventory (TAI), and BAI scores were also negatively associated with the N score (B=-0.367, -0.107, -0.281, and -0.851, respectively, all P<0.05). The KSS function score at the sixth month after surgery was negatively associated with TAI and N scores (B=-0.315 and -0.532, respectively, both P<0.05), but positively associated with the E score (B=0.215, P<0.05). The postoperative KSS joint score was positively associated with postoperative PCS (B=0.356, P<0.05). In conclusion, for TKR patients, the scores used for evaluating recovery of knee function and HRQL after 6 months are inversely associated with the presence of negative emotions.

  3. Negative emotions affect postoperative scores for evaluating functional knee recovery and quality of life after total knee replacement

    PubMed Central

    Qi, A.; Lin, C.; Zhou, A.; Du, J.; Jia, X.; Sun, L.; Zhang, G.; Zhang, L.; Liu, M.

    2015-01-01

    This study aimed to determine whether psychological factors affect health-related quality of life (HRQL) and recovery of knee function in total knee replacement (TKR) patients. A total of 119 TKR patients (male: 38; female: 81) completed the Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI), State Trait Anxiety Inventory (STAI), Eysenck Personality Questionnaire-revised (EPQR-S), Knee Society Score (KSS), and HRQL (SF-36). At 1 and 6 months after surgery, anxiety, depression, and KSS scores in TKR patients were significantly better compared with those preoperatively (P<0.05). SF-36 scores at the sixth month after surgery were significantly improved compared with preoperative scores (P<0.001). Preoperative Physical Component Summary Scale (PCS) and Mental Component Summary Scale (MCS) scores were negatively associated with extraversion (E score) (B=-0.986 and -0.967, respectively, both P<0.05). Postoperative PCS and State Anxiety Inventory (SAI) scores were negatively associated with neuroticism (N score; B=-0.137 and -0.991, respectively, both P<0.05). Postoperative MCS, SAI, Trait Anxiety Inventory (TAI), and BAI scores were also negatively associated with the N score (B=-0.367, -0.107, -0.281, and -0.851, respectively, all P<0.05). The KSS function score at the sixth month after surgery was negatively associated with TAI and N scores (B=-0.315 and -0.532, respectively, both P<0.05), but positively associated with the E score (B=0.215, P<0.05). The postoperative KSS joint score was positively associated with postoperative PCS (B=0.356, P<0.05). In conclusion, for TKR patients, the scores used for evaluating recovery of knee function and HRQL after 6 months are inversely associated with the presence of negative emotions. PMID:26577843

  4. Reliability of clinician scoring of the functional movement screen to assess movement patterns.

    PubMed

    Stobierski, Lisa M; Fayson, Shirleeah D; Minthorn, Lindsay M; Valovich McLeod, Tamara C; Welch, Cailee E

    2015-05-01

    Clinical Scenario: Injuries are inevitable in the physically active population. As a part of preventive medicine, health care professionals often seek clinical tools that can be used in real time to identify factors that may predispose individuals to these injuries. The Functional Movement Screen (FMS), a clinical tool consisting of 7 individual tasks, has been reported as useful in identifying individuals in various populations that may be susceptible to musculoskeletal injuries. If factors that may predispose physically active individuals to injury could be identified before participation, clinicians may be able to develop a training plan based on FMS scores, which could potentially decrease the likelihood of injury and overall time missed from physical activities. However, in order for a screening tool to be used clinically, it must demonstrate acceptable reliability. Focused Clinical Question: Are clinicians reliable at scoring the FMS, in real time, to assess movement patterns of physically active individuals?

  5. 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.

  6. 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

  7. 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

  8. Acoustic radiation force impulse elastography for chronic liver disease: comparison with ultrasound-based scores of experienced radiologists, Child-Pugh scores and liver function tests.

    PubMed

    Kim, Ji Eun; Lee, Jae Young; Kim, Yoon Jun; Yoon, Jung Hwan; Kim, Se Hyung; Lee, Jeong Min; Han, Joon Koo; Choi, Byung Ihn

    2010-10-01

    The purpose of our study was to investigate whether acoustic radiation force impulse (ARFI) elastography provides better diagnostic performance for diagnosis of chronic liver disease and correlates better with Child-Pugh scores and liver function tests, compared with an ultrasound (US) scoring system based on visual assessment of conventional B-mode US images by experienced radiologists. Five hundred and twenty-one patients with clinically proven chronic liver disease (n = 293), fatty liver (n = 95) or normal liver (n = 133) were included in this study. B-mode liver US and ARFI elastography were performed in all patients. ARFI elastography was performed at least five times, with each measurement obtained at a different area of the right hepatic lobe; mean shear wave velocity (SWV) was calculated for each patient. The mean SWV was compared with US-based scores from two radiologists (based on liver surface nodularity, parenchyma echotexture and hepatic vein contour), Child-Pugh scores and liver function tests. The mean SWV of the normal liver group was 1.08 m/s ± 0.15; of the fatty liver group, 1.02 m/s ± 0.16; and of the chronic liver disease group, 1.66 m/s ± 0.60 (p < 0.001). The area under the receiver operating characteristics curve of the mean SWV in ARFI elastography was significantly higher than that of the conventional B-mode US-based scores by two radiologists (0.89 vs. 0.74 and 0.77, p < 0.05), with a sensitivity of 75.4% and a specificity of 89.5% at the cut-off value of 1.22 m/s. The sensitivity of the mean SWV was significantly higher than the US-based scores (p < 0.001), although the specificity was not (p > 0.05). The mean SWV was better correlated with Child-Pugh scores and all liver function tests (except total protein) than the US-based scores from two radiologists. In conclusion, ARFI elastography showed better diagnostic performance than visual assessment of experienced radiologists for diagnosis of chronic liver disease, as well as for

  9. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data.

    PubMed

    Hawkins, Troy; Chitale, Meghana; Luban, Stanislav; Kihara, Daisuke

    2009-02-15

    Protein function prediction is a central problem in bioinformatics, increasing in importance recently due to the rapid accumulation of biological data awaiting interpretation. Sequence data represents the bulk of this new stock and is the obvious target for consideration as input, as newly sequenced organisms often lack any other type of biological characterization. We have previously introduced PFP (Protein Function Prediction) as our sequence-based predictor of Gene Ontology (GO) functional terms. PFP interprets the results of a PSI-BLAST search by extracting and scoring individual functional attributes, searching a wide range of E-value sequence matches, and utilizing conventional data mining techniques to fill in missing information. We have shown it to be effective in predicting both specific and low-resolution functional attributes when sufficient data is unavailable. Here we describe (1) significant improvements to the PFP infrastructure, including the addition of prediction significance and confidence scores, (2) a thorough benchmark of performance and comparisons to other related prediction methods, and (3) applications of PFP predictions to genome-scale data. We applied PFP predictions to uncharacterized protein sequences from 15 organisms. Among these sequences, 60-90% could be annotated with a GO molecular function term at high confidence (>or=80%). We also applied our predictions to the protein-protein interaction network of the Malaria plasmodium (Plasmodium falciparum). High confidence GO biological process predictions (>or=90%) from PFP increased the number of fully enriched interactions in this dataset from 23% of interactions to 94%. Our benchmark comparison shows significant performance improvement of PFP relative to GOtcha, InterProScan, and PSI-BLAST predictions. This is consistent with the performance of PFP as the overall best predictor in both the AFP-SIG '05 and CASP7 function (FN) assessments. PFP is available as a web service at http://dragon.bio.purdue.edu/pfp/.

  10. Graduate student WAIS-III scoring accuracy is a function of full scale IQ and complexity of examiner tasks.

    PubMed

    Hopwood, Christopher J; Richard, David C S

    2005-12-01

    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, recording, and scoring tasks have not been systematically varied. In this study, graduate student participants score a high (FSIQ = 112) and low (FSIQ = 85) IQ record form in one of two stimulus conditions: digitized film clips (N = 13) or partially completed record forms (N = 11). Results demonstrate that examiners are less accurate in the high IQ condition, and that recording examinee responses from scoring video clips results in more scoring errors. Obtained FSIQs are significantly higher than criterion IQ scores in the high IQ condition (8.46 for video condition, 2.55 for record form condition). Self-reported proficiency in WAIS-III administration and scoring is positively related to number of scoring errors.

  11. Functional neuroimaging of visuospatial working memory tasks enables accurate detection of attention deficit and hyperactivity disorder

    PubMed Central

    Hammer, Rubi; Cooke, Gillian E.; Stein, Mark A.; Booth, James R.

    2015-01-01

    Finding neurobiological markers for neurodevelopmental disorders, such as attention deficit and hyperactivity disorder (ADHD), is a major objective of clinicians and neuroscientists. We examined if functional Magnetic Resonance Imaging (fMRI) data from a few distinct visuospatial working memory (VSWM) tasks enables accurately detecting cases with ADHD. We tested 20 boys with ADHD combined type and 20 typically developed (TD) boys in four VSWM tasks that differed in feedback availability (feedback, no-feedback) and reward size (large, small). We used a multimodal analysis based on brain activity in 16 regions of interest, significantly activated or deactivated in the four VSWM tasks (based on the entire participants' sample). Dimensionality of the data was reduced into 10 principal components that were used as the input variables to a logistic regression classifier. fMRI data from the four VSWM tasks enabled a classification accuracy of 92.5%, with high predicted ADHD probability values for most clinical cases, and low predicted ADHD probabilities for most TDs. This accuracy level was higher than those achieved by using the fMRI data of any single task, or the respective behavioral data. This indicates that task-based fMRI data acquired while participants perform a few distinct VSWM tasks enables improved detection of clinical cases. PMID:26509111

  12. 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.

  13. 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.

  14. The functional SYNTAX score - a huge step forward or research in motion?

    PubMed

    Dehnee, Abed; Gerula, Christine; Mazza, Victor; Maher, James; Dhruvakumar, Sandiya; Kaluski, Edo

    2012-06-01

    In a recent manuscript in the Journal of the American College of Cardiology, the newly introduced "functional SYNTAX score" (FSS) was found to be a better tool to assess the extent and severity of coronary artery disease than the SYNTAX score (SS) and has reclassified 1/3 of the studied cohort into lower-risk categories. Besides being more invasive, costly, and time consuming, FSS still suffers from inherent deficiencies of its own. Like SS, FSS does not incorporate clinical risk predictors and consequently is a suboptimal tool for predicting PCI risk. FSS is not supported by a wealth of contemporary outcome data in a wide range of patient and lesions subsets. Key unanswered questions are whether PCI of hemodynamically significant lesions (FFR <0.80) is superior to optimal medical therapy (OMT) and whether complete revascularization yields considerably better outcomes than partial revascularization. Since partial revascularization is still an option, operational FSS (taking into account only the FSS of lesions subject to PCI) combined with a clinical risk score will probably better predict the procedural risk of the planned PCI.

  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. 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

  18. 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…

  19. Validation of functional fetal autonomic brain age score fABAS in 5 min short recordings.

    PubMed

    Hoyer, Dirk; Schneider, Uwe; Kowalski, Eva-Maria; Schmidt, Alexander; Witte, Otto W; Schleußner, Ekkehard; Hatzmann, Wolfgang; Grönemeyer, Dietrich Hw; van Leeuwen, Peter

    2015-11-01

    With the objective of evaluating the functional maturation age and developmental disturbances we have previously introduced the fetal autonomic brain age score (fABAS) using 30 min fetal magnetocardiographic recordings (fMCG, Jena). The score is based on heart rate pattern indices that are related to universal principles of developmental biology. The present work aims at the validation of the fABAS methodology on 5 min recordings from an independent database (fMCG, Bochum).We found high agreement of fABAS obtained from Jena normal fetuses (5 min subsets, n =  364) and Bochum recordings (n =  322, normal fetuses). fABAS of 48 recordings from fetuses with intra-uterine growth restriction (IUGR, Bochum) was reduced in most of the cases, a result consistent with IUGR fetuses from Jena previously reported. fABAS calculated from 5 min snapshots only partly covers the accuracy when compared to fABAS from 30 min recordings. More precise diagnosis requires longer recordings.fABAS obtained from fMCG recordings is a strong candidate for standardized assessment of functional maturation age and developmental disturbances. Even 5 min recordings seem to be valuable for screening for maturation problems.

  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

    2014-09-04

    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.

  1. Accurate dispersion interactions from standard density-functional theory methods with small basis sets.

    PubMed

    Mackie, Iain D; Dilabio, Gino A

    2010-06-21

    B971, PBE and PBE1 density functionals with 6-31G(d) basis sets are shown to accurately describe the binding in dispersion bound dimers. This is achieved through the use of dispersion-correcting potentials (DCPs) in conjunction with counterpoise corrections. DCPs resemble and are applied like conventional effective core potentials that can be used with most computational chemistry programs without code modification. Rather, DCPs are implemented by simple appendage to the input files for these types of programs. Binding energies are predicted to within ca. 11% and monomer separations to within ca. 0.06 A of high-level wavefunction data using B971/6-31G(d)-DCP. Similar results are obtained for PBE and PBE1 with the 6-31G(d) basis sets and DCPs. Although results found using the 3-21G(d) are not as impressive, they never-the-less show promise as a means of initial study for a wide variety of dimers, including those dominated by dispersion, hydrogen-bonding and a mixture of interactions. Notable improvement is found in comparison to M06-2X/6-31G(d) data, e.g., mean absolute deviations for the S22-set of dimers of ca. 13.6 and 16.5% for B971/6-31G(d)-DCP and M06-2X, respectively. However, it should be pointed out that the latter data were obtained using a larger integration grid size since a smaller grid results in different binding energies and geometries for simple dispersion-bound dimers such as methane and ethene.

  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. 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

  4. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    PubMed

    Li, Liqi; Cui, Xiang; 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.

  5. 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

  6. Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.

    PubMed

    Tsuchiya, Yuko; Kanamori, Eiji; Nakamura, Haruki; Kinoshita, Kengo

    2009-01-01

    Protein-protein docking simulations can provide the predicted complex structural models. In a docking simulation, several putative structural models are selected by scoring functions from an ensemble of many complex models. Scoring functions based on statistical analyses of heterodimers are usually designed to select the complex model with the most abundant interaction mode found among the known complexes, as the correct model. However, because the formation schemes of heterodimers are extremely diverse, a single scoring function does not seem to be sufficient to describe the fitness of the predicted models other than the most abundant interaction mode. Thus, it is necessary to classify the heterodimers in terms of their individual interaction modes, and then to construct multiple scoring functions for each heterodimer type. In this study, we constructed the classification method of heterodimers based on the discriminative characters between near-native and decoy models, which were found in the comparison of the interfaces in terms of the complementarities for the hydrophobicity, the electrostatic potential and the shape. Consequently, we found four heterodimer clusters, and then constructed the multiple scoring functions, each of which was optimized for each cluster. Our multiple scoring functions were applied to the predictions in the unbound docking.

  7. 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.

  8. [Videofluoroscopic Examination of Swallowing Using the AsR Score for Postoperative Swallowing Function in Oral Cancer Patients].

    PubMed

    Suzuki, Motoyuki; Fujii, Takashi; Yoshii, Tadashi; Otozai, Shinji; Kida, Kohta; Sugawa, Toshimitsu; Kitamura, Koji; Kanamura, Ryo; Koike, Ryosuke

    2015-07-01

    To evaluate the postoperative swallowing function in head and neck cancer patients, videofluoroscopic examination of swallowing (VF) proved useful as a qualitative evaluation, but was complex as a quantitative evaluation. We made use of the AsR score which consisted of a 10-point scale as a quantitative evaluation of VF. To identify the usefulness of the AsR score, 146 patients who had undergone extensive resection and reconstruction with free flaps or pedicle grafts were reviewed. The AsR score of VF for the first time after surgery was defined as "first score", and at the last time in the hospital was defined as "last score". The correlations between the first score and continuity of direct therapy, and between the last score and way of nutrition at the time of discharge were examined. Using the ROC (receiver operator characteristic) analysis and the AUC (area under the curve) the cut-off values of the AsR score were estimated. One hundred and thirty one patients could continue direct therapy after the first time of VF. The first score detected continuity of direct therapy with high accuracy (AUC = 0.946), furthermore using a cut-off of 5, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were about 96.2%, 86.6%, 98.4%, and 72.2%, respectively. At the time of discharge, 138 patients had no limitation of oral intake and 8 patients had a limitation e.g. PEG (n = 7) and a total laryngectomy for preventing aspiration (n = 1). The last score detected oral intake ability with no limitation with high accuracy (AUC = 0.925). Using a cut-off of 6, the sensitivity, specificity, PPV and NPV were about 82.6%, 87.5%, 99.1% and 22.6%, respectively. The AsR score is useful as a quantitative evaluation of postoperative swallowing function in oral cancer patients.

  9. CAD-score: a new contact area difference-based function for evaluation of protein structural models.

    PubMed

    Olechnovič, Kliment; Kulberkytė, Eleonora; Venclovas, Ceslovas

    2013-01-01

    Evaluation of protein models against the native structure is essential for the development and benchmarking of protein structure prediction methods. Although a number of evaluation scores have been proposed to date, many aspects of model assessment still lack desired robustness. In this study we present CAD-score, a new evaluation function quantifying differences between physical contacts in a model and the reference structure. The new score uses the concept of residue-residue contact area difference (CAD) introduced by Abagyan and Totrov (J Mol Biol 1997; 268:678-685). Contact areas, the underlying basis of the score, are derived using the Voronoi tessellation of protein structure. The newly introduced CAD-score is a continuous function, confined within fixed limits, free of any arbitrary thresholds or parameters. The built-in logic for treatment of missing residues allows consistent ranking of models of any degree of completeness. We tested CAD-score on a large set of diverse models and compared it to GDT-TS, a widely accepted measure of model accuracy. Similarly to GDT-TS, CAD-score showed a robust performance on single-domain proteins, but displayed a stronger preference for physically more realistic models. Unlike GDT-TS, the new score revealed a balanced assessment of domain rearrangement, removing the necessity for different treatment of single-domain, multi-domain, and multi-subunit structures. Moreover, CAD-score makes it possible to assess the accuracy of inter-domain or inter-subunit interfaces directly. In addition, the approach offers an alternative to the superposition-based model clustering. The CAD-score implementation is available both as a web server and a standalone software package at http://www.ibt.lt/bioinformatics/cad-score/.

  10. To examine the relationship between the Functional Movement Screen and the Landing Error Scoring System in an active collegiate population.

    PubMed

    Everard, E; Harrison, Aj; Lyons, M

    2016-07-25

    In recent years there has been an increasing focus on movement screening as the principal aspect of pre-participation testing. Two of the most common movement screening tools are the Functional Movement Screen (FMS) and the Landing Error Scoring System (LESS). Several studies have examined the reliability and validity of these tools but so far there have been no studies comparing the results of these two screening tools against each other. Therefore, the purpose of this study was to determine the relationship between Functional Movement Screen (FMS) scores and Landing Error Scoring System (LESS) scores. Ninety-eight male college athletes actively competing in sport (Gaelic games, soccer, athletics, boxing/mixed martial arts, Olympic weight lifting) participated in the study and performed the FMS and LESS screens. Both the 21 point and 100 point scoring systems were used to score the FMS. Spearman's correlation coefficients were used to determine the relationship between the two screening scores. The results showed a significant moderate correlation between FMS and LESS scores (rho 100 and 21 point = -.528; -.487; p< .001). In addition, r values of .26 and .23 indicate a poor shared variance between the two screens. The results indicate that performing well in one of the screens does not necessarily equate to performing well in the other. This has practical implications as it highlights that both screens may assess different movement patterns and should not be used as a substitute for each other.

  11. A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands

    NASA Astrophysics Data System (ADS)

    Kelemen, Ádám A.; Ferenczy, György G.; Keserű, György M.

    2015-01-01

    A physicochemical property-based desirability scoring scheme for fragment-based drug discovery was developed for class A aminergic GPCR targeted fragment libraries. Physicochemical property distributions of known aminergic GPCR-active fragments from the ChEMBL database were examined and used for a desirability function-based score. Property-distributions such as log D (at pH 7.4), PSA, pKa (strongest basic center), number of nitrogen atoms, number of oxygen atoms, and the number of rotatable bonds were combined into a desirability score (FrAGS). The validation of the scoring scheme was carried out using both public and proprietary experimental screening data. The scoring scheme is suitable for the design of aminergic GPCR targeted fragment libraries and might be useful for preprocessing fragments before structure based virtual or wet screening.

  12. Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.

    PubMed

    Hsieh, Meng-Juei; Luo, Ray

    2004-08-15

    A well-behaved physics-based all-atom scoring function for protein structure prediction is analyzed with several widely used all-atom decoy sets. The scoring function, termed AMBER/Poisson-Boltzmann (PB), is based on a refined AMBER force field for intramolecular interactions and an efficient PB model for solvation interactions. Testing on the chosen decoy sets shows that the scoring function, which is designed to consider detailed chemical environments, is able to consistently discriminate all 62 native crystal structures after considering the heteroatom groups, disulfide bonds, and crystal packing effects that are not included in the decoy structures. When NMR structures are considered in the testing, the scoring function is able to discriminate 8 out of 10 targets. In the more challenging test of selecting near-native structures, the scoring function also performs very well: for the majority of the targets studied, the scoring function is able to select decoys that are close to the corresponding native structures as evaluated by ranking numbers and backbone Calpha root mean square deviations. Various important components of the scoring function are also studied to understand their discriminative contributions toward the rankings of native and near-native structures. It is found that neither the nonpolar solvation energy as modeled by the surface area model nor a higher protein dielectric constant improves its discriminative power. The terms remaining to be improved are related to 1-4 interactions. The most troublesome term is found to be the large and highly fluctuating 1-4 electrostatics term, not the dihedral-angle term. These data support ongoing efforts in the community to develop protein structure prediction methods with physics-based potentials that are competitive with knowledge-based potentials.

  13. Comparing neural-network scoring functions and the state of the art: applications to common library screening.

    PubMed

    Durrant, Jacob D; Friedman, Aaron J; Rogers, Kathleen E; McCammon, J Andrew

    2013-07-22

    We compare established docking programs, AutoDock Vina and Schrödinger's Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statistically different than the mean performance obtained when docking and scoring with Glide. We further demonstrate that the Vina and NNScore docking scores both correlate with chemical properties like small-molecule size and polarizability. Compensating for these potential biases leads to improvements in virtual screen performance. Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design.

  14. Accurate calculation and Matlab based fast realization of merit function's Hesse matrix for the design of multilayer optical coating

    NASA Astrophysics Data System (ADS)

    Wu, Su-Yong; Long, Xing-Wu; Yang, Kai-Yong

    2009-09-01

    To improve the current status of home multilayer optical coating design with low speed and poor efficiency when a large layer number occurs, the accurate calculation and fast realization of merit function’s gradient and Hesse matrix is pointed out. Based on the matrix method to calculate the spectral properties of multilayer optical coating, an analytic model is established theoretically. And the corresponding accurate and fast computation is successfully achieved by programming with Matlab. Theoretical and simulated results indicate that this model is mathematically strict and accurate, and its maximal precision can reach floating-point operations in the computer, with short time and fast speed. Thus it is very suitable to improve the optimal search speed and efficiency of local optimization methods based on the derivatives of merit function. It has outstanding performance in multilayer optical coating design with a large layer number.

  15. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.

    PubMed

    Arnautova, Yelena A; Vorobjev, Yury N; Vila, Jorge A; Scheraga, Harold A

    2009-10-01

    Availability of energy functions which can discriminate native-like from non-native protein conformations is crucial for theoretical protein structure prediction and refinement of low-resolution protein models. This article reports the results of benchmark tests for scoring functions based on two all-atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent-accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent-accessible surface area model of Ooi et al. (Proc Natl Acad Sci USA 1987;84:3086-3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/FAMBEpH). Short Monte Carlo-with-Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native-like and non-native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native-like structures with C(alpha) root-mean-square-deviations below 3.5 A as lowest-energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein-solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native-like structures cannot be discriminated as those with low

  16. 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…

  17. Job Choice As a Function of SES and Achievement Scores For High School Students.

    ERIC Educational Resources Information Center

    Nelms, Charlie; And Others

    1982-01-01

    Investigated impact of socio-economic status (SES) and achievement scores on job choice for 128 participants in a Labor Market Orientation Training program. Neither SES nor the program measure ("World of Work") were significant, but "Wide Range Achievement Test" gain scores did significantly impact on job choice. (Author/BRR)

  18. Personnel Selection Procedures as a Function of Sample Size, Cut Scores, and Quartile Ranking.

    ERIC Educational Resources Information Center

    Ferrara, F. Felicia

    Cut scores, quartile ranking, sample size, and overall classification scheme were studied as personnel selection procedures in two samples. The first was 120 simulated observations of employee scores based on actual selection procedures for applicants for administrative assistant positions. The other sample was composed of test results for 73…

  19. Improving the full spectrum fitting method: accurate convolution with Gauss-Hermite functions

    NASA Astrophysics Data System (ADS)

    Cappellari, Michele

    2017-04-01

    I start by providing an updated summary of the penalized pixel-fitting (PPXF) method that is used to extract the stellar and gas kinematics, as well as the stellar population of galaxies, via full spectrum fitting. I then focus on the problem of extracting the kinematics when the velocity dispersion σ is smaller than the velocity sampling ΔV that is generally, by design, close to the instrumental dispersion σinst. The standard approach consists of convolving templates with a discretized kernel, while fitting for its parameters. This is obviously very inaccurate when σ ≲ ΔV/2, due to undersampling. Oversampling can prevent this, but it has drawbacks. Here I present a more accurate and efficient alternative. It avoids the evaluation of the undersampled kernel and instead directly computes its well-sampled analytic Fourier transform, for use with the convolution theorem. A simple analytic transform exists when the kernel is described by the popular Gauss-Hermite parametrization (which includes the Gaussian as special case) for the line-of-sight velocity distribution. I describe how this idea was implemented in a significant upgrade to the publicly available PPXF software. The key advantage of the new approach is that it provides accurate velocities regardless of σ. This is important e.g. for spectroscopic surveys targeting galaxies with σ ≪ σinst, for galaxy redshift determinations or for measuring line-of-sight velocities of individual stars. The proposed method could also be used to fix Gaussian convolution algorithms used in today's popular software packages.

  20. 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.

  1. Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening.

    PubMed

    Ain, Qurrat Ul; Aleksandrova, Antoniya; Roessler, Florian D; Ballester, Pedro J

    2015-01-01

    Docking tools to predict whether and how a small molecule binds to a target can be applied if a structural model of such target is available. The reliability of docking depends, however, on the accuracy of the adopted scoring function (SF). Despite intense research over the years, improving the accuracy of SFs for structure-based binding affinity prediction or virtual screening has proven to be a challenging task for any class of method. New SFs based on modern machine-learning regression models, which do not impose a predetermined functional form and thus are able to exploit effectively much larger amounts of experimental data, have recently been introduced. These machine-learning SFs have been shown to outperform a wide range of classical SFs at both binding affinity prediction and virtual screening. The emerging picture from these studies is that the classical approach of using linear regression with a small number of expert-selected structural features can be strongly improved by a machine-learning approach based on nonlinear regression allied with comprehensive data-driven feature selection. Furthermore, the performance of classical SFs does not grow with larger training datasets and hence this performance gap is expected to widen as more training data becomes available in the future. Other topics covered in this review include predicting the reliability of a SF on a particular target class, generating synthetic data to improve predictive performance and modeling guidelines for SF development. WIREs Comput Mol Sci 2015, 5:405-424. doi: 10.1002/wcms.1225 For further resources related to this article, please visit the WIREs website.

  2. Chronic kidney disease-epidemiology formula and model for end-stage liver disease score in the assessment of renal function in candidates for liver transplantation.

    PubMed

    Tinti, F; Lai, S; Umbro, I; Mordenti, M; Barile, M; Ginanni Corradini, S; Rossi, M; Poli, L; Nofroni, I; Berloco, P B; Mitterhofer, A P

    2010-05-01

    Assessment of renal function in patients with end-stage liver disease (ESLD) awaiting liver transplantation (OLT) is critical. Various conditions may cause renal damage in ESLD. Renal and liver functions are intertwined due to splanchnic hemodynamic relationships; renal failure rarely occurs in patients without advanced decompensated cirrhosis. The recent literature suggests that evaluation of renal function should include an assessment of liver function. The aim of this study was to evaluate different methods to estimate glomerular filtration rate (GFR) in patient among ESLD candidates for OLT over 1 year. We also correlated renal and hepatic functions. Fifty-two cirrhotic patients Model for End-Stage Liver Disease [MELD] > 10) were enrolled in the study. All patients were evaluated at baseline and every 4 months (T1-T4) thereafter for 1 year. The GFR was calculated by creatinine clearance, and estimated by Cockroft and Gault, Modified Diet Renal Disease (MDRD) 4 and 6 variable and Chronic Kidney Disease-Epidemiology (CKD-EPI) formulae. Hepatic functions were evaluated by MELD score, albumin, bilirubin, and International Normalized Ratio (INR). We observed not statistically significant increase mean value of MELD score, bilirubin, serum creatinine, and blood urea nitrogen and a reduced serum sodium. There were no significant differences among various methods to evaluate GFR at each time over 1 year. We did not observe any association between renal and hepatic function, except at T4 for MELD and GFR estimated with MDRD 4 (P = .009) and 6 (P = .008) parameters or CKD-EPI (P = .036), and MELD and sodium (P = .001). Our results showed that evaluation of renal function in cirrhosis should include an evaluation of hepatic function. In our case, MDRD and CKD-EPI seemed to be the more accurate formulae to evaluate renal function in relation to hepatic function.

  3. Unified treatment for accurate and fast evaluation of the Fermi-Dirac functions

    NASA Astrophysics Data System (ADS)

    Guseinov, I. I.; Mamedov, B. A.

    2010-05-01

    A new analytical approach to the computation of the Fermi-Dirac (FD) functions is presented, which was suggested by previous experience with various algorithms. Using the binomial expansion theorem, these functions are expressed through the binomial coefficients and familiar incomplete Gamma functions. This simplification and the use of the memory of the computer for the calculation of binomial coefficients may extend the limits to large arguments for users and result in speedier calculation, should such limits be required in practice. Some numerical results are presented for significant mapping examples and they are briefly discussed.

  4. A New Class of Highly Accurate Differentiation Schemes Based on the Prolate Spheroidal Wave Functions

    DTIC Science & Technology

    2011-04-07

    absolute and relative errors to approximate the derivatives of functions f : [−1, 1] → R with bandlimit roughly c with differentiation matrices constructed...of dimension N − 2 Ec = relative l2 error when D or DC is used to approximate the second derivatives of the functions sin(cx)− x sin(c) and cos(cx...dates back to the first half of the nineteenth century, is the finite difference method. It approximates the derivative of a function f : R → R at a

  5. 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

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

    PubMed

    Li, Yang; Yang, Jianyi

    2017-04-05

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

  7. Relationships between spatial activities and scores on the mental rotation test as a function of sex.

    PubMed

    Ginn, Sheryl R; Pickens, Stefanie J

    2005-06-01

    Previous results suggested that female college students' scores on the Mental Rotations Test might be related to their prior experience with spatial tasks. For example, women who played video games scored better on the test than their non-game-playing peers, whereas playing video games was not related to men's scores. The present study examined whether participation in different types of spatial activities would be related to women's performance on the Mental Rotations Test. 31 men and 59 women enrolled at a small, private church-affiliated university and majoring in art or music as well as students who participated in intercollegiate athletics completed the Mental Rotations Test. Women's scores on the Mental Rotations Test benefitted from experience with spatial activities; the more types of experience the women had, the better their scores. Thus women who were athletes, musicians, or artists scored better than those women who had no experience with these activities. The opposite results were found for the men. Efforts are currently underway to assess how length of experience and which types of experience are related to scores.

  8. Total Cerebral Small Vessel Disease MRI Score Is Associated with Cognitive Decline in Executive Function in Patients with Hypertension.

    PubMed

    Uiterwijk, Renske; van Oostenbrugge, Robert J; Huijts, Marjolein; De Leeuw, Peter W; Kroon, Abraham A; Staals, Julie

    2016-01-01

    Objectives: Hypertension is a major risk factor for white matter hyperintensities (WMH), lacunes, cerebral microbleeds, and perivascular spaces, which are MRI markers of cerebral small vessel disease (SVD). Studies have shown associations between these individual MRI markers and cognitive functioning and decline. Recently, a "total SVD score" was proposed in which the different MRI markers were combined into one measure of SVD, to capture total SVD-related brain damage. We investigated if this SVD score was associated with cognitive decline over 4 years in patients with hypertension. Methods: In this longitudinal cohort study, 130 hypertensive patients (91 patients with uncomplicated hypertension and 39 hypertensive patients with a lacunar stroke) were included. They underwent a neuropsychological assessment at baseline and after 4 years. The presence of WMH, lacunes, cerebral microbleeds, and perivascular spaces were rated on baseline MRI. Presence of each individual marker was added to calculate the total SVD score (range 0-4) in each patient. Results: Uncorrected linear regression analyses showed associations between SVD score and decline in overall cognition (p = 0.017), executive functioning (p < 0.001) and information processing speed (p = 0.037), but not with memory (p = 0.911). The association between SVD score and decline in overall cognition and executive function remained significant after adjustment for age, sex, education, anxiety and depression score, potential vascular risk factors, patient group, and baseline cognitive performance. Conclusion: Our study shows that a total SVD score can predict cognitive decline, specifically in executive function, over 4 years in hypertensive patients. This emphasizes the importance of considering total brain damage due to SVD.

  9. 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

  10. Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures

    NASA Astrophysics Data System (ADS)

    Tøndel, Kristin; Anderssen, Endre; Drabløs, Finn

    2006-03-01

    Protein Alpha Shape (PAS) Dock is a new empirical score function suitable for virtual library screening using homology modelled protein structures. Here, the score function is used in combination with the geometry search method Tabu search. A description of the protein binding site is generated using gaussian property fields like in Protein Alpha Shape Similarity Analysis (PASSA). Gaussian property fields are also used to describe the ligand properties. The overlap between the receptor and ligand hydrophilicity and lipophilicity fields is maximised, while minimising steric clashes. Gaussian functions introduce a smoothing of the property fields. This makes the score function robust against small structural variations, and therefore suitable for use with homology models. This also makes it less critical to include protein flexibility in the docking calculations. We use a fast and simplified version of the score function in the geometry search, while a more detailed version is used for the final prediction of the binding free energies. This use of a two-level scoring makes PAS-Dock computationally efficient, and well suited for virtual screening. The PAS-Dock score function is trained on 218 X-ray structures of protein- ligand complexes with experimental binding affinities. The performance of PAS-Dock is compared to two other docking methods, AutoDock and MOE-Dock, with respect to both accuracy and computational efficiency. According to this study, PAS-Dock is more computationally efficient than both AutoDock and MOE-Dock, and gives a better prediction of the free energies of binding. PAS-Dock is also more robust against structural variations than AutoDock.

  11. 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

  12. A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL

    NASA Astrophysics Data System (ADS)

    Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; García, Yamila; Puris, Amilkar; Bello, Rafael; Green, James; Sotomayor-Torres, Clivia M.

    2014-08-01

    Most successful structure prediction strategies use knowledge-based functions for global optimization, in spite of their intrinsic limited potential to create new folds, while physics-based approaches are often employed only during structure refinement steps. We here propose a physics-based scoring potential intended to perform global searches of the conformational space. We introduce a dynamic test to evaluate the discrimination power of our function, and compare it with predictions of targets from the CASP-ROLL competition. Results demonstrate that this dynamic test is able to generate 3D models which outrank 59% (according GDT_TS score) of models generated with ab initio structure prediction servers.

  13. PEER RATING VALIDITY AS A FUNCTION OF RATER INTELLIGENCE AND RATING SCORE RECEIVED

    DTIC Science & Technology

    intelligence there is little reason to take into consideration rather intelligence when concerned with the validity of the ratings he gives . This is also true for the Peer Rating score received by the rater.

  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. 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.

  16. 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.

  17. Total Cerebral Small Vessel Disease MRI Score Is Associated with Cognitive Decline in Executive Function in Patients with Hypertension

    PubMed Central

    Uiterwijk, Renske; van Oostenbrugge, Robert J.; Huijts, Marjolein; De Leeuw, Peter W.; Kroon, Abraham A.; Staals, Julie

    2016-01-01

    Objectives: Hypertension is a major risk factor for white matter hyperintensities (WMH), lacunes, cerebral microbleeds, and perivascular spaces, which are MRI markers of cerebral small vessel disease (SVD). Studies have shown associations between these individual MRI markers and cognitive functioning and decline. Recently, a “total SVD score” was proposed in which the different MRI markers were combined into one measure of SVD, to capture total SVD-related brain damage. We investigated if this SVD score was associated with cognitive decline over 4 years in patients with hypertension. Methods: In this longitudinal cohort study, 130 hypertensive patients (91 patients with uncomplicated hypertension and 39 hypertensive patients with a lacunar stroke) were included. They underwent a neuropsychological assessment at baseline and after 4 years. The presence of WMH, lacunes, cerebral microbleeds, and perivascular spaces were rated on baseline MRI. Presence of each individual marker was added to calculate the total SVD score (range 0–4) in each patient. Results: Uncorrected linear regression analyses showed associations between SVD score and decline in overall cognition (p = 0.017), executive functioning (p < 0.001) and information processing speed (p = 0.037), but not with memory (p = 0.911). The association between SVD score and decline in overall cognition and executive function remained significant after adjustment for age, sex, education, anxiety and depression score, potential vascular risk factors, patient group, and baseline cognitive performance. Conclusion: Our study shows that a total SVD score can predict cognitive decline, specifically in executive function, over 4 years in hypertensive patients. This emphasizes the importance of considering total brain damage due to SVD. PMID:28018214

  18. Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing

    NASA Astrophysics Data System (ADS)

    Paulechka, Eugene; Wassenaar, Tsjerk A.; Kroenlein, Kenneth; Kazakov, Andrei; Smolyanitsky, Alex

    2016-01-01

    We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions.We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07061a

  19. 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

  20. Benchmarking density-functional-theory calculations of rotational g tensors and magnetizabilities using accurate coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Lutnæs, Ola B.; Teale, Andrew M.; Helgaker, Trygve; Tozer, David J.; Ruud, Kenneth; Gauss, Jürgen

    2009-10-01

    An accurate set of benchmark rotational g tensors and magnetizabilities are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster single-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the results obtained is established for the rotational g tensors by careful comparison with experimental data, taking into account zero-point vibrational corrections. After an analysis of the basis sets employed, extrapolation techniques are used to provide estimates of the basis-set-limit quantities, thereby establishing an accurate benchmark data set. The utility of the data set is demonstrated by examining a wide variety of density functionals for the calculation of these properties. None of the density-functional methods are competitive with the CCSD or CCSD(T) methods. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of density-functional calculations constrained to give the same electronic density. The importance of current dependence in exchange-correlation functionals is discussed in light of this comparison.

  1. Efficient floating diffuse functions for accurate characterization of the surface-bound excess electrons in water cluster anions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2017-01-25

    In this work, the effect of diffuse function types (atom-centered diffuse functions versus floating functions and s-type versus p-type diffuse functions) on the structures and properties of three representative water cluster anions featuring a surface-bound excess electron is studied and we find that an effective combination of such two kinds of diffuse functions can not only reduce the computational cost but also, most importantly, considerably improve the accuracy of results and even avoid incorrect predictions of spectra and the EE shape. Our results indicate that (a) simple augmentation of atom-centered diffuse functions is beneficial for the vertical detachment energy convergence, but it leads to very poor descriptions for the singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) distributions of the water cluster anions featuring a surface-bound excess electron and thus a significant ultraviolet spectrum redshift; (b) the ghost-atom-based floating diffuse functions can not only contribute to accurate electronic calculations of the ground state but also avoid poor and even incorrect descriptions of the SOMO and the LUMO induced by excessive augmentation of atom-centered diffuse functions; (c) the floating functions can be realized by ghost atoms and their positions could be determined through an optimization routine along the dipole moment vector direction. In addition, both the s- and p-type floating functions are necessary to supplement in the basis set which are responsible for the ground (s-type character) and excited (p-type character) states of the surface-bound excess electron, respectively. The exponents of the diffuse functions should also be determined to make the diffuse functions cover the main region of the excess electron distribution. Note that excessive augmentation of such diffuse functions is redundant and even can lead to unreasonable LUMO characteristics.

  2. 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

    2010-12-13

    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.

  3. 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.

  4. 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

  5. Predictive validity of the UPDRS postural stability score and the Functional Reach Test, when compared with ecologically valid reaching tasks.

    PubMed

    Jenkins, M E; Johnson, A M; Holmes, J D; Stephenson, F F; Spaulding, S J

    2010-07-01

    Balance problems and falls are a common concern among individuals with Parkinson's disease (PD). Falls frequently occur during daily activities such as reaching into cupboards in the kitchen or bathroom. This study compared the correlation among two standard postural stability tests - the postural stability score on the Unified Parkinson's Disease Rating Scale (UPDRS) and the Functional Reach Test (FRT) - and ecologically valid reaching tasks that correspond to reaching at different cupboard heights among 20 individuals with PD and 20 age-matched controls. Both the FRT and the UPDRS postural stability tests are quick measures that can be performed during the clinical examination. The FRT, but not the postural stability score, demonstrated a significant correlation with the ecologically valid reaching tasks, among individuals with PD. Furthermore the FRT scores did not correlate with the UPDRS postural stability scores, indicating that these are measuring different aspects of balance. This study suggests that the FRT score may better predict the risk of postural instability encountered during daily activities among individuals with PD.

  6. Effects of a Story Map on Accelerated Reader Postreading Test Scores in Students with High-Functioning Autism

    ERIC Educational Resources Information Center

    Stringfield, Suzanne Griggs; Luscre, Deanna; Gast, David L.

    2011-01-01

    In this study, three elementary-aged boys with high-functioning autism (HFA) were taught to use a graphic organizer called a Story Map as a postreading tool during language arts instruction. Students learned to accurately complete the Story Map. The effect of the intervention on story recall was assessed within the context of a multiple-baseline…

  7. A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy.

    PubMed

    Moreira, Irina S; Martins, João M; Coimbra, João T S; Ramos, Maria J; Fernandes, Pedro A

    2015-01-28

    Protein-protein (P-P) 3D structures are fundamental to structural biology and drug discovery. However, most of them have never been determined. Many docking algorithms were developed for that purpose, but they have a very limited accuracy in generating native-like structures and identifying the most correct one, in particular when a single answer is asked for. With such a low success rate it is difficult to point out one docked structure as being native-like. Here we present a new, high accuracy, scoring method to identify the 3D structure of P-P complexes among a set of trial poses. It incorporates alanine scanning mutagenesis experimental data that need to be obtained a priori. The scoring scheme works by matching the computational and the experimental alanine scanning mutagenesis results. The size of the trial P-P interface area is also taken into account. We show that the method ranks the trial structures and identifies the native-like structures with unprecedented accuracy (∼94%), providing the correct P-P 3D structures that biochemists and molecular biologists need to pursue their studies. With such a success rate, the bottleneck of protein-protein docking moves from the scoring to searching algorithms.

  8. 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.

  9. 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,…

  10. Heightened clinical utility of smartphone versus body-worn inertial system for shoulder function B-B score

    PubMed Central

    Aminian, Kamiar; Ancey, Céline; Jaccard, Hervé; Lécureux, Estelle; Duc, Cyntia; Farron, Alain; Jolles, Brigitte M.; Gleeson, Nigel

    2017-01-01

    Background The B-B Score is a straightforward kinematic shoulder function score including only two movements (hand to the Back + lift hand as to change a Bulb) that demonstrated sound measurement properties for patients for various shoulder pathologies. However, the B-B Score results using a smartphone or a reference system have not yet been compared. Provided that the measurement properties are comparable, the use of a smartphone would offer substantial practical advantages. This study investigated the concurrent validity of a smartphone and a reference inertial system for the measurement of the kinematic shoulder function B-B Score. Methods Sixty-five patients with shoulder conditions (with rotator cuff conditions, adhesive capsulitis and proximal humerus fracture) and 20 healthy participants were evaluated using a smartphone and a reference inertial system. Measurements were performed twice, alternating between two evaluators. The B-B Score differences between groups, differences between devices, relationship between devices, intra- and inter-evaluator reproducibility were analysed. Results The smartphone mean scores (SD) were 94.1 (11.1) for controls and 54.1 (18.3) for patients (P < 0.01). The difference between devices was non-significant for the control (P = 0.16) and the patient group (P = 0.81). The analysis of the relationship between devices showed 0.97 ICC, −0.6 bias and −13.2 to 12.0 limits of agreement (LOA). The smartphone intra-evaluator ICC was 0.92, the bias 1.5 and the LOA −17.4 to 20.3. The smartphone inter-evaluator ICC was 0.92, the bias 1.5 and the LOA −16.9 to 20.0. Conclusions The B-B Score results measured with a smartphone were comparable to those of an inertial system. While single measurements diverged in some cases, the intra- and inter-evaluator reproducibility was excellent and was equivalent between devices. The B-B score measured with a smartphone is straightforward and as efficient as a reference inertial system

  11. Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.

    PubMed

    Peterson, Lenna X; Kim, Hyungrae; Esquivel-Rodriguez, Juan; Roy, Amitava; Han, Xusi; Shin, Woong-Hee; Zhang, Jian; Terashi, Genki; Lee, Matt; Kihara, Daisuke

    2017-03-01

    We report the performance of protein-protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community-wide assessment of state-of-the-art docking methods. Our prediction procedure uses a protein-protein docking program named LZerD developed in our group. LZerD represents a protein surface with 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The appropriate soft representation of protein surface with 3DZD makes the method more tolerant to conformational change of proteins upon docking, which adds an advantage for unbound docking. Docking was guided by interface residue prediction performed with BindML and cons-PPISP as well as literature information when available. The generated docking models were ranked by a combination of scoring functions, including PRESCO, which evaluates the native-likeness of residues' spatial environments in structure models. First, we discuss the overall performance of our group in the CAPRI prediction rounds and investigate the reasons for unsuccessful cases. Then, we examine the performance of several knowledge-based scoring functions and their combinations for ranking docking models. It was found that the quality of a pool of docking models generated by LZerD, that is whether or not the pool includes near-native models, can be predicted by the correlation of multiple scores. Although the current analysis used docking models generated by LZerD, findings on scoring functions are expected to be universally applicable to other docking methods. Proteins 2017; 85:513-527. © 2016 Wiley Periodicals, Inc.

  12. Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function.

    PubMed

    Yang, Zheng Rong; Thomson, Rebecca; Hodgman, T Charles; Dry, Jonathan; Doyle, Austin K; Narayanan, Ajit; Wu, XiKun

    2003-11-01

    This paper presents an algorithm which is able to extract discriminant rules from oligopeptides for protease proteolytic cleavage activity prediction. The algorithm is developed using genetic programming. Three important components in the algorithm are a min-max scoring function, the reverse Polish notation (RPN) and the use of minimum description length. The min-max scoring function is developed using amino acid similarity matrices for measuring the similarity between an oligopeptide and a rule, which is a complex algebraic equation of amino acids rather than a simple pattern sequence. The Fisher ratio is then calculated on the scoring values using the class label associated with the oligopeptides. The discriminant ability of each rule can therefore be evaluated. The use of RPN makes the evolutionary operations simpler and therefore reduces the computational cost. To prevent overfitting, the concept of minimum description length is used to penalize over-complicated rules. A fitness function is therefore composed of the Fisher ratio and the use of minimum description length for an efficient evolutionary process. In the application to four protease datasets (Trypsin, Factor Xa, Hepatitis C Virus and HIV protease cleavage site prediction), our algorithm is superior to C5, a conventional method for deriving decision trees.

  13. 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.

  14. SPARC: Accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory: Isolated clusters

    NASA Astrophysics Data System (ADS)

    Ghosh, Swarnava; Suryanarayana, Phanish

    2017-03-01

    As the first component of SPARC (Simulation Package for Ab-initio Real-space Calculations), we present an accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory (DFT) for isolated clusters. Specifically, utilizing a local reformulation of the electrostatics, the Chebyshev polynomial filtered self-consistent field iteration, and a reformulation of the non-local component of the force, we develop a framework using the finite-difference representation that enables the efficient evaluation of energies and atomic forces to within the desired accuracies in DFT. Through selected examples consisting of a variety of elements, we demonstrate that SPARC obtains exponential convergence in energy and forces with domain size; systematic convergence in the energy and forces with mesh-size to reference plane-wave result at comparably high rates; forces that are consistent with the energy, both free from any noticeable 'egg-box' effect; and accurate ground-state properties including equilibrium geometries and vibrational spectra. In addition, for systems consisting up to thousands of electrons, SPARC displays weak and strong parallel scaling behavior that is similar to well-established and optimized plane-wave implementations, but with a significantly reduced prefactor. Overall, SPARC represents an attractive alternative to plane-wave codes for practical DFT simulations of isolated clusters.

  15. 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.

  16. 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

  17. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

    PubMed

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-03-22

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  18. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches †

    PubMed Central

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-01-01

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  19. [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.

  20. Impaired Left Ventricular Diastolic Functions and Thickened Epicardial Adipose Tissue in Rheumatoid Arthritis Patients is Correlated with DAS-28 Score

    PubMed Central

    Alpaydın, Sertac; Buyukterzi, Zafer; Akkurt, Halil Ekrem; Yılmaz, Halim

    2017-01-01

    Background Rheumatoid arthritis (RA) is a chronic inflammatory disease that is known to be associated with high cardiovascular (CV) morbidity and mortality. In this study, we aimed to demonstrate whether RA disease activity reflected with disease activity score-28 (DAS-28) had an impact on left ventricular diastolic functions and epicardial adipose tissue (EAT) thickness in RA patients with no traditional CV risk factors. Methods In this retrospective study, 41 patients newly diagnosed with RA were included. In addition to medical history, detailed physical examination findings and laboratory tests, left ventricular systolic and diastolic functions, chamber dimensions, and EAT thickness were evaluated with transthoracic echocardiography in the study population. Results This study included 41 subjects with a median age of 45 years (38.00-55.50), of which 29.27% were male. In the binomial logistic regression analysis, DAS-28 score was found to be an independent associate of diastolic dysfunction, Additionally, DAS-28 was found to be independently associated with EAT thickness. Conclusions Patients with high DAS-28 score should be evaluated thoroughly for CV disease, and patients should undergo advanced diagnostic studies as required and receive appropriate treatment. PMID:28344422

  1. A scoring strategy combining statistics and functional genomics supports a possible role for common polygenic variation in autism

    PubMed Central

    Carayol, Jérôme; Schellenberg, Gerard D.; Dombroski, Beth; Amiet, Claire; Génin, Bérengère; Fontaine, Karine; Rousseau, Francis; Vazart, Céline; Cohen, David; Frazier, Thomas W.; Hardan, Antonio Y.; Dawson, Geraldine; Rio Frio, Thomas

    2014-01-01

    Autism spectrum disorders (ASD) are highly heritable complex neurodevelopmental disorders with a 4:1 male: female ratio. Common genetic variation could explain 40–60% of the variance in liability to autism. Because of their small effect, genome-wide association studies (GWASs) have only identified a small number of individual single-nucleotide polymorphisms (SNPs). To increase the power of GWASs in complex disorders, methods like convergent functional genomics (CFG) have emerged to extract true association signals from noise and to identify and prioritize genes from SNPs using a scoring strategy combining statistics and functional genomics. We adapted and applied this approach to analyze data from a GWAS performed on families with multiple children affected with autism from Autism Speaks Autism Genetic Resource Exchange (AGRE). We identified a set of 133 candidate markers that were localized in or close to genes with functional relevance in ASD from a discovery population (545 multiplex families); a gender specific genetic score (GS) based on these common variants explained 1% (P = 0.01 in males) and 5% (P = 8.7 × 10−7 in females) of genetic variance in an independent sample of multiplex families. Overall, our work demonstrates that prioritization of GWAS data based on functional genomics identified common variants associated with autism and provided additional support for a common polygenic background in autism. PMID:24600472

  2. A rapid method to score stream reaches based on the overall performance of their main ecological functions.

    PubMed

    Rowe, David K; Parkyn, Stephanie; Quinn, John; Collier, Kevin; Hatton, Chris; Joy, Michael K; Maxted, John; Moore, Stephen

    2009-06-01

    A method was developed to score the ecological condition of first- to third-order stream reaches in the Auckland region of New Zealand based on the performance of their key ecological functions. Such a method is required by consultants and resource managers to quantify the reduction in ecological condition of a modified stream reach relative to its unmodified state. This is a fundamental precursor for the determination of fair environmental compensation for achieving no-net-loss in overall stream ecological value. Field testing and subsequent use of the method indicated that it provides a useful measure of ecological condition related to the performance of stream ecological functions. It is relatively simple to apply compared to a full ecological study, is quick to use, and allows identification of the degree of impairment of each of the key ecological functions. The scoring system was designed so that future improvements in the measurement of stream functions can be incorporated into it. Although the methodology was specifically designed for Auckland streams, the principles can be readily adapted to other regions and stream types.

  3. Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy

    PubMed Central

    Rahaman, Obaidur; Estrada, Trilce P.; Doren, Douglas J.; Taufer, Michela; Brooks, Charles L.; Armen, Roger S.

    2011-01-01

    The performance of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for “step 2 discrimination” were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only “interacting” ligand atoms as the “effective size” of the ligand, and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and five-fold cross validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new dataset (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ dataset where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of

  4. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

    PubMed

    Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

    2011-09-26

    The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand

  5. The Effect of Specific Sling Exercises on the Functional Movement Screen Score in Adolescent Volleyball Players: A Preliminary Study

    PubMed Central

    Saulicz, Edward; Myśliwiec, Andrzej; Wójtowicz, Monika; Wolny, Tomasz

    2016-01-01

    Abstract The existing data indicate that the result of the Functional Movement Screen (FMS) test influences the likelihood of subsequent injury in professional athletes. Therefore, exercises increasing test scores of the FMS may be useful at various stages of sports activity. This study evaluated the effects of the NEURAC sling exercises method on the FMS test score in teenage volleyball players. The study was conducted on 15 volleyball players aged 14 years. The FMS test was performed three times interspersed with a two-month interval. Between the first and the second assessment, neither additional treatment nor training was applied, while between the second and the third assessment, the participants performed stabilisation exercises based on the NEURAC method. Training was carried out twice a week, for eight weeks. The analysis showed that between the first and the second measurement, no significant differences occurred. The use of specific sling exercises caused a significant improvement in FMS results (p ≤ 0.01) between the first and the third, as well as the second and the third measurement. The applied stabilisation exercises based on the NEURAC method positively influenced the FMS test result in male subjects practicing volleyball. Performance of such exercises also resulted in more than 90% of the subjects having a total FMS test score ≥ 17, which may be important in the prevention of injuries. The preliminary results indicate that this type of exercise should be included in a teenage volleyball training routine. PMID:28031760

  6. Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

    NASA Astrophysics Data System (ADS)

    Morley, S. David; Afshar, Mohammad

    2004-03-01

    We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock®, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection (`enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome. Abbreviations: ACD - Available Chemicals Directory; AMP - adenosine monophosphate; EF - enrichment factor; FMN - flavin mononucleotide; FRET - fluorescence resonance energy transfer; RMSD - root mean square deviation; TAR - trans-activation response element; Tat - transcriptional activator protein.

  7. 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

  8. 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…

  9. The effect of gluteus medius strengthening on the knee joint function score and pain in meniscal surgery patients

    PubMed Central

    Kim, Eun-Kyung

    2016-01-01

    [Purpose] The purpose of this study was to analyze the effect of gluteus medius activity strengthening due to squat with isometric hip adduction and hip abduction in side-lying exercise on knee joint function index and pain in meniscal surgery patients. [Subjects and Methods] This study selected sample of 26 patients who had meniscal surgery more than 4 weeks ago. The patients were divided into squat with isometric hip adduction exercise group I (n=8), hip abduction in side-lying exercise group II (n=9), and combined exercise group III. The lysholm score was used to evaluate knee joint function and visual analog scale was used to evaluate pain index of knee joint. [Results] Two-way repeated measures ANOVA was used to analyze the lysholm score and visual analog scale and showed significant interaction between the groups and durations. [Conclusion] Strengthening vastus medialis oblique and gluteus medius improved functional recovery and pain reduction of knee joint in meniscal injury surgery patients. Gluteus medius strengthening exercise is essential to meniscal injury surgery patients and should be included in rehabilitation program in early stages to be conducted systematically. PMID:27821928

  10. 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.

  11. 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.

  12. 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…

  13. Accurate and efficient calculation of van der Waals interactions within density functional theory by local atomic potential approach.

    PubMed

    Sun, Y Y; Kim, Yong-Hyun; Lee, Kyuho; Zhang, S B

    2008-10-21

    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.

  14. Validation of the BETA-2 Score: An Improved Tool to Estimate Beta Cell Function After Clinical Islet Transplantation Using a Single Fasting Blood Sample.

    PubMed

    Forbes, S; Oram, R A; Smith, A; Lam, A; Olateju, T; Imes, S; Malcolm, A J; Shapiro, A M J; Senior, P A

    2016-09-01

    The beta score, a composite measure of beta cell function after islet transplantation, has limited sensitivity because of its categorical nature and requires a mixed-meal tolerance test (MMTT). We developed a novel score based on a single fasting blood sample. The BETA-2 score used stepwise forward linear regression incorporating glucose (in millimoles per liter), C-peptide (in nanomoles per liter), hemoglobin A1c (as a percentage) and insulin dose (U/kg per day) as continuous variables from the original beta score data set (n = 183 MMTTs). Primary and secondary analyses assessed the score's ability to detect glucose intolerance (90-min MMTT glucose ≥8 mmol/L) and insulin independence, respectively. A validation cohort of islet transplant recipients (n = 114 MMTTs) examined 12 mo after transplantation was used to compare the score's ability to detect these outcomes. The BETA-2 score was expressed as follows (range 0-42): [Formula: see text] A score <20 and ≥15 detected glucose intolerance and insulin independence, respectively, with >82% sensitivity and specificity. The BETA-2 score demonstrated greater discrimination than the beta score for these outcomes (p < 0.05). Using a fasting blood sample, the BETA-2 score estimates graft function as a continuous variable and shows greater discrimination of glucose intolerance and insulin independence after transplantation versus the beta score, allowing frequent assessments of graft function. Studies examining its utility to track long-term graft function are required.

  15. Apgar Scores

    MedlinePlus

    ... because she is blue and not pink. Most newborn infants have Apgar scores greater than 7. Because their ... between 8 and 10. A small percentage of newborns have Apgar scores of less than ... low scores than infants with normal births. These scores may reflect difficulties ...

  16. Evaluation of functional ability of rheumatoid arthritis based on HAQ score and BMD among South Indian patients.

    PubMed

    Snekhalatha, U; Anburajan, M

    2012-07-01

    Aim of this study is to analyze the functional ability of rheumatoid arthritis among South Indian male and female patients based on HAQ score and forearm ulna-BMD measurement by peripheral DXA, and to investigate the correlation between forearm ulna-BMD and HAQ score among RA patients. Sixty-four patients with RA and 64 age- and sex-matched healthy controls were included in this study. The health assessment questionnaire test was self administered by each RA patients. The bone mineral density (BMD) in forearm ulna region was measured using peripheral Dual energy X-ray absorptiometry (osteometer model-DTX200 Meditech.Inc, Hawthorn, California, USA) both for RA patients and for healthy control group. RA patients (n = 64) and age- and sex-matched healthy controls (n = 64) were selected, of which 46 (72%) patients were women and 18 (28%) were men. The mean age was 47.75 ± 11.37 years, and a majority of the patients were in the age group of 30-75 years. The mean age of healthy controls was 46.42 ± 10.67 years. For male RA patients, U-BMD shows moderate significance with healthy controls (0.371 ± 0.05 (g cm(2)) [mean ± SD], 0.413 ± 0.05 (g cm(2)), P = 0.03). For female RA patients, U-BMD was highly significant with that of healthy controls (0.300 ± 0.132 (g cm(2)), 0.376 ± 0.05 (g cm(2)), P = 0.0006). Because as U-BMD decreases for RA patients, HAQ score increases, hence, Pearson correlation analysis revealed that U-BMD was negatively correlated with HAQ score (r = -0.732, P < 0.0001). Forearm U-BMD for RA patients is significantly lower than the healthy controls both for male and for female patients. There was a negative correlation found between HAQ score and P-DXA forearm U-BMD.

  17. Study Protocol - Accurate assessment of kidney function in Indigenous Australians: aims and methods of the eGFR Study

    PubMed Central

    2010-01-01

    Background There is an overwhelming burden of cardiovascular disease, type 2 diabetes and chronic kidney disease among Indigenous Australians. In this high risk population, it is vital that we are able to measure accurately kidney function. Glomerular filtration rate is the best overall marker of kidney function. However, differences in body build and body composition between Indigenous and non-Indigenous Australians suggest that creatinine-based estimates of glomerular filtration rate derived for European populations may not be appropriate for Indigenous Australians. The burden of kidney disease is borne disproportionately by Indigenous Australians in central and northern Australia, and there is significant heterogeneity in body build and composition within and amongst these groups. This heterogeneity might differentially affect the accuracy of estimation of glomerular filtration rate between different Indigenous groups. By assessing kidney function in Indigenous Australians from Northern Queensland, Northern Territory and Western Australia, we aim to determine a validated and practical measure of glomerular filtration rate suitable for use in all Indigenous Australians. Methods/Design A cross-sectional study of Indigenous Australian adults (target n = 600, 50% male) across 4 sites: Top End, Northern Territory; Central Australia; Far North Queensland and Western Australia. The reference measure of glomerular filtration rate was the plasma disappearance rate of iohexol over 4 hours. We will compare the accuracy of the following glomerular filtration rate measures with the reference measure: Modification of Diet in Renal Disease 4-variable formula, Chronic Kidney Disease Epidemiology Collaboration equation, Cockcroft-Gault formula and cystatin C- derived estimates. Detailed assessment of body build and composition was performed using anthropometric measurements, skinfold thicknesses, bioelectrical impedance and a sub-study used dual-energy X-ray absorptiometry. A

  18. 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.

  19. 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

  20. 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.

  1. Scores on the safe functional motion test are associated with prevalent fractures and fall history.

    PubMed

    Recknor, Chris P; Grant, Stephanie L; Recknor, Julie C; Macintyre, Norma J

    2013-01-01

    Objectif : Le test fonctionnel de mouvement (Safe Functional Motiontest, SFM) a été créé pour mesurer les mécanismes corporels et le mouvement fonctionnel associés à la sollicitation de la colonne vertébrale, à l'équilibre, à la force et à la souplesse au cours des activités quotidiennes, afin d'établir un profil des risques modifiables de fracture ostéoporotique. Cette étude transversale a évalué les associations entre les pointages obtenus au SFM et l'historique de fractures de compression vertébrale (FCV), de fracture de la hanche et de chutes préjudiciables qui sont autant de signes avant-coureurs confirmés de risques futurs. Méthode : Une recherche a été effectuée dans la base de données d'une clinique de l'ostéoporose afin de répertorier des adultes dont les résultats initiaux au SFM de départ, les données correspondantes et la densité minérale osseuse du col du fémur (DMOcf) prédisposaient à une FCV ou à une fracture de la hanche, ou qui possédaient des antécédents de chute préjudiciable (n=847). De multiples régressions logistiques, adaptées en fonction de l'âge, du sexe et de la DMOcf (et des chutes préjudiciables de l'analyse des risques de fractures) ont été utilisées pour déterminer si les associations entre les résultats du SFM et la prévalence des FCV, des fractures à la hanche et des chutes préjudiciables existent effectivement. Résultats : Les résultats du SFM ont été associés avec des FCV prévalentes (risque relatif approché [RRA]=0,89; 95 % d'IC, 0,79–0,99; p=0,036), des fractures de la hanche prévalentes (RRA=0,77; 95 % d'IC, 0,65–0,92; p=0,004) et des antécédents de chute préjudiciable (RRA=0,80; 95 % d'IC, 0,70–0,93; p=0,003) après ajustement d'autres covariables importantes. Conclusions : Les adultes dont les résultats au SFM étaient plus élevés (« mouvements sûrs » au cours de l'exécution de tâches courantes) couraient moins de risques d'afficher des ant

  2. 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.

  3. 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

  4. 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.

  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. On expedient properties of common biological score functions for multi-modality, adaptive and 4D dose optimization.

    PubMed

    Sobotta, B; Söhn, M; Shaw, W; Alber, M

    2011-05-21

    Frequently, radiotherapy treatments are comprised of several dose distributions computed or optimized in different patient geometries. Therefore, the need arises to compute the comprehensive biological effect or physical figure of merit of the combined dose of a number of distinct geometry instances. For that purpose the dose is typically accumulated in a reference geometry through deformation fields obtained from deformable image registration. However, it is difficult to establish precise voxel-by-voxel relationships between different anatomical images in many cases. In this work, the mathematical properties of commonly used score functions are exploited to derive an upper boundary for the maximum effect for normal tissue and a lower boundary for the minimum effect for the target of accumulated doses on multiple geometry instances.

  7. 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.

  8. Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins

    PubMed Central

    2015-01-01

    Background Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Despite intense efforts in developing conventional SFs, which are either force-field based, knowledge-based, or empirical, their limited docking power (or ability to successfully identify the correct pose) has been a major impediment to cost-effective drug discovery. Therefore, in this work, we explore a range of novel SFs employing different machine-learning (ML) approaches in conjunction with physicochemical and geometrical features characterizing protein-ligand complexes to predict the native or near-native pose of a ligand docked to a receptor protein's binding site. We assess the docking accuracies of these new ML SFs as well as those of conventional SFs in the context of the 2007 PDBbind benchmark dataset on both diverse and homogeneous (protein-family-specific) test sets. Further, we perform a systematic analysis of the performance of the proposed SFs in identifying native poses of ligands that are docked to novel protein targets. Results and conclusion We find that the best performing ML SF has a success rate of 80% in identifying poses that are within 1 Å root-mean-square deviation from the native poses of 65 different protein families. This is in comparison to a success rate of only 70% achieved by the best conventional SF, ASP, employed in the commercial docking software GOLD. In addition, the proposed ML SFs perform better on novel proteins that they were never trained on before. We also observed steady gains in the performance of these scoring functions as the training set size and number of features were increased by considering more protein-ligand complexes and/or more computationally-generated poses for each complex. PMID:25916860

  9. A composite score for executive functioning, validated in Alzheimer's Disease Neuroimaging Initiative (ADNI) participants with baseline mild cognitive impairment.

    PubMed

    Gibbons, Laura E; Carle, Adam C; Mackin, R Scott; Harvey, Danielle; Mukherjee, Shubhabrata; Insel, Philip; Curtis, S McKay; Mungas, Dan; Crane, Paul K

    2012-12-01

    The Alzheimer's Disease Neuroimaging Initiative (ADNI) measures abilities broadly related to executive function (EF), including WAIS-R Digit Symbol Substitution, Digit Span Backwards, Trails A and B, Category Fluency, and Clock Drawing. This study investigates whether a composite executive function measure based on these multiple indicators has better psychometric characteristics than the widely used individual components. We applied item response theory methods to 800 ADNI participants to derive an EF composite score (ADNI-EF) from the above measures. We then compared ADNI-EF with component measures in 390 longitudinally-followed participants with mild cognitive impairment (MCI) with respect to: (1) Ability to detect change over time; (2) Ability to predict conversion to dementia; (3) Strength of cross-sectional association with MRI-derived measures of structures involved in frontal systems, and (4) Strength of baseline association with cerebrospinal fluid (CSF) levels of amyloid β₁₋₄₂, total tau, and phosphorylated tau(181P). ADNI-EF showed the greatest change over time, followed closely by Category Fluency. ADNI-EF needed a 40 % smaller sample size to detect change. ADNI-EF was the strongest predictor of AD conversion. ADNI-EF was the only measure significantly associated with all the MRI regions, though other measures were more strongly associated in a few of the regions. ADNI-EF was associated with all the CSF measures. ADNI-EF appears to be a useful composite measure of EF in MCI, as good as or better than any of its composite parts. This study demonstrates an approach to developing a psychometrically sophisticated composite score from commonly-used tests.

  10. NPPD: A Protein-Protein Docking Scoring Function Based on Dyadic Differences in Networks of Hydrophobic and Hydrophilic Amino Acid Residues

    PubMed Central

    Shih, Edward S. C.; Hwang, Ming-Jing

    2015-01-01

    Protein-protein docking (PPD) predictions usually rely on the use of a scoring function to rank docking models generated by exhaustive sampling. To rank good models higher than bad ones, a large number of scoring functions have been developed and evaluated, but the methods used for the computation of PPD predictions remain largely unsatisfactory. Here, we report a network-based PPD scoring function, the NPPD, in which the network consists of two types of network nodes, one for hydrophobic and the other for hydrophilic amino acid residues, and the nodes are connected when the residues they represent are within a certain contact distance. We showed that network parameters that compute dyadic interactions and those that compute heterophilic interactions of the amino acid networks thus constructed allowed NPPD to perform well in a benchmark evaluation of 115 PPD scoring functions, most of which, unlike NPPD, are based on some sort of protein-protein interaction energy. We also showed that NPPD was highly complementary to these energy-based scoring functions, suggesting that the combined use of conventional scoring functions and NPPD might significantly improve the accuracy of current PPD predictions. PMID:25811640

  11. 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

  12. 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

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

    PubMed

    Zhang, Zhongheng; Ji, Xuqing

    2016-10-13

    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.

  14. Normative data for functional assessment of cancer therapy--general scale and its use for the interpretation of quality of life scores in cancer survivors.

    PubMed

    Holzner, Bernhard; Kemmler, Georg; Cella, David; De Paoli, Christina; Meraner, Verena; Kopp, Martin; Greil, Richard; Fleischhacker, W Wolfgang; Sperner-Unterweger, Barbara

    2004-01-01

    The aims of this study were to derive population-based reference values for the Functional Assessment of Cancer Therapy Scale-General (FACT-G) and to investigate the impact of sociodemographic variables (e.g. age, sex, health status) on these quality of life (QOL) scores, and to compare the normative QOL scores with those of various groups of cancer survivors. A random sample of 2 000 members of the Austrian public were sent questionnaires containing the FACT-G and questions relating to demographic data and health status. A total of 968 questionnaires were returned giving an overall response rate of 50.6% (females 48.3%, age 49.3 +/- 16.8). Subjects with higher education reported higher QOL values; divorced and widowed persons had significantly lower QOL scores. Higher age was also associated with lower QOL scores. After bone marrow transplantation, patients generally showed lower QOL scores than the age- and sex-matched population-based sample, whilst in breast cancer survivors there was reduced QOL regarding social well-being. Survivors of Hodgkin's disease were found to have higher functional and social well-being scores than those of the general population sample. Sociodemographic variables should always be taken into consideration when interpreting QOL scores. Furthermore, unless patient data are compared with normative values, phenomena such as adaptation and response shift might be missed or misinterpreted.

  15. 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.

  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. Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success.

    PubMed

    Xiao, Xingqing; Agris, Paul F; Hall, Carol K

    2016-05-01

    A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search.

  18. 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.

  19. Accurate localized resolution of identity approach for linear-scaling hybrid density functionals and for many-body perturbation theory

    NASA Astrophysics Data System (ADS)

    Ihrig, Arvid Conrad; Wieferink, Jürgen; Zhang, Igor Ying; Ropo, Matti; Ren, Xinguo; Rinke, Patrick; Scheffler, Matthias; Blum, Volker

    2015-09-01

    A key component in calculations of exchange and correlation energies is the Coulomb operator, which requires the evaluation of two-electron integrals. For localized basis sets, these four-center integrals are most efficiently evaluated with the resolution of identity (RI) technique, which expands basis-function products in an auxiliary basis. In this work we show the practical applicability of a localized RI-variant (‘RI-LVL’), which expands products of basis functions only in the subset of those auxiliary basis functions which are located at the same atoms as the basis functions. We demonstrate the accuracy of RI-LVL for Hartree-Fock calculations, for the PBE0 hybrid density functional, as well as for RPA and MP2 perturbation theory. Molecular test sets used include the S22 set of weakly interacting molecules, the G3 test set, as well as the G2-1 and BH76 test sets, and heavy elements including titanium dioxide, copper and gold clusters. Our RI-LVL implementation paves the way for linear-scaling RI-based hybrid functional calculations for large systems and for all-electron many-body perturbation theory with significantly reduced computational and memory cost.

  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.

  1. Accurate Prediction of Protein Functional Class From Sequence in the Mycobacterium Tuberculosis and Escherichia Coli Genomes Using Data Mining

    PubMed Central

    Karwath, Andreas; Clare, Amanda; Dehaspe, Luc

    2000-01-01

    The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli. PMID:11119305

  2. Predicting Musculoskeletal Injury in National Collegiate Athletic Association Division II Athletes From Asymmetries and Individual-Test Versus Composite Functional Movement Screen Scores

    PubMed Central

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

    2016-01-01

    Context:  Functional Movement Screen (FMS) scores of ≤14 have been used to predict injury in athletic populations. Movement asymmetries and poor-quality movement patterns in other functional tests have been shown to predict musculoskeletal injury (MSI). Therefore, movement asymmetry or poor-quality movement patterns on the FMS may have more utility in predicting MSI than the composite score. Objective:  To determine if an asymmetry or score of 1 on an individual FMS test would predict MSI in collegiate athletes. Design:  Cohort study. Setting:  National Collegiate Athletic Association Division II university athletic program. Patients or Other Participants:  A total of 84 Division II rowers, volleyball players, and soccer players (men: n = 20, age = 20.4 ± 1.3 years, height = 1.77 ± 0.04 m, mass = 73.5 ± 4.8 kg; women: n = 64, age = 19.1 ± 1.2 years, height = 1.69 ± 0.09 m, mass = 64.8 ± 9.4 kg). Main Outcome Measure(s):  The FMS was administered during preseason preparticipation examinations. Injury-incidence data were tracked for an academic year by each team's certified athletic trainer via computer software. An MSI was defined as physical damage to the body secondary to athletic activity or an event for which the athlete sought medical care, and resulted in modified training or required protective splitting or taping. Composite FMS scores were categorized as low (≤14) or high (>14). Pearson χ2 analyses were used to determine if MSI could be predicted by the composite FMS score or an asymmetry or score of 1 on an individual FMS test (P < .05). Results:  Athletes with FMS scores of ≤14 were not more likely to sustain an injury than those with higher scores (relative risk = 0.68, 95% confidence interval = 0.39, 1.19; P = .15). However, athletes with an asymmetry or individual score of 1 were 2.73 times more likely to sustain an injury than those without (relative risk = 2.73, 95% confidence interval = 1.36, 5.4; P = .001). Conclusions

  3. 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.

  4. 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.

  5. Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function.

    PubMed

    Raychaudhuri, Soumya; Korn, Joshua M; McCarroll, Steven A; Altshuler, David; Sklar, Pamela; Purcell, Shaun; Daly, Mark J

    2010-09-09

    Investigators have linked rare copy number variation (CNVs) to neuropsychiatric diseases, such as schizophrenia. One hypothesis is that CNV events cause disease by affecting genes with specific brain functions. Under these circumstances, we expect that CNV events in cases should impact brain-function genes more frequently than those events in controls. Previous publications have applied "pathway" analyses to genes within neuropsychiatric case CNVs to show enrichment for brain-functions. While such analyses have been suggestive, they often have not rigorously compared the rates of CNVs impacting genes with brain function in cases to controls, and therefore do not address important confounders such as the large size of brain genes and overall differences in rates and sizes of CNVs. To demonstrate the potential impact of confounders, we genotyped rare CNV events in 2,415 unaffected controls with Affymetrix 6.0; we then applied standard pathway analyses using four sets of brain-function genes and observed an apparently highly significant enrichment for each set. The enrichment is simply driven by the large size of brain-function genes. Instead, we propose a case-control statistical test, cnv-enrichment-test, to compare the rate of CNVs impacting specific gene sets in cases versus controls. With simulations, we demonstrate that cnv-enrichment-test is robust to case-control differences in CNV size, CNV rate, and systematic differences in gene size. Finally, we apply cnv-enrichment-test to rare CNV events published by the International Schizophrenia Consortium (ISC). This approach reveals nominal evidence of case-association in neuronal-activity and the learning gene sets, but not the other two examined gene sets. The neuronal-activity genes have been associated in a separate set of schizophrenia cases and controls; however, testing in independent samples is necessary to definitively confirm this association. Our method is implemented in the PLINK software package.

  6. 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.

  7. An accurate density functional theory calculation for electronic excitation energies: the least-squares support vector machine.

    PubMed

    Gao, Ting; Sun, Shi-Ling; Shi, Li-Li; Li, Hui; Li, Hong-Zhi; Su, Zhong-Min; Lu, Ying-Hua

    2009-05-14

    Support vector machines (SVMs), as a novel type of learning machine, has been very successful in pattern recognition and function estimation problems. In this paper we introduce least-squares (LS) SVMs to improve the calculation accuracy of density functional theory. As a demonstration, this combined quantum mechanical calculation with LS-SVM correction approach has been applied to evaluate the electronic excitation energies of 160 organic molecules. The newly introduced LS-SVM approach reduces the root-mean-square deviation of the calculated electronic excitation energies of 160 organic molecules from 0.32 to 0.11 eV for the B3LYP/6-31G(d) calculation. Thus, the LS-SVM correction on top of B3LYP/6-31G(d) is a better method to correct electronic excitation energies and can be used as the approximation of experimental results which are impossible to obtain experimentally.

  8. 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…

  9. RBANS memory percentage retention: No evidence of incremental validity beyond RBANS scores for diagnostic classification of mild cognitive impairment and dementia and for prediction of daily function.

    PubMed

    Jodouin, Kara A; O'Connell, Megan E; Morgan, Debra G

    2016-06-09

    RBANS percentage retention scores may be useful for diagnosis, but their incremental validity is unclear. Percentage retention versus RBANS immediate and delayed memory subtests and delayed index scores were compared for diagnostic classification and for prediction of function. Data from 173 memory clinic patients with an interdisciplinary diagnosis (no cognitive impairment, amnestic mild cognitive impairment [aMCI], and dementia due to Alzheimer's disease [AD]) and complete RBANS data were analyzed. Across diagnostic contrasts, list percentage retention classification accuracy was similar to List Learning delayed recall, but below the Delayed Memory Index (DMI). Similarly, for classifying no cognitive impairment versus aMCI or dementia due to AD, story percentage retention was similar to Story Memory subtests and below the DMI. For classifying aMCI versus AD; however, Story Memory exceeded the DMI, but was similar to Story Memory subtest scores. Similarly, for prediction of function percentage retention measures did not predict variance beyond that predicted by the RBANS subtest or index scores. In sum, there is no evidence that calculation of percentage retention for RBANS adds clinical utility beyond those provided by the standard RBANS scores.

  10. Accurate prediction of the electronic properties of low-dimensional graphene derivatives using a screened hybrid density functional.

    PubMed

    Barone, Veronica; Hod, Oded; Peralta, Juan E; Scuseria, Gustavo E

    2011-04-19

    Over the last several years, low-dimensional graphene derivatives, such as carbon nanotubes and graphene nanoribbons, have played a central role in the pursuit of a plausible carbon-based nanotechnology. Their electronic properties can be either metallic or semiconducting depending purely on morphology, but predicting their electronic behavior has proven challenging. The combination of experimental efforts with modeling of these nanometer-scale structures has been instrumental in gaining insight into their physical and chemical properties and the processes involved at these scales. Particularly, approximations based on density functional theory have emerged as a successful computational tool for predicting the electronic structure of these materials. In this Account, we review our efforts in modeling graphitic nanostructures from first principles with hybrid density functionals, namely the Heyd-Scuseria-Ernzerhof (HSE) screened exchange hybrid and the hybrid meta-generalized functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh). These functionals provide a powerful tool for quantitatively studying structure-property relations and the effects of external perturbations such as chemical substitutions, electric and magnetic fields, and mechanical deformations on the electronic and magnetic properties of these low-dimensional carbon materials. We show how HSE and TPSSh successfully predict the electronic properties of these materials, providing a good description of their band structure and density of states, their work function, and their magnetic ordering in the cases in which magnetism arises. Moreover, these approximations are capable of successfully predicting optical transitions (first and higher order) in both metallic and semiconducting single-walled carbon nanotubes of various chiralities and diameters with impressive accuracy. This versatility includes the correct prediction of the trigonal warping splitting in metallic nanotubes. The results predicted

  11. 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.

  12. LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.

    PubMed

    Hallen, Mark A; Jou, Jonathan D; Donald, Bruce R

    2016-09-28

    Most protein design algorithms search over discrete conformations and an energy function that is residue-pairwise, that is, a sum of terms that depend on the sequence and conformation of at most two residues. Although modeling of continuous flexibility and of non-residue-pairwise energies significantly increases the accuracy of protein design, previous methods to model these phenomena add a significant asymptotic cost to design calculations. We now remove this cost by modeling continuous flexibility and non-residue-pairwise energies in a form suitable for direct input to highly efficient, discrete combinatorial optimization algorithms such as DEE/A* or branch-width minimization. Our novel algorithm performs a local unpruned tuple expansion (LUTE), which can efficiently represent both continuous flexibility and general, possibly nonpairwise energy functions to an arbitrary level of accuracy using a discrete energy matrix. We show using 47 design calculation test cases that LUTE provides a dramatic speedup in both single-state and multistate continuously flexible designs.

  13. Validation of criterion-referenced archery cutting scores.

    PubMed

    Ishee, J H; Titlow, L W

    1993-04-01

    This study investigated an empirical method for setting optimal cutting scores for a criterion-referenced archery test. The classification-outcome probabilities and approaches to validity suggested by Berk were utilized. Pretest scores were obtained on 35 uninstructed college-age women on six ends (six arrows each) from 20 yards (18.3 m) after an unrecorded warm-up end. Posttest scores were after 15 weeks of instruction. Score distributions were the primary determinant for accurately classifying students as true mastery and true nonmastery. Accuracy is a function of the amount of overlap between distributions. Using the point at which the distributions overlapped, classification accuracy was estimated. Probabilities associated with 80 points were p(TM) + p(TN) = .83 and p(FM) + p(FN) = .14. Scores above and below 80 points had lower probabilities of classification accuracy. Reliability estimated using Kappa was .59. Statistical validity of the cutting score (phi) was .68.

  14. Scoring Guidelines.

    ERIC Educational Resources Information Center

    Tamir, Pinchas; Doran, Rodney L.

    1992-01-01

    Scoring guidelines are given for four forms of the practical skills tests of the Second International Association for the Evaluation of Educational Improvement Science Study conducted in the following countries in the 1980s: (1) Hungary; (2) Japan; (3) Korea; (4) Singapore; (5) Israel; and (6) the United States. (SLD)

  15. 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…

  16. 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…

  17. Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments.

    PubMed

    Pavelcík, Frantisek; Václavík, Jirí

    2010-09-01

    The automatic building of protein structures with tripeptidic and tetrapeptidic fragments was investigated. The oligopeptidic conformers were positioned in the electron-density map by a phased rotation, conformation and translation function and refined by a real-space refinement. The number of successfully located fragments lay within the interval 75-95% depending on the resolution and phase quality. The overlaps of partially located fragments were analyzed. The correctly positioned fragments were connected into chains. Chains formed in this way were extended directly into the electron density and a sequence was assigned. In the initial stage of the model building the number of located fragments was between 60% and 95%, but this number could be increased by several cycles of reciprocal-space refinement and automatic model rebuilding. A nearly complete structure can be obtained on the condition that the resolution is reasonable. Computer graphics will only be needed for a final check and small corrections.

  18. Accurate Ground-State Energies of Solids and Molecules from Time-Dependent Density-Functional Theory

    NASA Astrophysics Data System (ADS)

    Olsen, Thomas; Thygesen, Kristian S.

    2014-05-01

    We demonstrate that ground-state energies approaching chemical accuracy can be obtained by combining the adiabatic-connection fluctuation-dissipation theorem with time-dependent density-functional theory. The key ingredient is a renormalization scheme, which eliminates the divergence of the correlation hole characteristic of any local kernel. This new class of renormalized kernels gives a significantly better description of the short-range correlations in covalent bonds compared to the random phase approximation (RPA) and yields a fourfold improvement of RPA binding energies in both molecules and solids. We also consider examples of barrier heights in chemical reactions, molecular adsorption, and graphene interacting with metal surfaces, which are three examples where the RPA has been successful. In these cases, the renormalized kernel provides results that are of equal quality or even slightly better than the RPA, with a similar computational cost.

  19. Anticoagulation Stability Depends on CHADS2 Score and Hepatorenal Function in Warfarin-treated Patients, Including Those with Atrial Fibrillation

    PubMed Central

    Odashiro, Keita; Fukata, Mitsuhiro; Arita, Takeshi; Maruyama, Toru; Akashi, Koichi

    2017-01-01

    Aim: Although warfarin remains important despite the widespread use of nonvitamin K antagonist oral anticoagulants (NOACs), to date, the reality of warfarin use in the “NOACs era” is unclear. This multicenter observational study aimed to clarify the key factors contributing to warfarin treatment stability. Methods: The practical use of warfarin, stability of warfarin therapy, and factors contributing to this stability were investigated in community-based hospitals through a real-world study. Clinical data were retrospectively extracted from the medical records of warfarin-treated Japanese patients (age, 71.3 ± 5.5 years) with atrial fibrillation (AF), prosthetic heart valve, or other concerns requiring anticoagulation. Treatment stability was considered as time in therapeutic range of international normalized ratio of prothrombin time (TTR: %). The factors contributing to TTR were investigated, including CHADS2 score components. Results: Mean CHADS2 score was highest (1.38 ± 0.88, p < 0.001), and most CHADS2 score components in addition to hepatorenal dysfunction were factors contributing to the low TTR in patients with AF (n = 176). The similarity was found in overall patients who were prescribed warfarin (n = 518). TTR decreased according to the CHADS2 score component accumulation. Gender, dose and prescription interval of warfarin, and co-administration of antiplatelet agents did not correlate with the low TTR. Conclusions: This retrospective study demonstrated that the CHADS2 score component accumulation and hepatorenal dysfunction are factors significantly contributing to the low TTR, which is indicative of poor warfarin treatment stability, in patients such as those with AF. PMID:27319745

  20. 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

  1. 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.

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

    PubMed

    Liu, Jie; Herbert, John M

    2015-07-21

    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.

  3. 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.

  4. Accurate Analytic Potential Energy Function and Spectroscopic Study for G1Πg State of Dimer 7Li2

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Ma, Heng; Sun, Jin-Feng; Zhu, Zun-Lue

    2007-06-01

    The reasonable dissociation limit for the G1Πg state of dimer 7Li2 is determined. The equilibrium internuclear distance, dissociation energy, harmonic frequency, vibrational zero energy, and adiabatic excitation energy are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space in Gaussian03 program package at such numerous basis sets as 6-311++G, 6-311++G(2df,2pd), 6-311++G(2df,p), cc-PVTZ, 6-311++G(3df,3pd), CEP-121G, 6-311++G(2df,pd), 6-311++G(d,p),6-311G(3df,3pd), D95(3df,3pd), 6-311++G(3df,2p), 6-311++G(2df), 6-311++G(df,pd) D95V++, and DGDZVP. The complete potential energy curves are obtained at these sets over a wide internuclear distance range and have least squares fitted to Murrell-Sorbie function. The conclusion shows that the basis set 6-311++G(2df,p) is a most suitable one for the G1Πg state. At this basis set, the calculated spectroscopic constants Te, De, E0, Re, ωe, ωeχe, αe, and Be are of 3.9523 eV, 0.813 06 eV, 113.56 cm-1, 0.320 15 nm, 227.96 cm-1, 1.6928 cm-1, 0.004 436 cm-1, and 0.4689 cm-1, respectively, which are in good agreement with measurements whenever available. The total 50 vibrational levels and corresponding inertial rotation constants are for the first time calculated and compared with available RKR data. And good agreement with measurements is obtained.

  5. 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.

  6. 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.

  7. Robust dynamic myocardial perfusion CT deconvolution for accurate residue function estimation via adaptive-weighted tensor total variation regularization: a preclinical study

    NASA Astrophysics Data System (ADS)

    Zeng, Dong; Gong, Changfei; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Niu, Shanzhou; Zhang, Zhang; Liang, Zhengrong; Feng, Qianjin; Chen, Wufan; Ma, Jianhua

    2016-11-01

    Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for quick diagnosis and risk stratification of coronary artery disease. However, one major drawback of dynamic MPCT imaging is the heavy radiation dose to patients due to its dynamic image acquisition protocol. In this work, to address this issue, we present a robust dynamic MPCT deconvolution algorithm via adaptive-weighted tensor total variation (AwTTV) regularization for accurate residue function estimation with low-mA s data acquisitions. For simplicity, the presented method is termed ‘MPD-AwTTV’. More specifically, the gains of the AwTTV regularization over the original tensor total variation regularization are from the anisotropic edge property of the sequential MPCT images. To minimize the associative objective function we propose an efficient iterative optimization strategy with fast convergence rate in the framework of an iterative shrinkage/thresholding algorithm. We validate and evaluate the presented algorithm using both digital XCAT phantom and preclinical porcine data. The preliminary experimental results have demonstrated that the presented MPD-AwTTV deconvolution algorithm can achieve remarkable gains in noise-induced artifact suppression, edge detail preservation, and accurate flow-scaled residue function and MPHM estimation as compared with the other existing deconvolution algorithms in digital phantom studies, and similar gains can be obtained in the porcine data experiment.

  8. Towards accurate estimates of the spin-state energetics of spin-crossover complexes within density functional theory: a comparative case study of cobalt(II) complexes.

    PubMed

    Vargas, Alfredo; Krivokapic, Itana; Hauser, Andreas; Lawson Daku, Latévi Max

    2013-03-21

    We report a detailed DFT study of the energetic and structural properties of the spin-crossover Co(ii) complex [Co(tpy)(2)](2+) (tpy = 2,2':6',2''-terpyridine) in the low-spin (LS) and the high-spin (HS) states, using several generalized gradient approximation and hybrid functionals. In either spin-state, the results obtained with the functionals are consistent with one another and in good agreement with available experimental data. Although the different functionals correctly predict the LS state as the electronic ground state of [Co(tpy)(2)](2+), they give estimates of the HS-LS zero-point energy difference which strongly depend on the functional used. This dependency on the functional was also reported for the DFT estimates of the zero-point energy difference in the HS complex [Co(bpy)(3)](2+) (bpy = 2,2'-bipyridine) [A. Vargas, A. Hauser and L. M. Lawson Daku, J. Chem. Theory Comput., 2009, 5, 97]. The comparison of the and estimates showed that all functionals correctly predict an increase of the zero-point energy difference upon the bpy → tpy ligand substitution, which furthermore weakly depends on the functionals, amounting to . From these results and basic thermodynamic considerations, we establish that, despite their limitations, current DFT methods can be applied to the accurate determination of the spin-state energetics of complexes of a transition metal ion, or of these complexes in different environments, provided that the spin-state energetics is accurately known in one case. Thus, making use of the availability of a highly accurate ab initio estimate of the HS-LS energy difference in the complex [Co(NCH)(6)](2+) [L. M. Lawson Daku, F. Aquilante, T. W. Robinson and A. Hauser, J. Chem. Theory Comput., 2012, 8, 4216], we obtain for [Co(tpy)(2)](2+) and [Co(bpy)(3)](2+) best estimates of and , in good agreement with the known magnetic behaviour of the two complexes.

  9. 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).

  10. Poor sleep quality predicts decreased cognitive function independently of chronic mountain sickness score in young soldiers with polycythemia stationed in Tibet.

    PubMed

    Kong, Fan-Yi; Li, Qiang; Liu, Shi-Xiang

    2011-01-01

    Little is known about the association between poor sleep and cognitive function in people with polycythemia at high altitude. The aim of this study was to survey the sleep quality of individuals with polycythemia at high altitude and determine its association with cognitive abilities. We surveyed 230 soldiers stationed in Tibet (all men; mean age 21-52±4.30 yr) at altitudes ranging from 3658 to 3996 m. All participants were given a blood tests for hemoglobin level and a questionnaire survey of cognitive function. Polycythemia was defined as excessive erythrocytosis (Hb≥21 g/dL in men or ≥19 g/dL in women). Poor sleepers were defined as having a global Pittsburgh Sleep Quality Index score (PSQI)>5. Cognitive abilities were determined by the Chinese revision of the Wechsler Adult Intelligence Scale and the Benton Visual Retention Test. Multiple linear regression analysis was used to determine the association between the PSQI and cognitive function. Logistic regression analysis was performed to determine the independent effect of sleep quality on cognitive function. The global PSQI score of enrolled participants was 8.14±3.79. Seventy-five (32.6%) soldiers were diagnosed with polycythemia. The proportion of poor sleepers was 1.45 times greater in those with polycythemia compared with those without polycythemia [95% (confidence interval) CI 1.82-2.56], and they had a statistically significant lower score for cognitive function. Multiple linear regression analysis showed that the global PSQI score was negatively associated with IQ (β=0.11, 95% CI -0.16 to -0.05) and digit symbol scores (β=0.66, 95% CI -0.86 to -0.44). Poor sleep quality was determined to be an independent predictor of impaired IQ [odds ratio (OR) 1.59, 95% CI 1.30-1.95] and digit symbol score (OR 1.18, 95% CI 1.07-1.31) in logistic regression analysis. The present study showed that for young soldiers with polycythemia at high altitude impaired subjective sleep quality was an independent

  11. 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,…

  12. 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

  13. 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.

  14. 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

  15. An accurate prognostic staging system for hepatocellular carcinoma patients after curative hepatectomy

    PubMed Central

    TOKUMITSU, YUKIO; TAMESA, TAKAO; MATSUKUMA, SATOSHI; HASHIMOTO, NORIAKI; MAEDA, YOSHINARI; TOKUHISA, YOSHIHIRO; SAKAMOTO, KAZUHIKO; UENO, TOMIO; HAZAMA, SHOICHI; OGIHARA, HIROYUKI; FUJITA, YUSUKE; HAMAMOTO, YOSHIHIKO; OKA, MASAAKI; IIZUKA, NORIO

    2015-01-01

    The aim of this study was to develop an accurate predictive system for prognosis of hepatocellular carcinoma (HCC) patients after hepatectomy. We pooled data of clinicopathological features of 234 HCC patients who underwent curative hepatectomy. On the basis of the pooled data, we established a simple predictive staging system (PS score) scored by the mathematical product of tumor number and size, and degree of liver function. We compared the prognostic abilities of the PS score (score 0–3) with those of six well-known clinical staging systems. Then, we found that there were significant differences (P<0.05) in both disease-free survival (DFS) and overall survival (OS) between patients with different PS scores (PS score 0 vs. 1; PS score 1 vs. 2), and there was a significant difference in DFS, but not OS, between patients with PS score 2 and those with PS score 3. Moreover, the PS score had smaller values of the Akaike information criterion for both DFS and OS than any of the six well-known clinical staging systems. These results suggest that the PS score serves as a simple, accurate predictor for the prognosis of HCC patients after hepatectomy. PMID:25524574

  16. Rapid and accurate measurement of left ventricular function with a new second-harmonic fast-rotating transducer and semi-automated border detection.

    PubMed

    Krenning, Boudewijn J; Voormolen, Marco M; van Geuns, Robert-Jan; Vletter, W B; Lancée, Charles T; de Jong, Nico; Ten Cate, Folkert J; van der Steen, Anton F W; Roelandt, Jos R T C

    2006-07-01

    Measurement of left ventricular (LV) volume and function are the most common clinical referral questions to the echocardiography laboratory. A fast, practical, and accurate method would offer important advantages to obtain this important information. To validate a new practical method for rapid measurement of LV volume and function. We developed a continuous fast-rotating transducer, with second-harmonic capabilities, for three-dimensional echocardiography (3DE). Fifteen cardiac patients underwent both 3DE and magnetic resonance imaging (reference method) on the same day. 3DE image acquisition was performed during a 10-second breath-hold with a frame rate of 100 frames/sec and a rotational speed of 6 rotations/sec. The individual images were postprocessed with Matlab software using multibeat data fusion. Subsequently, with these images, 12 datasets per cardiac cycle were reconstructed, each comprising seven equidistant cross-sectional images for analysis in the new TomTec 4DLV analysis software, which uses a semi-automated border detection (ABD) algorithm. The ABD requires an average analysis time of 15 minutes per patient. A strong correlation was found between LV end-diastolic volume (r = 0.99; y = 0.95x - 1.14 ml; SEE = 6.5 ml), LV end-systolic volume (r = 0.96; y = 0.89x + 7.91 ml; SEE = 7.0 ml), and LV ejection fraction (r = 0.93; y = 0.69x + 13.36; SEE = 2.4%). Inter- and intraobserver agreement for all measurements was good. The fast-rotating transducer with new ABD software is a dedicated tool for rapid and accurate analysis of LV volume and function.

  17. SARC‐F: a symptom score to predict persons with sarcopenia at risk for poor functional outcomes

    PubMed Central

    Miller, Douglas K.; Simonsick, Eleanor M.; Ferrucci, Luigi; Morley, John E.

    2015-01-01

    Background A brief, inexpensive screening test for sarcopenia would be helpful for clinicians and their patients. To screen for persons with sarcopenia, we developed a simple five‐item questionnaire (SARC‐F) based on cardinal features or consequences of sarcopenia. Methods We investigated the utility of SARC‐F in the African American Health (AAH) study, Baltimore Longitudinal Study of Aging (BLSA), and National Health and Nutrition Examination Survey (NHANES). Internal consistency reliability for SARC‐F was determined using Cronbach's alpha. We evaluated SARC‐F factorial validity using principal components analysis and criterion validity by examining its association with exam‐based indicators of sarcopenia. Construct validity was examined using cross‐sectional and longitudinal differences among those with high (≥4) vs. low (<4) SARC‐F scores for mortality and health outcomes. Results SARC‐F exhibited good internal consistency reliability and factorial, criterion, and construct validity. AAH participants with SARC‐F scores ≥ 4 had more Instrumental Activity of Daily Living (IADL) deficits, slower chair stand times, lower grip strength, lower short physical performance battery scores, and a higher likelihood of recent hospitalization and of having a gait speed of <0.8 m/s. SARC‐F scores ≥ 4 in AAH also were associated with 6 year IADL deficits, slower chair stand times, lower short physical performance battery scores, having a gait speed of <0.8 m/s, being hospitalized recently, and mortality. SARC‐F scores ≥ 4 in the BLSA cohort were associated with having more IADL deficits and lower grip strength (both hands) in cross‐sectional comparisons and with IADL deficits, lower grip strength (both hands), and mortality at follow‐up. NHANES participants with SARC‐F scores ≥ 4 had slower 20 ft walk times, had lower peak force knee extensor strength, and were more likely to have been hospitalized recently in

  18. 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…

  19. 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).

  20. Benchmarking density-functional theory calculations of NMR shielding constants and spin-rotation constants using accurate coupled-cluster calculations.

    PubMed

    Teale, Andrew M; Lutnæs, Ola B; Helgaker, Trygve; Tozer, David J; Gauss, Jürgen

    2013-01-14

    Accurate sets of benchmark nuclear-magnetic-resonance shielding constants and spin-rotation constants are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the calculated coupled-cluster constants is established by a careful comparison with experimental data, taking into account zero-point vibrational corrections. Coupled-cluster basis-set convergence is analyzed and extrapolation techniques are employed to estimate basis-set-limit quantities, thereby establishing an accurate benchmark data set. Together with the set provided for rotational g-tensors and magnetizabilities in our previous work [O. B. Lutnæs, A. M. Teale, T. Helgaker, D. J. Tozer, K. Ruud, and J. Gauss, J. Chem. Phys. 131, 144104 (2009)], it provides a substantial source of consistently calculated high-accuracy data on second-order magnetic response properties. The utility of this benchmark data set is demonstrated by examining a wide variety of Kohn-Sham exchange-correlation functionals for the calculation of these properties. None of the existing approximate functionals provide an accuracy competitive with that provided by CCSD or CCSD(T) theory. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of Kohn-Sham calculations constrained to give the same electronic density. Routes to future improvements are discussed in light of this comparison.

  1. Cognitive and Functional Correlates of NPI-Q Scores and Symptom Clusters in Mildly Demented Alzheimer Patients.

    PubMed

    Travis Seidl, Jennifer N; Massman, Paul J

    2016-01-01

    Previous research has demonstrated an association between the emotional and behavioral symptoms of dementia, known as neuropsychiatric symptoms, and cognitive and functional decline among patients with Alzheimer disease (AD). The present study aimed to identify associations between neuropsychiatric symptoms as measured by the Neuropsychiatric Inventory-Questionnaire (NPI-Q) and cognitive and functional performance. Participants were 256 AD patients enrolled in the Alzheimer's Disease and Memory Disorders Center at Baylor College of Medicine. An exploratory factor analysis of the NPI-Q indicated a 2-factor structure consisting of Negative/Oppositional and Anxiety/Restlessness factors. Regression analyses revealed significant associations between greater total severity of neuropsychiatric symptoms and poorer performance on basic and Instrumental Activities of Daily Living. Greater severity of Anxiety/Restlessness symptoms was associated with poor performance on measures of visuospatial functioning and basic and instrumental activities of daily living. The Negative/Oppositional factor was not related to cognition or functioning. In summary, neuropsychiatric symptoms (particularly Anxiety/Restlessness symptoms) were related to cognition and everyday functioning. Proper assessment and treatment of these symptoms is essential for improving cognition and functioning in AD patients.

  2. 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

  3. Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development.

    PubMed

    Neeb, Zachary T; Hogan, Daniel J; Katzman, Sol; Zahler, Alan M

    2017-01-01

    During its sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes. Hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and replicated dozens of times to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a function of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are either expressed constitutively or are expressed at different times during macronuclear development, including many components of the RNA polymerase II machinery and homologous recombination complexes. Hundreds of macronuclear development-specific genes encode proteins that are well-conserved among multicellular eukaryotes, including many with links to germline functions or development. Our work implicates dozens of DNA and RNA-binding proteins with diverse evolutionary trajectories in macronuclear development in O. trifallax. It suggests functional connections between the process of macronuclear development in unicellular ciliates and germline specialization and differentiation in multicellular organisms, and argues that gene duplication is a key source of evolutionary innovation in this process.

  4. Validation of a questionnaire assessing patient's aesthetic and functional outcome after nasal reconstruction: the patient NAFEQ-score.

    PubMed

    Moolenburgh, S E; Mureau, M A M; Duivenvoorden, H J; Hofer, S O P

    2009-05-01

    In determining patient satisfaction with functional and aesthetic outcome after reconstructive surgery, including nasal reconstruction, standardised assessment instruments are very important. These standardised tools are needed to adequately evaluate and compare outcome results. Since no such instrument existed for nasal reconstruction, a standardised evaluation questionnaire was developed to assess aesthetic and functional outcome after nasal reconstruction. Items of the Nasal Appearance and Function Evaluation Questionnaire (NAFEQ) were derived from both the literature and experiences with patients. The NAFEQ was validated on 30 nasal reconstruction patients and a reference group of 175 people. A factor analysis confirmed the arrangement of the questionnaire in two subscales: functional and aesthetic outcome. High Cronbach's alpha values (>0.70) for both subscales showed that the NAFEQ was an internally consistent instrument. This study demonstrated that the NAFEQ can be used as a standardised questionnaire for detailed evaluation of aesthetic and functional outcome after nasal reconstruction. Its widespread use would enable comparison of results achieved by different techniques, surgeons and centres in a standardised fashion.

  5. Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development

    PubMed Central

    Katzman, Sol

    2017-01-01

    During its sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes. Hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and replicated dozens of times to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a function of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are either expressed constitutively or are expressed at different times during macronuclear development, including many components of the RNA polymerase II machinery and homologous recombination complexes. Hundreds of macronuclear development-specific genes encode proteins that are well-conserved among multicellular eukaryotes, including many with links to germline functions or development. Our work implicates dozens of DNA and RNA-binding proteins with diverse evolutionary trajectories in macronuclear development in O. trifallax. It suggests functional connections between the process of macronuclear development in unicellular ciliates and germline specialization and differentiation in multicellular organisms, and argues that gene duplication is a key source of evolutionary innovation in this process. PMID:28207760

  6. 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…

  7. Impact of the accurateness of bidirectional reflectance distribution function data on the intensity and luminance distributions of a light-emitting diode mixing chamber as obtained by simulations

    NASA Astrophysics Data System (ADS)

    Audenaert, Jan; Leloup, Frédéric B.; Van Giel, Bart; Durinck, Guy; Deconinck, Geert; Hanselaer, Peter

    2013-09-01

    The reliability of ray tracing simulations is strongly dependent on the accuracy of the input data such as the bidirectional reflectance distribution function (BRDF). Software developers offer the possibility to implement BRDF data in different ways, ranging from simple predefined functions to detailed tabulated data. The impact of the accuracy of the implemented reflectance model on ray tracing simulations has been investigated. A light-emitting diode device including a frequently employed diffuse reflector [microcellular polyethylene terephthalate (MCPET)] was constructed. The luminous intensity distribution (LID) and luminance distribution from a specific viewpoint were measured with a near-field goniophotometer. Both distributions were also simulated by use of ray tracing software. Three different reflection models of MCPET were introduced, varying in complexity: a diffuse model, a diffuse/specular model, and a model containing tabulated BRDF data. A good agreement between the measured and simulated LID was found irrespective of the applied model. However, the luminance distributions only corresponded when the most accurate BRDF model was applied. This proves that even for diffuse reflective materials, a simple BRDF model may only be employed for simulations of the LID; for evaluation of luminance distributions, more complex models are needed.

  8. On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

    PubMed Central

    2014-01-01

    Background Protein sequence similarities to any types of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc. where either positional sequence conservation is the result of a very simple, physically induced pattern or rather integral sequence properties are critical) are pertinent sources for mistaken homologies. Regretfully, these considerations regularly escape attention in large-scale annotation studies since, often, there is no substitute to manual handling of these cases. Quantitative criteria are required to suppress events of function annotation transfer as a result of false homology assignments. Results The sequence homology concept is based on the similarity comparison between the structural elements, the basic building blocks for conferring the overall fold of a protein. We propose to dissect the total similarity score into fold-critical and other, remaining contributions and suggest that, for a valid homology statement, the fold-relevant score contribution should at least be significant on its own. As part of the article, we provide the DissectHMMER software program for dissecting HMMER2/3 scores into segment-specific contributions. We show that DissectHMMER reproduces HMMER2/3 scores with sufficient accuracy and that it is useful in automated decisions about homology for instructive sequence examples. To generalize the dissection concept for cases without 3D structural information, we find that a dissection based on alignment quality is an appropriate surrogate. The approach was applied to a large-scale study of SMART and PFAM domains in the space of seed sequences and in the space of UniProt/SwissProt. Conclusions Sequence similarity core dissection with regard to fold-critical and other contributions systematically suppresses false hits and, additionally, recovers previously obscured homology relationships such as the one between aquaporins and formate/nitrite transporters that, so far, was only

  9. The Correlation of Serum Metal Ions with Functional Outcome Scores at Three-to-Six Years following Large Head Metal-on-Metal Hip Arthroplasty

    PubMed Central

    Patange Subbarao, Sheethal Prasad; Malek, Ibrahim A.; Mohanty, Khitish; Thomas, Phillip; John, Alun

    2013-01-01

    Based on success of hip resurfacing, large head Metal on Metal (MoM) hip arthroplasty has gained significant popularity in recent years. There are growing concerns about metal ions related soft tissue abnormalities. The aim of this study was to define a correlation of metal ions with various functional outcome scores following large head MoM hip arthroplasty. Consecutive cohort of 70 patients (76 hips) with large head MoM hip arthroplasty using SL-Plus femoral stem and Cormet acetabular component were prospectively followed up. An independent observer assessed the patients which included serology for metal ion levels and collection of Oxford Hip, Harris hip, WOMAC, SF-36 & modified UCLA scores. Median serum cobalt and chromium levels were 3.10 μg/L (0.35–62.92) and 4.21 μg/L (0.73–69.27) with total of median 7.30 μg/L (2.38–132.19). The median Oxford, Harris, WOMAC, SF-36 and modified UCLA scores were 36 (6–48), 87 (21–100), 36 (24–110), 104 (10–125), and 3 (1–9), respectively. Seventeen patients had elevated serum cobalt and chromium levels ≥7 μg/L. There was no significant correlation between serum metal ion levels with any of these outcome scores. We recommend extreme caution during follow up of these patients with large head MoM arthroplasty. PMID:24959353

  10. 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

  11. Early changes in scores of chronic damage on transplant kidney protocol biopsies reflect donor characteristics, but not future graft function.

    PubMed

    Caplin, Ben; Veighey, Kristin; Mahenderan, Arundathi; Manook, Miriam; Henry, Joanne; Nitsch, Dorothea; Harber, Mark; Dupont, Peter; Wheeler, David C; Jones, Gareth; Fernando, Bimbi; Howie, Alexander J; Veitch, Peter

    2013-01-01

    The amount of irreversible injury on renal allograft biopsy predicts function, but little is known about the early evolution of this damage. In a single-center cohort, we examined the relationship between donor-, recipient-, and transplantation-associated factors and change in a morphometric index of chronic damage (ICD) between protocol biopsies performed at implantation and at 2-3 months. We then investigated whether early delta ICD predicted subsequent biochemical outcomes. We found little evidence to support differences between the study group, who had undergone serial biopsies, and a contemporaneous control group, who had not. In allografts with serial biopsies (n = 162), there was an increase in ICD between implantation (median: 2%, IQR:0-8) and 2-3 months post-transplant (median 8% IQR:4-15; p < 0.0001). Donation from younger or live donors was independently associated with smaller early post-transplant increases in ICD. There was no evidence for a difference in delta ICD between donation after cardiac death vs. donation after brain death, nor association with length of cold ischemia. After adjustment for GFR at the time of the second biopsy, delta ICD after three months did not predict allograft function at one yr. These findings suggest that graft damage develops shortly after transplantation and reflects donor factors, but does not predict future biochemical outcomes.

  12. An accurate density functional theory for the vapor-liquid interface of associating chain molecules based on the statistical associating fluid theory for potentials of variable range

    NASA Astrophysics Data System (ADS)

    Gloor, Guy J.; Jackson, George; Blas, Felipe J.; del Río, Elvira Martín; de Miguel, Enrique

    2004-12-01

    A Helmholtz free energy density functional is developed to describe the vapor-liquid interface of associating chain molecules. The functional is based on the statistical associating fluid theory with attractive potentials of variable range (SAFT-VR) for the homogenous fluid [A. Gil-Villegas, A. Galindo, P. J. Whitehead, S. J. Mills, G. Jackson, and A. N. Burgess, J. Chem. Phys. 106, 4168 (1997)]. A standard perturbative density functional theory (DFT) is constructed by partitioning the free energy density into a reference term (which incorporates all of the short-range interactions, and is treated locally) and an attractive perturbation (which incorporates the long-range dispersion interactions). In our previous work [F. J. Blas, E. Martı´n del Rı´o, E. de Miguel, and G. Jackson, Mol. Phys. 99, 1851 (2001); G. J. Gloor, F. J. Blas, E. Martı´n del Rı´o, E. de Miguel, and G. Jackson, Fluid Phase Equil. 194, 521 (2002)] we used a mean-field version of the theory (SAFT-HS) in which the pair correlations were neglected in the attractive term. This provides only a qualitative description of the vapor-liquid interface, due to the inadequate mean-field treatment of the vapor-liquid equilibria. Two different approaches are used to include the correlations in the attractive term: in the first, the free energy of the homogeneous fluid is partitioned such that the effect of correlations are incorporated in the local reference term; in the second, a density averaged correlation function is incorporated into the perturbative term in a similar way to that proposed by Toxvaerd [S. Toxvaerd, J. Chem. Phys. 64, 2863 (1976)]. The latter is found to provide the most accurate description of the vapor-liquid surface tension on comparison with new simulation data for a square-well fluid of variable range. The SAFT-VR DFT is used to examine the effect of molecular chain length and association on the surface tension. Different association schemes (dimerization, straight and

  13. FUNCTIONAL HOP TESTS AND TUCK JUMP ASSESSMENT SCORES BETWEEN FEMALE DIVISION I COLLEGIATE ATHLETES PARTICIPATING IN HIGH VERSUS LOW ACL INJURY PRONE SPORTS: A CROSS SECTIONAL ANALYSIS

    PubMed Central

    Hoog, Philipp; Warren, Meghan; Smith, Craig A.

    2016-01-01

    Background Although functional tests including the single leg hop (SLH), triple hop (TH), cross over hop (COH) for distance, and the tuck jump assessment (TJA) are used for return to play (RTP) criteria for post anterior cruciate ligament (ACL) injury, sport-specific baseline measurements are limited. Purpose The purpose of this study was to examine differences in SLH, TH, and COH distance and limb symmetry index (LSI), as well as total scores, number of jumps, and individual flaws of the TJA in 97 injury-free Division I (DI) collegiate female student athletes participating in ACL injury prone vs. non ACL injury prone sports. The hypothesis was that significant mean differences and asymmetries (LSI) would exist between the two groups in SLH, TH, COH and TJA. Study Design Cross sectional. Methods Due to research suggesting inherent ACL injury risk associated with specific sport involvement, participants were grouped into high (HR, n=57) and low (LR, n=40) ACL injury risk based on participating in a sport with high or low ACL injury rates. The HR group was composed of athletes participating in soccer, basketball, and volleyball, while the LR group athletes participated in diving, cross country, and track and field. Participants performed all standard functional tests (SFT) and side-to-side differences for each participant as well as between group differences were assessed for the hop tests. The LSI, a ratio frequently used to gauge athletes’ readiness for RTP post injury, was also assessed for between group differences. The TJA was compared between the groups on individual flaws, overall scores, and number of jumps performed. Results No between group differences for hop distances were found, with medium to large effect sizes for SLH, TH, and COH. The HR group had a higher TJA score, number of jumps, and higher proportion of the flaw of ‘foot placement not shoulder width apart’. Conclusion Although most SFT's showed no significant differences between athlete

  14. Accurate estimation of global and regional cardiac function by retrospectively gated multidetector row computed tomography: comparison with cine magnetic resonance imaging.

    PubMed

    Belge, Bénédicte; Coche, Emmanuel; Pasquet, Agnès; Vanoverschelde, Jean-Louis J; Gerber, Bernhard L

    2006-07-01

    Retrospective reconstruction of ECG-gated images at different parts of the cardiac cycle allows the assessment of cardiac function by multi-detector row CT (MDCT) at the time of non-invasive coronary imaging. We compared the accuracy of such measurements by MDCT to cine magnetic resonance (MR). Forty patients underwent the assessment of global and regional cardiac function by 16-slice MDCT and cine MR. Left ventricular (LV) end-diastolic and end-systolic volumes estimated by MDCT (134+/-51 and 67+/-56 ml) were similar to those by MR (137+/-57 and 70+/-60 ml, respectively; both P=NS) and strongly correlated (r=0.92 and r=0.95, respectively; both P<0.001). Consequently, LV ejection fractions by MDCT and MR were also similar (55+/-21 vs. 56+/-21%; P=NS) and highly correlated (r=0.95; P<0.001). Regional end-diastolic and end-systolic wall thicknesses by MDCT were highly correlated (r=0.84 and r=0.92, respectively; both P<0.001), but significantly lower than by MR (8.3+/-1.8 vs. 8.8+/-1.9 mm and 12.7+/-3.4 vs. 13.3+/-3.5 mm, respectively; both P<0.001). Values of regional wall thickening by MDCT and MR were similar (54+/-30 vs. 51+/-31%; P=NS) and also correlated well (r=0.91; P<0.001). Retrospectively gated MDCT can accurately estimate LV volumes, EF and regional LV wall thickening compared to cine MR.

  15. 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.

  16. Physiotherapy needs assessment of people with stroke following discharge from hospital, stratified by acute functional independence measure score.

    PubMed

    Depaul, Vincent G; Moreland, Julie D; Dehueck, Amy L

    2013-01-01

    Objectif : Établir les besoins en physiothérapie des personnes ayant subi un accident vasculaire cérébrale (AVC) lors de leur congé de l'hôpital, 6 mois après leur congé et 1 an après leur congé, et examiner les résultats stratifiés en fonction des pointages de mesure de l'autonomie fonctionnelle aigüe (Functional Independence Measure, FIM). Méthodologie : On a recruté en tout 241 adultes ayant récemment subi un ACV pour cette étude longitudinale de cohorte. En plus de participer à une entrevue semi-structurée comprenant des questions sur leurs besoins et sur les obstacles en matière de mobilité, les participants ont dû remplir et retourner un sondage d'évaluation des besoins avec questions fermées. Résultats : Au cours de l'entrevue, les participants ont fait part de besoins et d'obstacles liés au contrôle de leur motricité, à la marche, aux escaliers, à la fatigue, à la prévention des chutes et à l'accès à des services de physiothérapie. Le sondage a permis d'établir de nombreux autres besoins, dont la nécessité de transferts, l'utilisation d'un fauteuil roulant, un plus grand équilibre et de plus grandes habiletés motrices ainsi que l'accès à la physiothérapie et à des installations adaptées à leurs besoins en exercice. La fréquence des besoins et des obstacles avait tendance à diminuer chez les participants qui avaient obtenu des pointages plus élevés à l'échelle FIM. On n'a observé aucune tendance constante de diminution des besoins et des obstacles au fil du temps. Conclusions : Au cours de la première année suivant le congé de l'hôpital, les personnes qui ont subi un AVC font état d'un grand nombre de besoins variés et persistants en matière de mobilité. Les physiothérapeutes doivent faire pression pour des services de suivi adéquat et doivent contribuer à l'inclusion des besoins des patients qui ont subi un AVC dans les politiques en matière de santé.

  17. 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).

  18. Changes in Millon Clinical Multiaxial Inventory scores among opiate addicts as a function of retention in methadone maintenance treatment and recent drug use.

    PubMed

    Calsyn, D A; Wells, E A; Fleming, C; Saxon, A J

    2000-05-01

    The Millon Clinical Multiaxial Inventory (MCMI) was administered to 144 men and 86 women within 1 month of admission to methadone maintenance treatment and was readministered 18 months following admission. Based on prior research, we hypothesized there would be significant decreases on scales measuring affective disturbance, anxiety, and social isolation and little change in scales measuring antisocial and narcissistic traits. In addition, it was hypothesized that changes on the MCMI would be related to retention in treatment and illicit drug use during the interim between initial assessment and follow-up. Data were analyzed using a multivariate analysis of variance (MANOVA) for repeated measures. There was an overall decrease in MCMI scores, indicating less psychopathology between initial assessment and follow-up. MCMI scales did not change as a function of retention status, but decreases in MCMI scale scores were greater for subjects who were light drug users in the 6 months prior to the follow-up compared to heavy users. Inspection of individual MCMI scales supported our hypothesis; there were decreases on scales measuring affective disturbance, anxiety, and social isolation, but not on scales measuring antisocial and narcissistic traits.

  19. FILMPAR: A parallel algorithm designed for the efficient and accurate computation of thin film flow on functional surfaces containing micro-structure

    NASA Astrophysics Data System (ADS)

    Lee, Y. C.; Thompson, H. M.; Gaskell, P. H.

    2009-12-01

    FILMPAR is a highly efficient and portable parallel multigrid algorithm for solving a discretised form of the lubrication approximation to three-dimensional, gravity-driven, continuous thin film free-surface flow over substrates containing micro-scale topography. While generally applicable to problems involving heterogeneous and distributed features, for illustrative purposes the algorithm is benchmarked on a distributed memory IBM BlueGene/P computing platform for the case of flow over a single trench topography, enabling direct comparison with complementary experimental data and existing serial multigrid solutions. Parallel performance is assessed as a function of the number of processors employed and shown to lead to super-linear behaviour for the production of mesh-independent solutions. In addition, the approach is used to solve for the case of flow over a complex inter-connected topographical feature and a description provided of how FILMPAR could be adapted relatively simply to solve for a wider class of related thin film flow problems. Program summaryProgram title: FILMPAR Catalogue identifier: AEEL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEL_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.: 530 421 No. of bytes in distributed program, including test data, etc.: 1 960 313 Distribution format: tar.gz Programming language: C++ and MPI Computer: Desktop, server Operating system: Unix/Linux Mac OS X Has the code been vectorised or parallelised?: Yes. Tested with up to 128 processors RAM: 512 MBytes Classification: 12 External routines: GNU C/C++, MPI Nature of problem: Thin film flows over functional substrates containing well-defined single and complex topographical features are of enormous significance, having a wide variety of engineering

  20. Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology

    NASA Astrophysics Data System (ADS)

    Eid, Sameh; Saleh, Noureldin; Zalewski, Adam; Vedani, Angelo

    2014-12-01

    Carbohydrates play a key role in a variety of physiological and pathological processes and, hence, represent a rich source for the development of novel therapeutic agents. Being able to predict binding mode and binding affinity is an essential, yet lacking, aspect of the structure-based design of carbohydrate-based ligands. We assembled a diverse data set comprising 273 carbohydrate-protein crystal structures with known binding affinity and evaluated the prediction accuracy of a large collection of well-established scoring and free-energy functions, as well as combinations thereof. Unfortunately, the tested functions were not capable of reproducing binding affinities in the studied complexes. To simplify the complex free-energy surface of carbohydrate-protein systems, we classified the studied proteins according to the topology and solvent exposure of the carbohydrate-binding site into five distinct categories. A free-energy model based on the proposed classification scheme reproduced binding affinities in the carbohydrate data set with an r 2 of 0.71 and root-mean-squared-error of 1.25 kcal/mol ( N = 236). The improvement in model performance underlines the significance of the differences in the local micro-environments of carbohydrate-binding sites and demonstrates the usefulness of calibrating free-energy functions individually according to binding-site topology and solvent exposure.

  1. Age-related commonalities and differences in the relationship between executive functions and intelligence: Analysis of the NAB executive functions module and WAIS-IV scores.

    PubMed

    Buczylowska, Dorota; Petermann, Franz

    2016-08-02

    Data from five subtests of the Executive Functions Module of the German Neuropsychological Assessment Battery (NAB) and all ten core subtests of the German Wechsler Adult Intelligence Scale - Fourth Edition (WAIS-IV) were used to examine the relationship between executive functions and intelligence in a comparison of two age groups: individuals aged 18-59 years and individuals aged 60-88 years. The NAB subtests Categories and Word Generation demonstrated a consistent correlation pattern for both age groups. However, the NAB Judgment subtest correlated more strongly with three WAIS-IV indices, the Full Scale IQ (FSIQ), and the General Ability Index (GAI) in the older adult group than in the younger group. Additionally, in the 60-88 age group, the Executive Functions Index (EFI) was more strongly correlated with the Verbal Comprehension Index (VCI) than with the Perceptual Reasoning Index (PRI). Both age groups demonstrated a strong association of the EFI with the FSIQ and the Working Memory Index (WMI). The results imply the potential diagnostic utility of the Judgment subtest and a significant relationship between executive functioning and crystallized intelligence at older ages. Furthermore, it may be concluded that there is a considerable age-independent overlap between the EFI and general intelligence, as well as between the EFI and working memory.

  2. 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.

  3. Test facilities for SCORE-D

    NASA Astrophysics Data System (ADS)

    Greuel, Dirk; Deeken, Jan; Suslov, Dmitry; Schäfer, Klaus; Schlechtriem, Stefan

    2013-06-01

    The LOX/LH2 Staged Combustion Rocket Engine Demonstrator (SCORE-D) is part of ESA's Future Launcher Preparatory Program (FLPP). SCORE-D serves as a technology demonstrator in perspective of the development of the High Thrust Engine (HTE), which is designated as a candidate for the main stage engine of the Next Generation Launcher (NGL). To develop and test the SCORE-D engine, ESA investigates configurations of the test benches P3.2 and P5 at DLR test site in Lampoldshausen. For the SCORE-D Hot Combustion Devices (HCD) development, i.e. Pre-burner (PB) and thrust chamber assembly (TCA), the P3.2 test facility has to be modified for further usage. Recently, the first steps in this endeavor have been made with the evaluation of the necessary modifications to the facility. To accommodate the SCORE-D engine, it is foreseen to modify the P5 test facility in the coming years. In the last year, DLR has started the design phase for these modifications. In preparatory test programs at the P8 test facility, Astrium has conducted sub-scale hot combustion devices tests. While Astrium designed and manufactured the sub-scale assembly of the pre-burner and the main combustion chamber (MCC) for SCORE-D, DLR operated the P8 test facility.

  4. 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…

  5. The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods

    NASA Astrophysics Data System (ADS)

    Jójárt, Balázs; Martinek, Tamás A.; Márki, Árpád

    2005-05-01

    Molecular docking and 3D-QSAR studies were performed to determine the binding mode for a series of benzoxazine oxytocin antagonists taken from the literature. Structural hypotheses were generated by docking the most active molecule to the rigid receptor by means of AutoDock 3.05. The cluster analysis yielded seven possible binding conformations. These structures were refined by using constrained simulated annealing, and the further ligands were aligned in the refined receptor by molecular docking. A good correlation was found between the estimated Δ G bind and the p K i values for complex F. The Connolly-surface analysis, CoMFA and CoMSIA models q CoMFA 2 = 0.653, q CoMSA 2 = 0.630 and r pred,CoMFA 2 = 0.852 , r pred,CoMSIA 2 = 0.815) confirmed the scoring function results. The structural features of the receptor-ligand complex and the CoMFA and CoMSIA fields are in closely connected. These results suggest that receptor-ligand complex F is the most likely binding hypothesis for the studied benzoxazine analogs.

  6. Pathway-specific polygenic risk scores as predictors of β-amyloid deposition and cognitive function in a sample at increased risk for Alzheimer’s disease

    PubMed Central

    Darst, Burcu F.; Koscik, Rebecca L.; Racine, Annie M.; Oh, Jennifer M.; Krause, Rachel A.; Carlsson, Cynthia M.; Zetterberg, Henrik; Blennow, Kaj; Christian, Bradley T.; Bendlin, Barbara B.; Okonkwo, Ozioma C.; Hogan, Kirk J.; Hermann, Bruce P.; Sager, Mark A.; Asthana, Sanjay; Johnson, Sterling C.; Engelman, Corinne D.

    2016-01-01

    Polygenic risk scores (PRSs) have been used to combine the effects of variants with small effects identified by genome-wide association studies. We explore the potential for using pathway-specific PRSs as predictors of early changes in Alzheimer’s disease (AD)-related biomarkers and cognitive function. Participants were from the Wisconsin Registry for Alzheimer’s Prevention, a longitudinal study of adults who were cognitively asymptomatic at enrollment and enriched for a parental history of AD. Using genes associated with AD in the International Genomics of Alzheimer’s Project’s meta-analysis, we identified clusters of genes that grouped into pathways involved in β-amyloid (Aβ) deposition and neurodegeneration: Aβ clearance, cholesterol metabolism, and immune response. Weighted pathway-specific and overall PRSs were developed and compared to APOE alone. Mixed models were used to assess whether each PRS was associated with cognition in 1,200 individuals, cerebral Aβ deposition measured using amyloid ligand (Pittsburgh compound B) positron emission imaging (PET) in 168 individuals, and cerebrospinal fluid (CSF) Aβ deposition, neurodegeneration, and tau pathology in 111 individuals, with replication performed in an independent sample. We found that PRSs including APOE appeared to be driven by the inclusion of APOE, suggesting that the pathway-specific PRSs used here were not more predictive than an overall PRS or APOE alone. However, pathway-specific PRSs could prove to be useful as more knowledge is gained on the genetic variants involved in specific biological pathways of AD. PMID:27662287

  7. 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

  8. 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

  9. 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.

  10. 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

    SciTech Connect

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

    2016-02-07

    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.

  11. Highly accurate first-principles benchmark data sets for the parametrization and validation of density functional and other approximate methods. Derivation of a robust, generally applicable, double-hybrid functional for thermochemistry and thermochemical kinetics.

    PubMed

    Karton, Amir; Tarnopolsky, Alex; Lamère, Jean-François; Schatz, George C; Martin, Jan M L

    2008-12-18

    We present a number of near-exact, nonrelativistic, Born-Oppenheimer reference data sets for the parametrization of more approximate methods (such as DFT functionals). The data were obtained by means of the W4 ab initio computational thermochemistry protocol, which has a 95% confidence interval well below 1 kJ/mol. Our data sets include W4-08, which are total atomization energies of over 100 small molecules that cover varying degrees of nondynamical correlations, and DBH24-W4, which are W4 theory values for Truhlar's set of 24 representative barrier heights. The usual procedure of comparing calculated DFT values with experimental atomization energies is hampered by comparatively large experimental uncertainties in many experimental values and compounds errors due to deficiencies in the DFT functional with those resulting from neglect of relativity and finite nuclear mass. Comparison with accurate, explicitly nonrelativistic, ab initio data avoids these issues. We then proceed to explore the performance of B2x-PLYP-type double hybrid functionals for atomization energies and barrier heights. We find that the optimum hybrids for hydrogen-transfer reactions, heavy-atoms transfers, nucleophilic substitutions, and unimolecular and recombination reactions are quite different from one another: out of these subsets, the heavy-atom transfer reactions are by far the most sensitive to the percentages of Hartree-Fock-type exchange y and MP2-type correlation x in an (x, y) double hybrid. The (42,72) hybrid B2K-PLYP, as reported in a preliminary communication, represents the best compromise between thermochemistry and hydrogen-transfer barriers, while also yielding excellent performance for nucleophilic substitutions. By optimizing for best overall performance on both thermochemistry and the DBH24-W4 data set, however, we find a new (36,65) hybrid which we term B2GP-PLYP. At a slight expense in performance for hydrogen-transfer barrier heights and nucleophilic substitutions, we

  12. Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis.

    PubMed

    Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

    2011-04-01

    Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore

  13. 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.

  14. 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.

  15. 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

  16. Ligand Identification Scoring Algorithm (LISA).

    PubMed

    Zheng, Zheng; Merz, Kenneth M

    2011-06-27

    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.

  17. Impact of geometric mean imaging in the accurate determination of partial function in MAG3 renal scanning in a patient with retroperitoneal mass.

    PubMed

    Takesh, Mustafa; Zechmann, Christian M; Haufe, Sabine; Giesel, Frederik L; Kratochwil, Clemens

    2011-01-01

    Liposarcoma frequently occurs in the retroperitoneum and lower extremities, accounting for 20% of all mesenchymal malignancies. Liposarcomas vary by histology and can be classified into four types. Those four types are well differentiated, myxoid/round cell, pleomorphic and dedifferentiated. Due to retroperitoneal location of this tumor, it is expected to affect the kidney position. Renography has provided a unique tool for noninvasive evaluation of various functional parameters e.g. relative renal function. Most renography studies are carried out using the posterior view, under the assumption that the depths of both kidneys are similar so that the radiotracer counts in the region of interest will be attenuated to the same extent. Errors in estimation of the relative renal function may arise if the kidneys are at different depths e.g. secondary to a pushing tumor. Geometric mean imaging from combined anterior and posterior views helps to overcome this issue. This case shows the impact of geometric mean imaging in the truthful determination of partial function in patients with retroperitoneal liposarcoma.

  18. Effects of resting ischemia assessed by thallium scintigraphy on QRS scoring system for estimating left ventricular function quantified by radionuclide angiography in acute myocardial infarction patients.

    PubMed

    DePace, N L; Hakki, A H; Iskandrian, A S

    1984-06-01

    The purpose of this study was to determine whether resting ischemia limits the usefulness of the QRS scoring system in predicting left ventricular (LV) ejection fraction (EF) in patients with acute infarction. We studied 48 patients after acute infarction by means of 12-lead ECG, thallium-201 scintigraphy, and radionuclide angiography. The thallium-201 scintigrams showed fixed defects in 25 patients, perfusion defects with partial or complete redistribution in the delayed images in 19 patients, and normal images in the remaining four patients. In the 48 patients there was a significant correlation between the QRS score and LVEF (r = -0.67; p less than 0.001). Patients with fixed defects showed a better correlation than patients with resting ischemia (r = -0.77 vs r = -0.60). A QRS score of 3 or less was used to separate patients with LVEF of 40% or greater from those with lower LVEF in patients with fixed defects (p = 0.0005), but this cutoff did not categorize patients with resting ischemia as to LVEF. Thus the presence of rest ischemia in patients with acute infarction may affect the correlation between QRS score and LVEF.

  19. 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…

  20. 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…

  1. 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.

  2. Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions

    PubMed Central

    2010-01-01

    Background In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translational accuracy and speed and is one of several factors optimizing cell growth. Whereas CUB and the overrepresentation of individual proteins have been studied in detail, it is still unclear which high-level metabolic categories are subject to translational optimization in different habitats. Results In a systematic study of 388 microbial species, we have identified for each genome a specific subset of genes characterized by a marked CUB, which we named the effectome. As expected, gene products related to protein synthesis are abundant in both archaeal and bacterial effectomes. In addition, enzymes contributing to energy production and gene products involved in protein folding and stabilization are overrepresented. The comparison of genomes from eleven habitats shows that the environment has only a minor effect on the composition of the effectomes. As a paradigmatic example, we detailed the effectome content of 37 bacterial genomes that are most likely exposed to strongest selective pressure towards translational optimization. These effectomes accommodate a broad range of protein functions like enzymes related to glycolysis/gluconeogenesis and the TCA cycle, ATP synthases, aminoacyl-tRNA synthetases, chaperones, proteases that degrade misfolded proteins, protectants against oxidative damage, as well as cold shock and outer membrane proteins. Conclusions We made clear that effectomes consist of specific subsets of the proteome being involved in several cellular functions. As expected, some functions are related to cell growth and affect speed and quality of protein synthesis. Additionally, the effectomes contain enzymes of central metabolic pathways and cellular functions sustaining microbial life under stress situations. These findings indicate that cell

  3. 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.

  4. 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.…

  5. 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.

  6. Accurate ab initio determination of the adiabatic potential energy function and the Born-Oppenheimer breakdown corrections for the electronic ground state of LiH isotopologues

    NASA Astrophysics Data System (ADS)

    Holka, Filip; Szalay, Péter G.; Fremont, Julien; Rey, Michael; Peterson, Kirk A.; Tyuterev, Vladimir G.

    2011-03-01

    High level ab initio potential energy functions have been constructed for LiH in order to predict vibrational levels up to dissociation. After careful tests of the parameters of the calculation, the final adiabatic potential energy function has been composed from: (a) an ab initio nonrelativistic potential obtained at the multireference configuration interaction with singles and doubles level including a size-extensivity correction and quintuple-sextuple ζ extrapolations of the basis, (b) a mass-velocity-Darwin relativistic correction, and (c) a diagonal Born-Oppenheimer (BO) correction. Finally, nonadiabatic effects have also been considered by including a nonadiabatic correction to the kinetic energy operator of the nuclei. This correction is calculated from nonadiabatic matrix elements between the ground and excited electronic states. The calculated vibrational levels have been compared with those obtained from the experimental data [J. A. Coxon and C. S. Dickinson, J. Chem. Phys. 134, 9378 (2004)]. It was found that the calculated BO potential results in vibrational levels which have root mean square (rms) deviations of about 6-7 cm-1 for LiH and ˜3 cm-1 for LiD. With all the above mentioned corrections accounted for, the rms deviation falls down to ˜1 cm-1. These results represent a drastic improvement over previous theoretical predictions of vibrational levels for all isotopologues of LiH.

  7. Accurate ab initio determination of the adiabatic potential energy function and the Born-Oppenheimer breakdown corrections for the electronic ground state of LiH isotopologues.

    PubMed

    Holka, Filip; Szalay, Péter G; Fremont, Julien; Rey, Michael; Peterson, Kirk A; Tyuterev, Vladimir G

    2011-03-07

    High level ab initio potential energy functions have been constructed for LiH in order to predict vibrational levels up to dissociation. After careful tests of the parameters of the calculation, the final adiabatic potential energy function has been composed from: (a) an ab initio nonrelativistic potential obtained at the multireference configuration interaction with singles and doubles level including a size-extensivity correction and quintuple-sextuple ζ extrapolations of the basis, (b) a mass-velocity-Darwin relativistic correction, and (c) a diagonal Born-Oppenheimer (BO) correction. Finally, nonadiabatic effects have also been considered by including a nonadiabatic correction to the kinetic energy operator of the nuclei. This correction is calculated from nonadiabatic matrix elements between the ground and excited electronic states. The calculated vibrational levels have been compared with those obtained from the experimental data [J. A. Coxon and C. S. Dickinson, J. Chem. Phys. 134, 9378 (2004)]. It was found that the calculated BO potential results in vibrational levels which have root mean square (rms) deviations of about 6-7 cm(-1) for LiH and ∼3 cm(-1) for LiD. With all the above mentioned corrections accounted for, the rms deviation falls down to ∼1 cm(-1). These results represent a drastic improvement over previous theoretical predictions of vibrational levels for all isotopologues of LiH.

  8. Accurate determination of pyridine-poly(amidoamine) dendrimer absolute binding constants with the OPLS-AA force field and direct integration of radial distribution functions.

    PubMed

    Peng, Yong; Kaminski, George A

    2005-08-11

    OPLS-AA force field and direct integration of intermolecular radial distribution functions (RDF) were employed to calculate absolute binding constants of pyridine molecules to amino group (NH2) and amide group hydrogen atoms in and first generation poly(amidoamine) dendrimers in chloroform. The average errors in the absolute and relative association constants, as predicted with the calculations, are 14.1% and 10.8%, respectively, which translate into ca. 0.08 and 0.06 kcal/mol errors in the absolute and relative binding free energies. We believe that this level of accuracy proves the applicability of the OPLS-AA, force field, in combination with the direct RDF integration, to reproducing and predicting absolute intermolecular association constants of low magnitudes (ca. 0.2-2.0 range).

  9. Accurate Determination of Pyridine -- Poly (Amidoamine) Dendrimer Absolute Binding Constants with the OPLS-AA Force Field and Direct Integration of Radial Distribution Functions

    NASA Astrophysics Data System (ADS)

    Peng, Yong; Kaminski, George

    2006-03-01

    OPLS-AA force field and direct integration of intermolecular radial distribution functions (RDF) were employed to calculate absolute binding constants of pyridine molecules to NH2 and amide group hydrogen atoms in 0th and 1st generation poly (amidoamine) dendrimers in chloroform. The average errors in the absolute and relative association constants, as predicted with the calculations, are 14.1% and 10.8%, respectively, which translate into ca. 0.08 kcal/mol and 0.06 kcal/mol errors in the absolute and relative binding free energies. We believe that this level of accuracy proves the applicability of the OPLS-AA, force field, in combination with the direct RDF integration, to reproducing and predicting absolute intermolecular association constants of low magnitudes (ca. 0.2 -- 2.0 range).

  10. Evaluation of Transient Elastography, Acoustic Radiation Force Impulse Imaging (ARFI), and Enhanced Liver Function (ELF) Score for Detection of Fibrosis in Morbidly Obese Patients

    PubMed Central

    Karlas, Thomas; Dietrich, Arne; Peter, Veronica; Wittekind, Christian; Lichtinghagen, Ralf; Garnov, Nikita; Linder, Nicolas; Schaudinn, Alexander; Busse, Harald; Prettin, Christiane; Keim, Volker; Tröltzsch, Michael; Schütz, Tatjana; Wiegand, Johannes

    2015-01-01

    Background Liver fibrosis induced by non-alcoholic fatty liver disease causes peri-interventional complications in morbidly obese patients. We determined the performance of transient elastography (TE), acoustic radiation force impulse (ARFI) imaging, and enhanced liver fibrosis (ELF) score for fibrosis detection in bariatric patients. Patients and Methods 41 patients (median BMI 47 kg/m2) underwent 14-day low-energy diets to improve conditions prior to bariatric surgery (day 0). TE (M and XL probe), ARFI, and ELF score were performed on days -15 and -1 and compared with intraoperative liver biopsies (NAS staging). Results Valid TE and ARFI results at day -15 and -1 were obtained in 49%/88% and 51%/90% of cases, respectively. High skin-to-liver-capsule distances correlated with invalid TE measurements. Fibrosis of liver biopsies was staged as F1 and F3 in n = 40 and n = 1 individuals. However, variations (median/range at d-15/-1) of TE (4.6/2.6–75 and 6.7/2.9–21.3 kPa) and ARFI (2.1/0.7–3.7 and 2.0/0.7–3.8 m/s) were high and associated with overestimation of fibrosis. The ELF score correctly classified 87.5% of patients. Conclusion In bariatric patients, performance of TE and ARFI was poor and did not improve after weight loss. The ELF score correctly classified the majority of cases and should be further evaluated. PMID:26528818

  11. Accurate density-functional calculation of core-electron binding energies with a scaled polarized triple-zeta basis set. (III). Extension to open-shell molecules

    NASA Astrophysics Data System (ADS)

    Hu, Ching-Han; Chong, Delano P.

    1997-03-01

    Density functional theory and the unrestricted generalized transition state (uGTS) model were applied to study the core-electron binding energies (CEBEs) of open-shell molecules. Basis set scaling based on Clementi and Raimondi's rules for atomic screening was used along with the cc-pVTZ basis set. The scaled pVTZ basis set is almost as good as the cc-pV5Z and complete basis set limit in predicting CEBEs. For small molecules (O 2, NO, NF 2 and NO 2) the average absolute deviation (aad) of our prediction (scaled pVTZ) is only 0.29 eV. For the larger molecule (CF 3) 2NO the aad is 0.56 eV, compared with experimental uncertainty of 0.5 eV. Theoretical predicted multiplet splittings for the small molecules agree quite well with experiment: the average deviation is -0.33 eV. For (CF 3) 2NO the calculated multiplet splittings are much smaller than the experimental ones. We also predict the CEBEs of PO, SN and SO, which have not been observed experimentally.

  12. 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

  13. Frequency Scale Factors for Some Double-Hybrid Density Functional Theory Procedures: Accurate Thermochemical Components for High-Level Composite Protocols.

    PubMed

    Chan, Bun; Radom, Leo

    2016-08-09

    In the present study, we have obtained geometries and frequency scale factors for a number of double-hybrid density functional theory (DH-DFT) procedures. We have evaluated their performance for obtaining thermochemical quantities [zero-point vibrational energies (ZPVE) and thermal corrections for 298 K enthalpies (ΔH298) and 298 K entropies (S298)] to be used within high-level composite protocols (using the W2X procedure as a probe). We find that, in comparison with the previously prescribed protocol for optimization and frequency calculations (B3-LYP/cc-pVTZ+d), the use of contemporary DH-DFT methods such as DuT-D3 and DSD-type procedures leads to a slight overall improved performance compared with B3-LYP. A major strength of this approach, however, lies in the better robustness of the DH-DFT methods in that the largest deviations are notably smaller than those for B3-LYP. In general, the specific choices of the DH-DFT procedure and the associated basis set do not drastically change the performance. Nonetheless, we find that the DSD-PBE-P86/aug'-cc-pVTZ+d combination has a very slight edge over the others that we have examined, and we recommend its general use for geometry optimization and vibrational frequency calculations, in particular within high-level composite methods such as the higher-level members of the WnX series of protocols. The scale factors determined for DSD-PBE-P86/aug'-cc-pVTZ+d are 0.9830 (ZPVE), 0.9876 (ΔH298), and 0.9923 (S298).

  14. 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.

  15. Conditional Reliability Coefficients for Test Scores.

    PubMed

    Nicewander, W Alan

    2017-04-06

    The most widely used, general index of measurement precision for psychological and educational test scores is the reliability coefficient-a ratio of true variance for a test score to the true-plus-error variance of the score. In item response theory (IRT) models for test scores, the information function is the central, conditional index of measurement precision. In this inquiry, conditional reliability coefficients for a variety of score types are derived as simple transformations of information functions. It is shown, for example, that the conditional reliability coefficient for an ordinary, number-correct score, X, is equal to, ρ(X,X'|θ)=I(X,θ)/[I(X,θ)+1] Where: θ is a latent variable measured by an observed test score, X; p(X, X'|θ) is the conditional reliability of X at a fixed value of θ; and I(X, θ) is the score information function. This is a surprisingly simple relationship between the 2, basic indices of measurement precision from IRT and classical test theory (CTT). This relationship holds for item scores as well as test scores based on sums of item scores-and it holds for dichotomous as well as polytomous items, or a mix of both item types. Also, conditional reliabilities are derived for computerized adaptive test scores, and for θ-estimates used as alternatives to number correct scores. These conditional reliabilities are all related to information in a manner similar-or-identical to the 1 given above for the number-correct (NC) score. (PsycINFO Database Record

  16. 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.

  17. Establishing Passing Scores.

    ERIC Educational Resources Information Center

    McLarty, Joyce R.

    The problem of establishing appropriate passing scores is one of evaluation rather than estimation and not amenable to exact solution. It must therefore be approached by (1) identifying criteria for judging the acceptability of the passing score, (2) collecting the data appropriate to assessing each relevant criterion, and (3) judging how well the…

  18. 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…

  19. 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…

  20. 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

  1. Mortality scoring in ITU.

    PubMed

    Niewiński, Grzegorz; Kański, Andrzej

    2012-01-01

    Chronic shortage of ITU beds makes decisions on admission difficult and responsible. The use of computer-based mortality scoring should help in decision-making and for this purpose, a number of different scoring systems have been created; in principle, they should be easy to use, adaptable to all populations of patients and suitable for predicting the risk of mortality during both ITU and hospital stay. Most of existing scales and scoring systems were included in this review. They are frequently used in ITUs and become a necessary tool to describe ITU populations and to explain differences in mortality. As there are several pitfalls related to the interpretation of the numbers supplied by the systems, they should be used with the knowledge on the severity scoring science. Moreover, the cost and significant workload limit the use of scoring systems; in many cases an extra person has to be employed for collection and analysis of data only.

  2. FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data.

    PubMed

    Pearlman, David A; Rao, B Govinda; Charifson, Paul

    2008-05-15

    We demonstrate a new approach to the development of scoring functions through the formulation and parameterization of a new function, which can be used both for rapidly ranking the binding of ligands to proteins and for estimating relative aqueous molecular solubilities. The intent of this work is to introduce a new paradigm for creation of scoring functions, wherein we impose the following criteria upon the function: (1) simple; (2) intuitive; (3) requires no postparameterization tweaking; (4) can be applied (without reparameterization) to multiple target systems; and (5) can be rapidly evaluated for any potential ligand. Following these criteria, a new function, FURSMASA (function for rapid scoring using an MD-averaged grid and the accessible surface area) has been developed. Three novel features of the function include: (1) use of an MD-averaged potential energy grid for ligand-protein interactions, rather than a simple static grid; (2) inclusion of a term that depends on the change in the solvent-accessible surface area changes on an atomic (not molecular) basis; and (3) use of the recently derived predictive index (PI) target when optimizing the function, which focuses the function on its intended purpose of relative ranking. A genetic algorithm is used to optimize the function against test data sets that include ligands for the following proteins: IMPDH, p38, gyrase B, HIV-1, and TACE, as well as the Syracuse Research solubility database. We find that the function is predictive, and can simultaneously fit all the test data sets with cross-validated predictive indices ranging from 0.68 to 0.82. As a test of the ability of this function to predict binding for systems not in the training set, the resulting fitted FURSAMA function is then applied to 23 ligands of the COX-2 enzyme. Comparing the results for COX-2 against those obtained using a variety of well-known rapid scoring functions demonstrates that FURSMASA outperforms all of them in terms of the PI and

  3. Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?

    PubMed

    Ballester, Pedro J; Schreyer, Adrian; Blundell, Tom L

    2014-03-24

    Predicting the binding affinities of large sets of diverse molecules against a range of macromolecular targets is an extremely challenging task. The scoring functions that attempt such computational prediction are essential for exploiting and analyzing the outputs of docking, which is in turn an important tool in problems such as structure-based drug design. Classical scoring functions assume a predetermined theory-inspired functional form for the relationship between the variables that describe an experimentally determined or modeled structure of a protein-ligand complex and its binding affinity. The inherent problem of this approach is in the difficulty of explicitly modeling the various contributions of intermolecular interactions to binding affinity. New scoring functions based on machine-learning regression models, which are able to exploit effectively much larger amounts of experimental data and circumvent the need for a predetermined functional form, have already been shown to outperform a broad range of state-of-the-art scoring functions in a widely used benchmark. Here, we investigate the impact of the chemical description of the complex on the predictive power of the resulting scoring function using a systematic battery of numerical experiments. The latter resulted in the most accurate scoring function to date on the benchmark. Strikingly, we also found that a more precise chemical description of the protein-ligand complex does not generally lead to a more accurate prediction of binding affinity. We discuss four factors that may contribute to this result: modeling assumptions, codependence of representation and regression, data restricted to the bound state, and conformational heterogeneity in data.

  4. 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.

  5. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...

    EPA Pesticide Factsheets

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad

  6. 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)

  7. 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)

  8. Accurate spectral color measurements

    NASA Astrophysics Data System (ADS)

    Hiltunen, Jouni; Jaeaeskelaeinen, Timo; Parkkinen, Jussi P. S.

    1999-08-01

    Surface color measurement is of importance in a very wide range of industrial applications including paint, paper, printing, photography, textiles, plastics and so on. For a demanding color measurements spectral approach is often needed. One can measure a color spectrum with a spectrophotometer using calibrated standard samples as a reference. Because it is impossible to define absolute color values of a sample, we always work with approximations. The human eye can perceive color difference as small as 0.5 CIELAB units and thus distinguish millions of colors. This 0.5 unit difference should be a goal for the precise color measurements. This limit is not a problem if we only want to measure the color difference of two samples, but if we want to know in a same time exact color coordinate values accuracy problems arise. The values of two instruments can be astonishingly different. The accuracy of the instrument used in color measurement may depend on various errors such as photometric non-linearity, wavelength error, integrating sphere dark level error, integrating sphere error in both specular included and specular excluded modes. Thus the correction formulas should be used to get more accurate results. Another question is how many channels i.e. wavelengths we are using to measure a spectrum. It is obvious that the sampling interval should be short to get more precise results. Furthermore, the result we get is always compromise of measuring time, conditions and cost. Sometimes we have to use portable syste or the shape and the size of samples makes it impossible to use sensitive equipment. In this study a small set of calibrated color tiles measured with the Perkin Elmer Lamda 18 and the Minolta CM-2002 spectrophotometers are compared. In the paper we explain the typical error sources of spectral color measurements, and show which are the accuracy demands a good colorimeter should have.

  9. Benchmark calculations with correlated molecular wave functions. V. The determination of accurate [ital ab] [ital initio] intermolecular potentials for He[sub 2], Ne[sub 2], and Ar[sub 2

    SciTech Connect

    Woon, D.E. )

    1994-02-15

    Dimer interactions of helium, neon, and argon have been studied using the augmented correlation consistent basis sets of Dunning and co-workers. Two correlation methods have been employed throughout; Moller--Plesset perturbation theory through fourth-order (MP4) and single and double excitation coupled-cluster theory with perturbative treatment of triple excitations [CCSD(T)]. Full configuration interaction (FCI) calculations were performed on He[sub 2] for some basis sets. In general, only valence electrons were correlated, although some calculations which also correlated the [ital n]=2 shell of Ar[sub 2] were performed. Dimer potential energy curves were determined using the supermolecule method with and without the counterpoise correction. A series of additional basis sets beyond the augmented correlation consistent sets were explored in which the diffuse region of the radial function space has been systematically saturated. In combination with the systematic expansion across angular function space which is inherent to the correlation consistent prescription, this approach guarantees very accurate atomic polarizabilities and hyperpolarizabilities and should lead to an accurate description of dispersion forces. The best counterpoise-corrected MP4 values for the well depths of the three dimers are (in microhartrees, empirical values in parentheses) He[sub 2], 31.9 (34.6); Ne[sub 2], 123 (134); and Ar[sub 2], 430 (454). The corresponding CCSD(T) values are He[sub 2], 33.1; Ne[sub 2], 128; and Ar[sub 2], 417. Although these values are very good, the nearly exponential convergence of well depth as a function of basis quality afforded by using the various series of correlation consistent basis sets allows estimation of complete basis set (CBS) limiting values. The MP4 estimated CBS limits are He[sub 2], 32.2; Ne[sub 2], 126; and Ar[sub 2], 447.

  10. Benchmarking singlet and triplet excitation energies of molecular semiconductors for singlet fission: Tuning the amount of HF exchange and adjusting local correlation to obtain accurate functionals for singlet-triplet gaps

    NASA Astrophysics Data System (ADS)

    Brückner, Charlotte; Engels, Bernd

    2017-01-01

    Vertical and adiabatic singlet and triplet excitation energies of molecular p-type semiconductors calculated with various DFT functionals and wave-function based approaches are benchmarked against MS-CASPT2/cc-pVTZ reference values. A special focus lies on the singlet-triplet gaps that are very important in the process of singlet fission. Singlet fission has the potential to boost device efficiencies of organic solar cells, but the scope of existing singlet-fission compounds is still limited. A computational prescreening of candidate molecules could enlarge it; yet it requires efficient methods accurately predicting singlet and triplet excitation energies. Different DFT formulations (Tamm-Dancoff approximation, linear response time-dependent DFT, Δ-SCF) and spin scaling schemes along with several ab initio methods (CC2, ADC(2)/MP2, CIS(D), CIS) are evaluated. While wave-function based methods yield rather reliable singlet-triplet gaps, many DFT functionals are shown to systematically underestimate triplet excitation energies. To gain insight, the impact of exact exchange and correlation is in detail addressed.

  11. Accurate ab Initio Spin Densities.

    PubMed

    Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus

    2012-06-12

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

  12. Computer Health Score

    SciTech Connect

    2016-08-03

    The algorithm develops a single health score for office computers, today just Windows, but we plan to extend this to Apple computers. The score is derived from various parameters, including: CPU Utilization Memory Utilization Various Error logs Disk Problems Disk write queue length It then uses a weighting scheme to balance these parameters and provide an overall health score. By using these parameters, we are not just assessing the theoretical performance of the components of the computer, rather we are using actual performance metrics that are selected to be a more realistic representation of the experience of the person using the computer. This includes compensating for the nature of their use. If there are two identical computers and the user of one places heavy demands on their computer compared with the user of the second computer, the former will have a lower health score. This allows us to provide a 'fit for purpose' score tailored to the assigned user. This is very helpful data to inform the mangers when individual computers need to be replaced. Additionally it provides specific information that can facilitate the fixing of the computer, to extend it's useful lifetime. This presents direct financial savings, time savings for users transferring from one computer to the next, and better environmental stewardship.

  13. On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra

    PubMed Central

    2015-01-01

    Identifying the peptide responsible for generating an observed fragmentation spectrum requires scoring a collection of candidate peptides and then identifying the peptide that achieves the highest score. However, analysis of a large collection of such spectra requires that the score assigned to one spectrum be well-calibrated with respect to the scores assigned to other spectra. In this work, we define the notion of calibration in the context of shotgun proteomics spectrum identification, and we introduce a simple, albeit computationally intensive, technique to calibrate an arbitrary score function. We demonstrate that this calibration procedure yields an increased number of identified spectra at a fixed false discovery rate (FDR) threshold. We also show that proper calibration of scores has a surprising effect on a previously described FDR estimation procedure, making the procedure less conservative. Finally, we provide empirical results suggesting that even partial calibration, which is much less computationally demanding, can yield significant increases in spectrum identification. Overall, we argue that accurate shotgun proteomics analysis requires careful attention to score calibration. PMID:25482958

  14. Circulating plasmalogen levels and Alzheimer Disease Assessment Scale–Cognitive scores in Alzheimer patients

    PubMed Central

    Wood, Paul L.; Mankidy, Rishikesh; Ritchie, Shawn; Heath, Doug; Wood, Julie A.; Flax, John; Goodenowe, Dayan B.

    2010-01-01

    Background Plasmalogens, which are key structural phospholipids in brain membranes, are decreased in the brain and serum of patients with Alzheimer disease (AD). We performed this pilot study to evaluate the relation between the levels of circulating plasmalogens and Alzheimer Disease Assessment Scale–Cognitive (ADAS-Cog) scores in patients with AD. Methods We evaluated participants’ ADAS-Cog scores and serum plasmalogen levels. For the 40 included AD patients with an ADAS-Cog score between 20 and 46, we retested their ADAS-Cog score 1 year later. The levels of docosahexaenoic acid plasmalogen were measured by use of liquid chromatography–tandem mass spectrometry. Results We found that the ADAS-Cog score increased significantly in AD patients with circulating plasmalogen levels that were ≤ 75% of that of age-matched controls at entry into the study. There was no change in score among participants with normal serum plasmalogen levels at baseline (> 75%). Limitations This was a pilot study with 40 patients, and the results require validation in a larger population. Conclusion Our study demonstrates that decreased levels of plasmalogen precursors in the central nervous system correlate with functional decline (as measured by ADAS-Cog scores) in AD patients. The use of both ADAS-Cog and serum plasmalogen data may be a more accurate way of predicting cognitive decline in AD patients, and may be used to decrease the risk of including patients with no cognitive decline in the placebo arm of a drug trial. PMID:20040248

  15. Discovery of Novel Disruptor of Silencing Telomeric 1-Like (DOT1L) Inhibitors using a Target-Specific Scoring Function for the (S)-Adenosyl-l-methionine (SAM)-Dependent Methyltransferase Family.

    PubMed

    Wang, Yulan; Li, Linjuan; Zhang, Bidong; Xing, Jing; Chen, Shijie; Wan, Wei; Song, Yakai; Jiang, Hao; Jiang, Hualiang; Luo, Cheng; Zheng, Mingyue

    2017-02-21

    The disruptor of telomeric silencing 1-like (DOT1L) protein is a histone H3K79 methyltransferase that plays a key role in transcriptional elongation and cell cycle regulation and is required for the development and maintenance of MLL-rearranged mixed lineage leukemia. Much effort has been dedicated toward discovering novel scaffold DOT1L inhibitors using different strategies. Here, we report the development and application of a target-specific scoring function, the SAM score, for (S)-adenosyl-l-methionine (SAM)-dependent methyltransferases, for the discovery of novel DOT1L inhibitors. On the basis of the SAM score, we successfully identified a novel class of DOT1L inhibitors with a scaffold of [1,2,4]-triazolo-[3,4-b][1,3,4]-thiadiazole, in which compound 6 exhibits an IC50 value of 8.3 μM with selectivity versus other tested SAM-dependent methyltransferases. In cellular studies, 6 selectively targets DOT1L, blocks the proliferation of mixed lineage leukemia cell lines, and causes cell cycle arrest and apoptosis. Moreover, we analyzed the putative binding modes of 6 and its analogues obtained by molecular docking, which may assist with the future development of DOT1L inhibitors with improved potency and selectivity profiles.

  16. Understanding and Interpreting Pharmacy College Admission Test Scores

    PubMed Central

    2017-01-01

    To fairly and accurately interpret candidates’ Pharmacy College Admission Test (PCAT) scores as listed on their official transcripts, it is important to understand how these scores reflect candidates’ performances on cognitive tasks involving the identification, interpretation, analysis, and evaluation of information assumed to have been covered in pre-pharmacy science, math, and general education coursework. This paper attempts to facilitate this understanding by explaining how candidates’ responses to PCAT test items relate to their scaled scores and percentile ranks and how their writing scores reflect their performance. This paper also suggests how differences between candidates’ PCAT subtest scores may reflect different personal experiences, educational backgrounds, and cognitive abilities. PMID:28289307

  17. Walk Score®

    PubMed Central

    Brown, Scott C.; Pantin, Hilda; Lombard, Joanna; Toro, Matthew; Huang, Shi; Plater-Zyberk, Elizabeth; Perrino, Tatiana; Perez-Gomez, Gianna; Barrera-Allen, Lloyd; Szapocznik, José

    2013-01-01

    Background Walk Score® is a nationally and publicly available metric of neighborhood walkability based on proximity to amenities (e.g., retail, food, schools). However, few studies have examined the relationship of Walk Score to walking behavior. Purpose To examine the relationship of Walk Score to walking behavior in a sample of recent Cuban immigrants, who overwhelmingly report little choice in their selection of neighborhood built environments when they arrive in the U.S. Methods Participants were 391 recent healthy Cuban immigrants (M age=37.1 years) recruited within 90 days of arrival in the U.S., and assessed within 4 months of arrival (M=41.0 days in the U.S.), who resided throughout Miami-Dade County FL. Data on participants’ addresses, walking and sociodemographics were collected prospectively from 2008 to 2010. Analyses conducted in 2011 examined the relationship of Walk Score for each participant’s residential address in the U.S. to purposive walking, controlling for age, gender, education, BMI, days in the U.S., and habitual physical activity level in Cuba. Results For each 10-point increase in Walk Score, adjusting for covariates, there was a significant 19% increase in the likelihood of purposive walking, a 26% increase in the likelihood of meeting physical activity recommendations by walking, and 27% more minutes walked in the previous week. Conclusions Results suggest that Walk Score is associated with walking in a sample of recent immigrants who initially had little choice in where they lived in the U.S. These results support existing guidelines indicating that mixed land use (such as parks and restaurants near homes) should be included when designing walkable communities. PMID:23867028

  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. 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.

  20. 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

  1. A score model for the continuous grading of early allograft dysfunction severity.

    PubMed

    Pareja, Eugenia; Cortes, Miriam; Hervás, David; Mir, José; Valdivieso, Andrés; Castell, José V; Lahoz, Agustín

    2015-01-01

    Early allograft dysfunction (EAD) dramatically influences graft and patient outcomes. A lack of consensus on an EAD definition hinders comparisons of liver transplant outcomes and management of recipients among and within centers. We sought to develop a model for the quantitative assessment of early allograft function [Model for Early Allograft Function Scoring (MEAF)] after transplantation. A retrospective study including 1026 consecutive liver transplants was performed for MEAF score development. Multivariate data analysis was used to select a small number of postoperative variables that adequately describe EAD. Then, the distribution of these variables was mathematically modeled to assign a score for each actual variable value. A model, based on easily obtainable clinical parameters (ie, alanine aminotransferase, international normalized ratio, and bilirubin) and scoring liver function from 0 to 10, was built. The MEAF score showed a significant association with patient and graft survival at 3-, 6- and 12-month follow-ups. Hepatic steatosis and age for donors; cold/warm ischemia times and postreperfusion syndrome for surgery; and intensive care unit and hospital stays, Model for End-Stage Liver Disease and Child-Pugh scores, body mass index, and fresh frozen plasma transfusions for recipients were factors associated significantly with EAD. The model was satisfactorily validated by its application to an independent set of 200 patients who underwent liver transplantation at a different center. In conclusion, a model for the quantitative assessment of EAD severity has been developed and validated for the first time. The MEAF provides a more accurate graft function assessment than current categorical classifications and may help clinicians to make early enough decisions on retransplantation benefits. Furthermore, the MEAF score is a predictor of recipient and graft survival. The standardization of the criteria used to define EAD may allow reliable comparisons of

  2. ATP system target for performance scoring

    NASA Astrophysics Data System (ADS)

    Tamerler, Timothy; Dowling, James A.; Dillow, Michael A.; Sebesta, Henry R.

    1997-06-01

    The US Air Force Phillips Laboratory is developing the High Altitude Balloon Experiment (HABE) to investigate acquisition, tracking, and pointing concepts to be employed in engagements against boosting missiles in near-space environments. In its most stressing test, HABE employs the Inertial Pseudo Star Reference Unit to provide inertially stabilized line-of-sights (LOSs) for an illuminator laser, active fine track camera, and the marker scoring. The latter serves to measure and score the payload's laser pointing performance. HABE's LOS stabilization subsystem and marker laser pointing are required to demonstrate jitter and drift which is below 1 (mu) rad RMS, a requirement which stresses testing capabilities. At present, a system does not exist to characterize and score the lasers used on this and other experiments at the target plane. This paper will address a concept to provide accurate characterization of laser systems in the far-field target plane.

  3. 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)

  4. Test Score Reporting Referenced to Doubly-Moderated Cut Scores Using Splines

    ERIC Educational Resources Information Center

    Schafer, William D.; Hou, Xiaodong

    2011-01-01

    This study discusses and presents an example of a use of spline functions to establish and report test scores using a moderated system of any number of cut scores. Our main goals include studying the need for and establishing moderated standards and creating a reporting scale that is referenced to all the standards. Our secondary goals are to make…

  5. Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression.

    PubMed

    Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

    2009-10-01

    An accurate scoring function is required for protein structure prediction. The scoring function should distinguish the native structure among model structures (decoys) and it also should have correlation with the quality of the decoys. However, we had observed the trade-off between the two requirements for seven all-atom distance dependent potentials in the previous study, where the native structure could be discriminated by examining the fine atomic details, whereas the correlation could be improved by examining coarse-grained interactions, To overcome this problem, in this study, we tried to make an improved scoring function by combining the seven potentials. First, the seven potentials were normalized by the expected energy values of the native and reference states of the target protein. Second, the relationship between the seven normalized energies and the quality (GDT_TS) of the structure were learned using support vector regression with the decoy sets of CASP6 as the training set. Then the meta-score was obtained as the predicted GDT_TS and it was tested with the decoys of the CASP7 experiment. The meta-score showed improvement in correlations with the GDT_TS and in the Z-score of the native structure. It also showed comparable performances in the GDT and enrichment criteria, with the best component potentials. The meta-score could be also used as the absolute quality of the structures. Our study suggests the benefit of combining several different scoring functions for model evaluation.

  6. Empirical Bayes Estimates of Domain Scores under Binomial and Hypergeometric Distributions for Test Scores.

    ERIC Educational Resources Information Center

    Lin, Miao-Hsiang; Hsiung, Chao A.

    1994-01-01

    Two simple empirical approximate Bayes estimators are introduced for estimating domain scores under binomial and hypergeometric distributions respectively. Criteria are established regarding use of these functions over maximum likelihood estimation counterparts. (SLD)

  7. [Scoring--criteria for operability].

    PubMed

    Oestern, H J

    1997-01-01

    For therapeutic recommendations three different kinds of scores are essential: 1. The severity scores for trauma; 2. Severity scores for mangled extremities; 3. Intensive care scores. The severity of polytrauma patients is measurable by the AIS, ISS, RTS, PTS and TRISS which is a combination of RTS, ISS, age, and mechanism of injury. For mangled extremities there are also different scores available: MESI (Mangled Extremity Syndrome Index) and MESS (Mangled Extremity Severity Score). The aim of these scores is to assist in the indication with regard to amputate or to save the extremity. These scoring indices can be used to evaluate the severity of a systemic inflammatory reaction syndrome with respect to multiple organ failure. All scores are dynamic values which are variable with improvement of therapy.

  8. 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…

  9. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, D. C.; Goorvitch, D.; Witteborn, Fred C. (Technical Monitor)

    1995-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schrodinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  10. Using Subpopulation Invariance to Assess Test Score Equity

    ERIC Educational Resources Information Center

    Dorans, Neil J.

    2004-01-01

    Score equity assessment (SEA) is introduced, and placed within a fair assessment context that includes differential prediction or fair selection and differential item functioning. The notion of subpopulation invariance of linking functions is central to the assessment of score equity, just as it has been for differential item functioning and…

  11. 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.

  12. 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…

  13. 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…

  14. Definition of True Score Appropriate for Estimated True Scores

    ERIC Educational Resources Information Center

    Stanley, Julian C.

    1970-01-01

    It is shown that all obtained scores must meet the requirements for classical test-score theory with respect to definitions of true scores and errors of measurement if that frame of reference is to yield valid variance errors of measurement. (DG)

  15. 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)

  16. Risk scores-the modern Oracle of Delphi?

    PubMed

    Kronenberg, Florian; Schwaiger, Johannes P

    2017-03-01

    Recently, 4 new risk scores for the prediction of mortality and cardiovascular events were especially tailored for hemodialysis patients; these scores performed much better than previous scores. Tripepi et al. found that these risk scores were even more predictive for all-cause and cardiovascular death than the measurement of the left ventricular mass index was. Nevertheless, the investigation of left ventricular mass and function has its own place for other reasons.

  17. 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%.

  18. 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)

  19. On The Factor Score Controversy

    ERIC Educational Resources Information Center

    Green, Bert F. Jr.

    1976-01-01

    A summary and interpretation of the recent literature on the indeterminancy of factor scores is given in simple terms. A good index of factor score determinancy is the squared multiple correlation of the factor with the observed variables. (Author)

  20. 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

    2015-08-03

    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.

  1. Developmental Sentence Scoring for Japanese

    ERIC Educational Resources Information Center

    Miyata, Susanne; MacWhinney, Brian; Otomo, Kiyoshi; Sirai, Hidetosi; Oshima-Takane, Yuriko; Hirakawa, Makiko; Shirai, Yasuhiro; Sugiura, Masatoshi; Itoh, Keiko

    2013-01-01

    This article 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 Lee's English Developmental Sentence Scoring model. Using this measure, the authors calculated DSSJ scores for 84 children divided into six age groups between 2;8…

  2. 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)

  3. An accurate registration technique for distorted images

    NASA Technical Reports Server (NTRS)

    Delapena, Michele; Shaw, Richard A.; Linde, Peter; Dravins, Dainis

    1990-01-01

    Accurate registration of International Ultraviolet Explorer (IUE) images is crucial because the variability of the geometrical distortions that are introduced by the SEC-Vidicon cameras ensures that raw science images are never perfectly aligned with the Intensity Transfer Functions (ITFs) (i.e., graded floodlamp exposures that are used to linearize and normalize the camera response). A technique for precisely registering IUE images which uses a cross correlation of the fixed pattern that exists in all raw IUE images is described.

  4. Protein-specific scoring method for ligand discovery.

    PubMed

    Lu, I-Lin; Wang, Hsiuying

    2012-11-01

    Protein-based virtual screening plays an important role in modern drug discovery process. Most protein-based virtual screening experiments are carried out with docking programs. The accuracy of a docking program highly relies on the incorporated scoring function based on various energy terms. The existing scoring functions deal all the energy terms with the equal weight function or other weight function derived by physical characteristics. These existing scoring functions are not protein dependent. We expect that a protein-specific scoring function, which can reflect the protein characteristics, may improve the docking results. Therefore, we propose a protein-specific rescoring approach to select potential ligands by adjusting the weights of energy terms. The protein-specific scoring function is based on the linear regression analysis associated with an outlier detection approach. The scoring function incorporated in DOCK program is used as the model system. The performance of our method was evaluated by the DUD docked data set, which contains 40 protein targets. The study results show that this method can improve the enrichment factors for most of the 40 protein targets. We further expend the protein-specific scoring function to a larger database, and the results also show significant improvement. Our method is not limited to improving the DOCK scoring function. It can be adopted to improve other programs such as GOLD and Glide. We believe that this method can be applied to virtual screening experiments and elevates the hits rate significantly, which can be beneficial to the modern drug discovery process.

  5. Egy-Score as a Noninvasive Score for the Assessment of Hepatic Fibrosis in Chronic Hepatitis C: A Preliminary Approach

    PubMed Central

    Alboraie, Mohamed; Khairy, Marwa; Elsharkawy, Aisha; Elsharkawy, Marwa; Asem, Noha; El-Seoud, Amany R. Abo; Elghamry, Fathy G.; Esmat, Gamal

    2014-01-01

    Background and Aims: Egy-Score is a new noninvasive score for prediction of severe hepatic fibrosis in patients with chronic liver diseases. The aim of this study was to validate Egy-Score as a noninvasive score for predicting stage of hepatic fibrosis in a group of Egyptian chronic hepatitis C patients. Patients and Methods: One hundred Egyptian patients with chronic hepatitis C were enrolled. Mean age was 40.25 ± 9.39 years. They were subjected to CA19-9, alpha-2-macroglobulin, total bilirubin, platelet count and albumin, liver biopsy, and histopathological staging of hepatic fibrosis according to METAVIR scoring system as part of their assessment for treatment. Egy-Score was calculated according to the following formula: Egy-Score = 3.52 + 0.0063 × CA19-9 + 0.0203 × age + 0.4485 × alpha-2-macroglobulin + 0.0303 × bilirubin – 0.0048 × platelet – 0.0462 × albumin. Egy-Score results were correlated to the stage of hepatic fibrosis. Results: Egy-Score correlates positively with the stage of hepatic fibrosis (F0–F4). Egy-Score was able to differentiate significant hepatic fibrosis, severe hepatic fibrosis, and cirrhosis accurately. Cutoff values of Egy-Score were 2.91850 (for significant fibrosis), 3.28624 (for severe fibrosis), and 3.67570 (for cirrhosis). Sensitivity, specificity, and areas-under-ROC curve (AUROCs) were 75.8%, 68.42%, and 0.776 (for significant fibrosis “≥F2”), 91.67%, 77.63%, and 0.875 (for severe fibrosis “≥F3”), and 81.82%, 86.52%, and 0.874 (for cirrhosis “F4”), respectively. Conclusion: Egy-Score is a useful noninvasive panel of surrogate biomarkers that could accurately predict different stages of hepatic fibrosis in patients with chronic hepatitis C. PMID:24976280

  6. Increasing Score Reliability with Item-Pattern Scoring: An Empirical Study in Several Score Metrics.

    ERIC Educational Resources Information Center

    Yen, Wendy M.; Candell, Gregory L.

    Reliabilities are compared for two types of test score data: number correct, and item response patterns. Item-pattern scoring using three-parameter item response theory takes into account how many and which items a student answers correctly. This procedure theoretically results in greater reliability than does number-correct scoring. Empirical…

  7. 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.

  8. Counselor Simulation by Film in Test Score Reporting Interviews

    ERIC Educational Resources Information Center

    Collins, Tom

    1972-01-01

    The responsible and innovative utilization of media, not only in test score reporting but also in other guidance functions, may assist the counselor in permitting him more time to function with clients in counseling relationships. (Author)

  9. The SCoRE residual: a quality index to assess the accuracy of joint estimations.

    PubMed

    Ehrig, Rainald M; Heller, Markus O; Kratzenstein, Stefan; Duda, Georg N; Trepczynski, Adam; Taylor, William R

    2011-04-29

    The determination of an accurate centre of rotation (CoR) from skin markers is essential for the assessment of abnormal gait patterns in clinical gait analysis. Despite the many functional approaches to estimate CoRs, no non-invasive analytical determination of the error in the reconstructed joint location is currently available. The purpose of this study was therefore to verify the residual of the symmetrical centre of rotation estimation (SCoRE) as a reliable indirect measure of the error of the computed joint centre. To evaluate the SCoRE residual, numerical simulations were performed to evaluate CoR estimations at different ranges of joint motion. A statistical model was developed and used to determine the theoretical relationships among the SCoRE residual, the magnitude of the skin marker artefact, the corrections to the marker positions, and the error of the CoR estimations to the known centre of rotation. We found that the equation err=0.5r(s) provides a reliable relationship among the CoR error, err, and the scaled SCoRE residual, r(s), providing that any skin marker artefact is first minimised using the optimal common shape technique (OCST). Measurements on six healthy volunteers showed a reduction of SCoRE residual from 11 to below 6mm and therefore demonstrated consistency of the theoretical considerations and numerical simulations with the in vivo data. This study also demonstrates the significant benefit of the OCST for reducing skin marker artefact and thus for predicting the accuracy of determining joint centre positions in functional gait analysis. For the first time, this understanding of the SCoRE residual allows a measure of error in the non-invasive assessment of joint centres. This measure now enables a rapid assessment of the accuracy of the CoR as well as an estimation of the reproducibility and repeatability of skeletal motion patterns.

  10. Accuracy of harm scores entered into an event reporting system.

    PubMed

    Abbasi, Toni; Adornetto-Garcia, Debra; Johnston, Patricia A; Segovia, Julie H; Summers, Barbara

    2015-04-01

    This quality improvement project evaluated the accuracy of harm scores entered into an event reporting system by inpatient nursing staff at a National Cancer Institute-designated comprehensive cancer center. Nurses scored 10 safety scenarios using 2 versions of the Agency for Healthcare Research and Quality scale to determine interrater reliability. Results indicated inconsistency in the way nurses scored the scenarios, suggesting that the event reporting system may not accurately portray the severity of harm in patient safety events. Nurse executives can use this information to guide the development and implementation of incident reporting systems.

  11. 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…

  12. 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

  13. [Overview of regulatory aspects guiding tablet scoring].

    PubMed

    Teixeira, Maíra Teles; Sá-Barreto, Lívia Cristina Lira; Silva, Dayde Lane Mendonça; Cunha-Filho, Marcílio Sergio Soares

    2016-06-01

    Tablet scoring is a controversial but common practice used to adjust doses, facilitate drug intake, or lower the cost of drug treatment, especially in children and the elderly. The risks of tablet scoring are mainly related to inaccuracies in the resulting dose and stability problems. The aim of this article is to provide an overview of worldwide guidelines regarding tablet scoring. We found that regulatory health agencies in Mercosur countries as well as other South American countries do not have published standards addressing tablet splitting. Among the surveyed health agencies, the Food and Drug Administration (FDA) in the United States is the only one to present standards, ranging from splitting instructions to regulation of the manufacturing process. The concept of functional scoring implemented by the FDA has introduced some level of guarantee as to the ability of tablets to be split. In conclusion, technical and scientific bases are still insufficient to guide health rules on this subject, making the decision on scoring, in certain situations, random and highly risky to public health. The need for more detailed regulation is vital to ensure the safety of tablet medications.

  14. 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.

  15. 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…

  16. 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,…

  17. 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…

  18. What is propensity score modelling?

    PubMed

    Campbell, Michael J

    2017-03-01

    Propensity score methodology is being increasingly used to try and make inferences about treatments when randomised trials are either impossible or not conducted and the only data are from observational studies. This paper reviews the basis of propensity scores and the current state of knowledge about them. It uses and critiques a current paper in the Emergency Medicine Journal to illustrate the methodology.

  19. 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…

  20. Hedonism or Higher Test Scores?

    ERIC Educational Resources Information Center

    Wold, Donald C.

    2004-01-01

    In the 20 years since the federal report on education "A Nation at Risk" appeared, much has been written on test scores of students in the United States versus their counterparts elsewhere. One of the issues is whether their scores are in fact inferior, or merely a statistical difference due to their universal schooling philosophy. Since…

  1. 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.…

  2. Guidelines for Improving SAT Scores.

    ERIC Educational Resources Information Center

    Thomson, Scott; DeLeonibus, Nancy

    The National Association of Secondary School Principals (NASSP) identified 34 high schools whose students maintained or improved their SAT scores from 1973 to 1976 or whose mean scores in 1973 were approximately the same as in 1965. In an open-ended questionnaire, the principals of these schools were asked to identify success factors. Their…

  3. 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.

  4. 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.…

  5. 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…

  6. Rapid and Accurate Identification of Candida albicans Isolates by Use of PNA FISHFlow▿

    PubMed Central

    Trnovsky, Jan; Merz, William; Della-Latta, Phyllis; Wu, Fann; Arendrup, Maiken Cavling; Stender, Henrik

    2008-01-01

    We developed the simple, rapid (1 h), and accurate PNA FISHFlow method for the identification of Candida albicans. The method exploits unique in solution in situ hybridization conditions under which the cells are simultaneously fixed and hybridized. This method facilitates the accurate identification of clinical yeast isolates using two scoring techniques: flow cytometry and fluorescence microscopy. PMID:18287325

  7. 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.

  8. 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.

  9. On numerically accurate finite element

    NASA Technical Reports Server (NTRS)

    Nagtegaal, J. C.; Parks, D. M.; Rice, J. R.

    1974-01-01

    A general criterion for testing a mesh with topologically similar repeat units is given, and the analysis shows that only a few conventional element types and arrangements are, or can be made suitable for computations in the fully plastic range. Further, a new variational principle, which can easily and simply be incorporated into an existing finite element program, is presented. This allows accurate computations to be made even for element designs that would not normally be suitable. Numerical results are given for three plane strain problems, namely pure bending of a beam, a thick-walled tube under pressure, and a deep double edge cracked tensile specimen. The effects of various element designs and of the new variational procedure are illustrated. Elastic-plastic computation at finite strain are discussed.

  10. 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

  11. Statistical Significance of Threading Scores

    PubMed Central

    Fayyaz Movaghar, Afshin; Launay, Guillaume; Schbath, Sophie; Gibrat, Jean-François

    2012-01-01

    Abstract We present a general method for assessing threading score significance. The threading score of a protein sequence, thread onto a given structure, should be compared with the threading score distribution of a random amino-acid sequence, of the same length, thread on the same structure; small p-values point significantly high scores. We claim that, due to general protein contact map properties, this reference distribution is a Weibull extreme value distribution whose parameters depend on the threading method, the structure, the length of the query and the random sequence simulation model used. These parameters can be estimated off-line with simulated sequence samples, for different sequence lengths. They can further be interpolated at the exact length of a query, enabling the quick computation of the p-value. PMID:22149633

  12. 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)

  13. Scoring system for prediction of metastatic spine tumor prognosis

    PubMed Central

    Tokuhashi, Yasuaki; Uei, Hiroshi; Oshima, Masashi; Ajiro, Yasumitsu

    2014-01-01

    Assessing the prognosis before treatment for metastatic spine tumor is extremely important in therapy selection. Therefore, we review some prognostic scoring systems and their outcomes. Articles with combinations of two keywords among “metastatic spine tumor” and “prognosis”, “score”, “scoring system”, “predicting”, or “life expectancy” were searched for in PubMed. As a result, 236 articles were extracted. Those referring to representative scoring systems about predicting the survival of patients with metastatic spine tumors were used. The significance and limits of these scoring systems, and the future perspectives were described. Tokuhashi score, Tomita score, Baur score, Linden score, Rades score, and Katagiri score were introduced. They are all scoring systems prepared by combining factors that affect prognosis. The primary site of cancer and visceral metastasis were common factors in all of these scoring systems. Other factors selected to influence the prognosis varied. They were useful to roughly predict the survival period, such as, “more than one year or not” or “more than six months or not”. In particular, they were utilized for decision-making about operative indications and avoidance of excessive medical treatment. Because the function depended on the survival period in the patients with metastatic spine tumor, it was also utilized in assessing functional prognosis. However, no scoring system had more than 90% consistency between the predicted and actual survival periods. Future perspectives should adopt more oncological viewpoints with adjustment of the process of treatment for metastatic spine tumor. PMID:25035829

  14. Factors Affecting Children's Math Achievement Scores in Preschool

    ERIC Educational Resources Information Center

    Kilday, Carolyn R.

    2010-01-01

    This dissertation contains three independently conducted studies on factors that affect the math achievement scores of preschool-aged children. The first study examined the associations between children's executive-functioning (EF) and math achievement scores at 54 months of age. Results suggest that EF is strongly associated with children's…

  15. Investigating an Invariant Item Ordering for Polytomously Scored Items

    ERIC Educational Resources Information Center

    Ligtvoet, Rudy; van der Ark, L. Andries; te Marvelde, Janneke M.; Sijtsma, Klaas

    2010-01-01

    This article discusses the concept of an invariant item ordering (IIO) for polytomously scored items and proposes methods for investigating an IIO in real test data. Method manifest IIO is proposed for assessing whether item response functions intersect. Coefficient H[superscript T] is defined for polytomously scored items. Given that an IIO…

  16. Comparison of Program Effects: The Use of Mastery Scores.

    ERIC Educational Resources Information Center

    Yeh, Jennie P.; Moy, Raymond

    The setting of a cut-off score on a mastery test usually involves a consideration of one or more of the following elements: (1) the distribution of observed test scores; (2) the type of mastery criterion used; (3) the level of acceptable risks of mis-classification; (4) the loss of functions of mis-classifications; and (5) the distribution of true…

  17. Untrained consumer assessment of the eating quality of beef: 1. A single composite score can predict beef quality grades.

    PubMed

    Bonny, S P F; Hocquette, J-F; Pethick, D W; Legrand, I; Wierzbicki, J; Allen, P; Farmer, L J; Polkinghorne, R J; Gardner, G E

    2016-11-10

    Quantifying consumer responses to beef across a broad range of demographics, nationalities and cooking methods is vitally important for any system evaluating beef eating quality. On the basis of previous work, it was expected that consumer scores would be highly accurate in determining quality grades for beef, thereby providing evidence that such a technique could be used to form the basis of and eating quality grading system for beef. Following the Australian MSA (Meat Standards Australia) testing protocols, over 19 000 consumers from Northern Ireland, Poland, Ireland, France and Australia tasted cooked beef samples, then allocated them to a quality grade; unsatisfactory, good-every-day, better-than-every-day and premium. The consumers also scored beef samples for tenderness, juiciness, flavour-liking and overall-liking. The beef was sourced from all countries involved in the study and cooked by four different cooking methods and to three different degrees of doneness, with each experimental group in the study consisting of a single cooking doneness within a cooking method for each country. For each experimental group, and for the data set as a whole, a linear discriminant function was calculated, using the four sensory scores which were used to predict the quality grade. This process was repeated using two conglomerate scores which are derived from weighting and combining the consumer sensory scores for tenderness, juiciness, flavour-liking and overall-liking, the original meat quality 4 score (oMQ4) (0.4, 0.1, 0.2, 0.3) and current meat quality 4 score (cMQ4) (0.3, 0.1, 0.3, 0.3). From the results of these analyses, the optimal weightings of the sensory scores to generate an 'ideal meat quality 4 score (MQ4)' for each country were calculated, and the MQ4 values that reflected the boundaries between the four quality grades were determined. The oMQ4 weightings were far more accurate in categorising European meat samples than the cMQ4 weightings, highlighting that

  18. Score Matrix for HWBI Forecast Model

    EPA Pesticide Factsheets

    2000-2010 Annual State-Scale Service and Domain scores used to support the approach for forecasting EPA's Human Well-Being Index. A modeling approach was developed based relationship function equations derived from select economic, social and ecosystem final goods and service scores and calculated human well-being index and related domain scores. These data are being used in a secondary capacity. The foundational data and scoring techniques were originally described in: a) U.S. EPA. 2012. Indicators and Methods for Constructing a U.S. Human Well-being Index (HWBI) for Ecosystem Services Research. Report. EPA/600/R-12/023. pp. 121; and b) U.S. EPA. 2014. Indicators and Methods for Evaluating Economic, Ecosystem and Social Services Provisioning. Report. EPA/600/R-14/184. pp. 174. Mode Smith, L. M., Harwell, L. C., Summers, J. K., Smith, H. M., Wade, C. M., Straub, K. R. and J.L. Case (2014).This dataset is associated with the following publication:Summers , K., L. Harwell , and L. Smith. A Model For Change: An Approach for Forecasting Well-Being From Service-Based Decisions. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 69: 295-309, (2016).

  19. Modification site localization scoring: strategies and performance.

    PubMed

    Chalkley, Robert J; Clauser, Karl R

    2012-05-01

    Using enrichment strategies many research groups are routinely producing large data sets of post-translationally modified peptides for proteomic analysis using tandem mass spectrometry. Although search engines are relatively effective at identifying these peptides with a defined measure of reliability, their localization of site/s of modification is often arbitrary and unreliable. The field continues to be in need of a widely accepted metric for false localization rate that accurately describes the certainty of site localization in published data sets and allows for consistent measurement of differences in performance of emerging scoring algorithms. In this article are discussed the main strategies currently used by software for modification site localization and ways of assessing the performance of these different tools. Methods for representing ambiguity are reviewed and a discussion of how the approaches transfer to different data types and modifications is presented.

  20. Prognostic Scores for Acute Pulmonary Embolism.

    PubMed

    Morillo, Raquel; Moores, Lisa; Jiménez, David

    2017-02-06

    Rapid and accurate risk stratification is critical in determining the optimal treatment strategy for patients with acute pulmonary embolism (PE). Early identification of patients with normal blood pressure and a favorable prognosis (low-risk PE) might select a subset of patients for outpatient treatment, which is associated with reduced cost and improved patient satisfaction, and has been shown to be effective and safe. Alternatively, identification of normotensive patients deemed as having a high risk for PE-related adverse clinical events (intermediate-high-risk PE) might select a subset of patients for close observation and consideration of escalation of therapy. Clinical prognostic scores have been gaining importance in the classification of patients into these categories. They should be derived and validated following strict methodological standards, and their use in clinical practice should be encouraged.

  1. Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

    PubMed Central

    Koes, David Ryan; Baumgartner, Matthew P.; Camacho, Carlos J.

    2013-01-01

    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 dataset, 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

  2. Quantification of protein group coherence and pathway assignment using functional association

    PubMed Central

    2011-01-01

    Background Genomics and proteomics experiments produce a large amount of data that are awaiting functional elucidation. An important step in analyzing such data is to identify functional units, which consist of proteins that play coherent roles to carry out the function. Importantly, functional coherence is not identical with functional similarity. For example, proteins in the same pathway may not share the same Gene Ontology (GO) terms, but they work in a coordinated fashion so that the aimed function can be performed. Thus, simply applying existing functional similarity measures might not be the best solution to identify functional units in omics data. Results We have designed two scores for quantifying the functional coherence by considering association of GO terms observed in two biological contexts, co-occurrences in protein annotations and co-mentions in literature in the PubMed database. The counted co-occurrences of GO terms were normalized in a similar fashion as the statistical amino acid contact potential is computed in the protein structure prediction field. We demonstrate that the developed scores can identify functionally coherent protein sets, i.e. proteins in the same pathways, co-localized proteins, and protein complexes, with statistically significant score values showing a better accuracy than existing functional similarity scores. The scores are also capable of detecting protein pairs that interact with each other. It is further shown that the functional coherence scores can accurately assign proteins to their respective pathways. Conclusion We have developed two scores which quantify the functional coherence of sets of proteins. The scores reflect the actual associations of GO terms observed either in protein annotations or in literature. It has been shown that they have the ability to accurately distinguish biologically relevant groups of proteins from random ones as well as a good discriminative power for detecting interacting pairs of

  3. 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.

  4. Crossover from in-plane to perpendicular anisotropy in Pt/CoFe/AlOx sandwiches as a function of Al oxidation: A very accurate control of the oxidation of tunnel barriers

    NASA Astrophysics Data System (ADS)

    Monso, S.; Rodmacq, B.; Auffret, S.; Casali, G.; Fettar, F.; Gilles, B.; Dieny, B.; Boyer, P.

    2002-06-01

    By measuring the extraordinary Hall effect on a series of naturally oxidized Pt3 nm/Co90Fe10 0.6 nm/Al tAl samples with 0accurate and convenient way to monitor the oxidation of the tunnel barrier in magnetic tunnel junctions. This technique is also applied to characterize the oxidation kinetics of various ultrathin metallic layers as well as the aging effect in alumina barriers.

  5. Optimally combining propensity score subclasses.

    PubMed

    Rudolph, Kara E; Colson, K Ellicott; Stuart, Elizabeth A; Ahern, Jennifer

    2016-11-30

    Propensity score methods, such as subclassification, are a common approach to control for confounding when estimating causal effects in non-randomized studies. Propensity score subclassification groups individuals into subclasses based on their propensity score values. Effect estimates are obtained within each subclass and then combined by weighting by the proportion of observations in each subclass. Combining subclass-specific estimates by weighting by the inverse variance is a promising alternative approach; a similar strategy is used in meta-analysis for its efficiency. We use simulation to compare performance of each of the two methods while varying (i) the number of subclasses, (ii) extent of propensity score overlap between the treatment and control groups (i.e., positivity), (iii) incorporation of survey weighting, and (iv) presence of heterogeneous treatment effects across subclasses. Both methods perform well in the absence of positivity violations and with a constant treatment effect with weighting by the inverse variance performing slightly better. Weighting by the proportion in subclass performs better in the presence of heterogeneous treatment effects across subclasses. We apply these methods to an illustrative example estimating the effect of living in a disadvantaged neighborhood on risk of past-year anxiety and depressive disorders among U.S. urban adolescents. This example entails practical positivity violations but no evidence of treatment effect heterogeneity. In this case, weighting by the inverse variance when combining across propensity score subclasses results in more efficient estimates that ultimately change inference. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Fabricating an Accurate Implant Master Cast: A Technique Report.

    PubMed

    Balshi, Thomas J; Wolfinger, Glenn J; Alfano, Stephen G; Cacovean, Jeannine N; Balshi, Stephen F

    2015-12-01

    The technique for fabricating an accurate implant master cast following the 12-week healing period after Teeth in a Day® dental implant surgery is detailed. The clinical, functional, and esthetic details captured during the final master impression are vital to creating an accurate master cast. This technique uses the properties of the all-acrylic resin interim prosthesis to capture these details. This impression captures the relationship between the remodeled soft tissue and the interim prosthesis. This provides the laboratory technician with an accurate orientation of the implant replicas in the master cast with which a passive fitting restoration can be fabricated.

  7. Finding Nearly Optimal GDT Scores

    PubMed Central

    Li, Shuai Cheng; Bu, Dongbo; Xu, Jinbo

    2011-01-01

    Abstract Global Distance Test (GDT) is one of the commonly accepted measures to assess the quality of predicted protein structures. Given a set of distance thresholds, GDT maximizes the percentage of superimposed (or matched) residue pairs under each threshold, and reports the average of these percentages as the final score. The computation of GDT score was conjectured to be NP-hard. All available methods are heuristic and do not guarantee the optimality of scores. These heuristic strategies usually result in underestimated GDT scores. Contrary to the conjecture, the problem can be solved exactly in polynomial time, albeit the method would be too slow for practical usage. In this paper we propose an efficient tool called OptGDT to obtain GDT scores with theoretically guaranteed accuracies. Denote ℓ as the number of matched residue pairs found by OptGDT for a given threshold d. Let ℓ′ be the optimal number of matched residues pairs for threshold d/(1 + ε), where ε is a parameter in our computation. OptGDT guarantees that ℓ ≥ ℓ′. We applied our tool to CASP8 (The eighth Critical Assessment of Structure Prediction Techniques) data. For 87.3% of the predicted models, better GDT scores are obtained when OptGDT is used. In some cases, the number of matched residue pairs were improved by at least 10%. The tool runs in time O(n3 log n/ε5) for a given threshold d and parameter ε. In the case of globular proteins, the tool can be improved to a randomized algorithm of O(n log2 n) runtime with probability at least 1 − O(1/n). Released under the GPL license and downloadable from http://bioinformatics.uwaterloo.ca/∼scli/OptGDT/. PMID:21554017

  8. 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

  9. 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.

  10. Accurate method for computing correlated color temperature.

    PubMed

    Li, Changjun; Cui, Guihua; Melgosa, Manuel; Ruan, Xiukai; Zhang, Yaoju; Ma, Long; Xiao, Kaida; Luo, M Ronnier

    2016-06-27

    For the correlated color temperature (CCT) of a light source to be estimated, a nonlinear optimization problem must be solved. In all previous methods available to compute CCT, the objective function has only been approximated, and their predictions have achieved limited accuracy. For example, different unacceptable CCT values have been predicted for light sources located on the same isotemperature line. In this paper, we propose to compute CCT using the Newton method, which requires the first and second derivatives of the objective function. Following the current recommendation by the International Commission on Illumination (CIE) for the computation of tristimulus values (summations at 1 nm steps from 360 nm to 830 nm), the objective function and its first and second derivatives are explicitly given and used in our computations. Comprehensive tests demonstrate that the proposed method, together with an initial estimation of CCT using Robertson's method [J. Opt. Soc. Am. 58, 1528-1535 (1968)], gives highly accurate predictions below 0.0012 K for light sources with CCTs ranging from 500 K to 106 K.

  11. 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…

  12. 24 CFR 902.63 - PHAS scoring.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... four PHAS indicators in this part will be scored individually, and then will be used to determine an overall score for the PHA. Components within each of the four PHAS indicators will be scored individually... indicators. (b) Adjustments to the PHAS score. (1) Adjustments to the score may be made after a PHA's...

  13. 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…

  14. Turning Merit Scores into Salaries.

    ERIC Educational Resources Information Center

    Becker, William E.

    1999-01-01

    Provides a single formula for merit-raise salary schemes based on either a fixed cash amount, a percentage of base salary, or any combination of the two. Explains that the formula makes explicit how merit scores, together with prior salaries and the money available for raises, determine individual salaries. (CMK)

  15. Developing Scoring Algorithms (Earlier Methods)

    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.

  16. 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…

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. Accurate density-functional calculation of core-electron binding energies with a scaled polarized triple-zeta basis set. Twelve test cases and application to three C 2H 4O 2 isomers

    NASA Astrophysics Data System (ADS)

    Chong, Delano P.; Hu, Ching-Han; Duffy, Patrick

    1996-02-01

    A scaling procedure based on Clementi and Raimondi's rules for atomic screening was proposed for atomic orbital basis sets in the unrestricted generalized transition state (uGTS) model of density functional calculation of core-electron binding energies (CEBEs). The exchange-correlation potential is based on a combined functional of Becke's exchange (B88) and Perdew's correlation (P86). This proposal was tested on CEBEs of twelve small molecules, including F 2, N 2 and H 2O, and applied to the computation of CEBEs of three isomers of C 2H 4O 2: acetic acid (CH 3COOH), methyl formate (HCOOCH 3), and glycolic aldehyde (CH 2OHCHO). In all cases, the new scaled pVTZ basis performs almost as well as the much larger cc-pV5Z and the average absolute difference between the results from the scaled pVTZ and estimated complete basis set limits is 0.04 eV.

  3. A method for increasing the scoring efficiency of the Farnsworth-Munsell 100-Hue test.

    PubMed

    Craven, B J

    1997-03-01

    This paper describes a method for scoring the Farnsworth-Munsell 100-Hue test, based on maximum-likelihood estimation, which in theory reduces test-to-test variability in scores and which is therefore better able to discriminate between different levels of overall colour discrimination than is the original Farnsworth scoring system. Error scores produced by the method are directly comparable to error scores produced by the traditional scoring system. It is hoped that this work will provoke further consideration of the efficiency of the scoring system as far as test-to-test variability is concerned, including the efficient detection of polarity in the subject's hue discrimination function.

  4. 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.

  5. Calibration of unified Parkinson's disease rating scale scores to Movement Disorder Society-unified Parkinson's disease rating scale scores.

    PubMed

    Goetz, Christopher G; Stebbins, Glenn T; Tilley, Barbara C

    2012-09-01

    The aim of this study was to develop formulas to convert the UPDRS to Movement Disorder Society (MDS)-UPDRS scores. The MDS-UPDRS is a revision of the UPDRS with sound clinimetric properties. Reliable formulas to recalculate UPDRS scores into MDS-UPDRS equivalents are pivotal to the practical transition and definitive adoption of the MDS-UPDRS. UPDRS and MDS-UPDRS scores were collected on 875 PD patients. A developmental sample was used to regress UPDRS scores on corresponding MDS-UPDRS scores based on three H & Y groupings (I/II, III, and IV/V). Regression weighting factors and intercept terms provided formulas for UPDRS conversions to be tested in a validation sample. Concordance between the true MDS-UPDRS Part scores and those derived from the formulas was compared using Bland-Altman's plots and Lin's concordance coefficient (LCC). Significant concordance between UPDRS-estimated MDS-UPDRS scores was achieved for Parts II (Motor Experiences of Daily Living) (LCC = 0.93) and III (Motor Examination) (LCC = 0.97). The formulas resulted in mean differences between the true MDS-UPDRS and estimated MDS-UPDRS scores of less than 1 point for both Parts II and III. Concordance was not achieved for Parts I and IV (Non-motor Experiences of Daily Living and Complications of Therapy). Formulas allow archival UPDRS Parts II and III individual patient data to be accurately transferred to MDS-UPDRS scores. Because Part I collects data on much more extensive information than the UPDRS, and because Part IV is structured differently in the two versions, old ratings for these parts cannot be converted. © 2012 Movement Disorder Society.

  6. "Score the Core" Web-based pathologist training tool improves the accuracy of breast cancer IHC4 scoring.

    PubMed

    Engelberg, Jesse A; Retallack, Hanna; Balassanian, Ronald; Dowsett, Mitchell; Zabaglo, Lila; Ram, Arishneel A; Apple, Sophia K; Bishop, John W; Borowsky, Alexander D; Carpenter, Philip M; Chen, Yunn-Yi; Datnow, Brian; Elson, Sarah; Hasteh, Farnaz; Lin, Fritz; Moatamed, Neda A; Zhang, Yanhong; Cardiff, Robert D

    2015-11-01

    Hormone receptor status is an integral component of decision-making in breast cancer management. IHC4 score is an algorithm that combines hormone receptor, HER2, and Ki-67 status to provide a semiquantitative prognostic score for breast cancer. High accuracy and low interobserver variance are important to ensure the score is accurately calculated; however, few previous efforts have been made to measure or decrease interobserver variance. We developed a Web-based training tool, called "Score the Core" (STC) using tissue microarrays to train pathologists to visually score estrogen receptor (using the 300-point H score), progesterone receptor (percent positive), and Ki-67 (percent positive). STC used a reference score calculated from a reproducible manual counting method. Pathologists in the Athena Breast Health Network and pathology residents at associated institutions completed the exercise. By using STC, pathologists improved their estrogen receptor H score and progesterone receptor and Ki-67 proportion assessment and demonstrated a good correlation between pathologist and reference scores. In addition, we collected information about pathologist performance that allowed us to compare individual pathologists and measures of agreement. Pathologists' assessment of the proportion of positive cells was closer to the reference than their assessment of the relative intensity of positive cells. Careful training and assessment should be used to ensure the accuracy of breast biomarkers. This is particularly important as breast cancer diagnostics become increasingly quantitative and reproducible. Our training tool is a novel approach for pathologist training that can serve as an important component of ongoing quality assessment and can improve the accuracy of breast cancer prognostic biomarkers.

  7. Resiliency scoring for business continuity plans.

    PubMed

    Olson, Anna; Anderson, Jamie

    Through this paper readers will learn of a scoring methodology, referred to as resiliency scoring, which enables the evaluation of business continuity plans based upon analysis of their alignment with a predefined set of criteria that can be customised and are adaptable to the needs of any organisation. This patent pending tool has been successful in driving engagement and is a powerful resource to improve reporting capabilities, identify risks and gauge organisational resilience. The role of business continuity professionals is to aid their organisations in planning and preparedness activities aimed at mitigating the impacts of potential disruptions and ensuring critical business functions can continue in the event of unforeseen circumstances. This may seem like a daunting task for what can typically be a small team of individuals. For this reason, it is important to be able to leverage industry standards, documented best practices and effective tools to streamline and support your continuity programme. The resiliency scoring methodology developed and implemented at Target has proven to be a valuable tool in taking the organisation's continuity programme to the next level. This paper will detail how the tool was developed and provide guidance on how it can be customised to fit your organisation's unique needs.

  8. Predicting neonatal morbidity after perinatal asphyxia: a scoring system.

    PubMed

    Portman, R J; Carter, B S; Gaylord, M S; Murphy, M G; Thieme, R E; Merenstein, G B

    1990-01-01

    Predicting immediate neonatal morbidity after perinatal asphyxia has been difficult. A review of asphyxiated neonates greater than or equal to 36 weeks' gestation admitted to The Children's Hospital Newborn Intensive Care Unit in 1983 was conducted to devise a scoring system that would rapidly predict organ dysfunction observed in the immediate neonatal period. Comparison of potential score components to morbidity by multiple regression analysis yielded significant association with abnormalities in fetal heart rate monitoring, the 5-minute Apgar score, and neonatal base deficit. A scoring system was devised whose sensitivity (93.8%) and specificity (81.3%) were more predictive than any of its individual components. Prospective analysis in a similar population in 1984 validated its ability to distinguish severe from moderate morbidity after asphyxia. Positive predictive value for the score in the combined study groups (n = 98) was 79% and the negative predictive value was 83%. The scoring system may offer a rapid and accurate prediction of organ dysfunction in the immediate neonatal period after asphyxia.

  9. [Scores and stages in pneumology].

    PubMed

    Kuhn, Max

    2013-10-01

    Useful scales and classifications for patients with pulmonary diseases are discussed. The modified Medical Research Council breathlessness scale (mMRC) is a measure of disability in lung patients. The GOLD classifications, the COPD-Assessment Test (CAT) and the BODE Index are important to classify the severity of COPD and to measure the disability of these patients. The Geneva score is a clinical prediction rule used in determining the pre-test probability of pulmonary embolism. The Pulmonary Embolism Severity Index (PESI) is a scoring system used to predict 30 day mortality in patients with pulmonary embolism. The Epworth Sleepiness Scale is intended to measure daytime sleepiness in patients with sleep apnea syndrome. The Asthma Controll Test (ACT) determines if asthma symptoms are well controlled.

  10. The Southampton Dupuytren's Scoring Scheme.

    PubMed

    Mohan, Arvind; Vadher, Jane; Ismail, Hiba; Warwick, David

    2014-02-01

    The aim of this study was to construct and validate a simple patient-related outcome score to quantify the disability caused by Dupuytren's disease (DD), thus enabling prioritisation of treatment, to allow reliable audit of surgical outcome and to support future research. The Southampton Dupuytren's Scoring System (SDSS) was developed in a staged fashion according to the recommendations of The Derby Outcomes Conference. (1) Item generation; (2) Item reduction; (3) Internal consistency; (4) Test-re-test; (5) Field management; (6) Sensitivity to change standardised response mean; and (7) Criterion validity: ability of the SDSS to measure what it is supposed to measure. Internal consistency measured with Cronbach's alpha indicated acceptable reliability. The test-re-test correlation coefficient showed high reliability with SDSS. Field-testing showed SDSS ratings to be higher than the QuickDASH (Disability of the arm, shoulder and hand) ratings evaluated by the patients who answered both questionnaires. Standardised response mean was more sensitive for SDSS compared with QuickDASH showing sensitivity to change. Criterion validity was used to assess if the SDSS was measuring what it is supposed to measure comparing the SDSS with QuickDASH. A highly significant correlation was found between the two scoring systems. SDSS is a disease-specific patient-related outcome measure with a good internal consistency and performs better than QuickDASH in terms of test-re-test reliability and sensitivity to change. SDSS shows better field-testing attributes suggesting that it is a relatively more patient and practitioner friendly scoring system. This study proposes to the SDSS is a useful patient-related outcome measure for DD.

  11. Concurrent validity of abbreviated WAIS-III index scores in geriatric outpatients with suspected dementia.

    PubMed

    Brooks, Brian L; Weaver, Linda E

    2006-04-01

    Assessments of older adults with suspected dementia can be time limited and clinicians might consider using abbreviated versions of measures. The present study examined the concurrent validity of abbreviated WAIS-III index scores in a sample of geriatric patients referred for assessment of suspected dementia (N=43; mean age=63.8 years). All 2-subtest estimates of the Verbal Comprehension, Perceptual Organization, and Working Memory index scores accurately estimated more than 80% of cases within +/-2 standard errors of measurement (S.E.M.), and in most cases, more than 90% of cases were accurate at this level. While none of the 1-subtest estimates of these index scores were as accurate, both of the 1-subtest estimates of the Processing Speed index had high clinical accuracy. Abbreviated versions of the four index scores can be substituted in situations with this clinical population where testing time is limited or a patient fatigues easily.

  12. GPU acceleration of Dock6's Amber scoring computation.

    PubMed

    Yang, Hailong; Zhou, Qiongqiong; Li, Bo; Wang, Yongjian; Luan, Zhongzhi; Qian, Depei; Li, Hanlu

    2010-01-01

    Dressing the problem of virtual screening is a long-term goal in the drug discovery field, which if properly solved, can significantly shorten new drugs' R&D cycle. The scoring functionality that evaluates the fitness of the docking result is one of the major challenges in virtual screening. In general, scoring functionality in docking requires a large amount of floating-point calculations, which usually takes several weeks or even months to be finished. This time-consuming procedure is unacceptable, especially when highly fatal and infectious virus arises such as SARS and H1N1, which forces the scoring task to be done in a limited time. This paper presents how to leverage the computational power of GPU to accelerate Dock6's (http://dock.compbio.ucsf.edu/DOCK_6/) Amber (J. Comput. Chem. 25: 1157-1174, 2004) scoring with NVIDIA CUDA (NVIDIA Corporation Technical Staff, Compute Unified Device Architecture - Programming Guide, NVIDIA Corporation, 2008) (Compute Unified Device Architecture) platform. We also discuss many factors that will greatly influence the performance after porting the Amber scoring to GPU, including thread management, data transfer, and divergence hidden. Our experiments show that the GPU-accelerated Amber scoring achieves a 6.5× speedup with respect to the original version running on AMD dual-core CPU for the same problem size. This acceleration makes the Amber scoring more competitive and efficient for large-scale virtual screening problems.

  13. Quality metric for accurate overlay control in <20nm nodes

    NASA Astrophysics Data System (ADS)

    Klein, Dana; Amit, Eran; Cohen, Guy; Amir, Nuriel; Har-Zvi, Michael; Huang, Chin-Chou Kevin; Karur-Shanmugam, Ramkumar; Pierson, Bill; Kato, Cindy; Kurita, Hiroyuki

    2013-04-01

    The semiconductor industry is moving toward 20nm nodes and below. As the Overlay (OVL) budget is getting tighter at these advanced nodes, the importance in the accuracy in each nanometer of OVL error is critical. When process owners select OVL targets and methods for their process, they must do it wisely; otherwise the reported OVL could be inaccurate, resulting in yield loss. The same problem can occur when the target sampling map is chosen incorrectly, consisting of asymmetric targets that will cause biased correctable terms and a corrupted wafer. Total measurement uncertainty (TMU) is the main parameter that process owners use when choosing an OVL target per layer. Going towards the 20nm nodes and below, TMU will not be enough for accurate OVL control. KLA-Tencor has introduced a quality score named `Qmerit' for its imaging based OVL (IBO) targets, which is obtained on the-fly for each OVL measurement point in X & Y. This Qmerit score will enable the process owners to select compatible targets which provide accurate OVL values for their process and thereby improve their yield. Together with K-T Analyzer's ability to detect the symmetric targets across the wafer and within the field, the Archer tools will continue to provide an independent, reliable measurement of OVL error into the next advanced nodes, enabling fabs to manufacture devices that meet their tight OVL error budgets.

  14. 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…

  15. 34 CFR 668.147 - Passing scores.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 3 2010-07-01 2010-07-01 false Passing scores. 668.147 Section 668.147 Education...; Specification of Passing Score; Approval of State Process § 668.147 Passing scores. Except as provided in §§ 668... education and training offered, the Secretary specifies that the passing score on each approved test is...

  16. The scoring bias in reverse docking and the score normalization strategy to improve success rate of target fishing

    PubMed Central

    Luo, Qiyao; Zhao, Liang; Hu, Jianxing; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren

    2017-01-01

    Target fishing often relies on the use of reverse docking to identify potential target proteins of ligands from protein database. The limitation of reverse docking is the accuracy of current scoring funtions used to distinguish true target from non-target proteins. Many contemporary scoring functions are designed for the virtual screening of small molecules without special optimization for reverse docking, which would be easily influenced by the properties of protein pockets, resulting in scoring bias to the proteins with certain properties. This bias would cause lots of false positives in reverse docking, interferring the identification of true targets. In this paper, we have conducted a large-scale reverse docking (5000 molecules to 100 proteins) to study the scoring bias in reverse docking by DOCK, Glide, and AutoDock Vina. And we found that there were actually some frequency hits, namely interference proteins in all three docking procedures. After analyzing the differences of pocket properties between these interference proteins and the others, we speculated that the interference proteins have larger contact area (related to the size and shape of protein pockets) with ligands (for all three docking programs) or higher hydrophobicity (for Glide), which could be the causes of scoring bias. Then we applied the score normalization method to eliminate this scoring bias, which was effective to make docking score more balanced between different proteins in the reverse docking of benchmark dataset. Later, the Astex Diver Set was utilized to validate the effect of score normalization on actual cases of reverse docking, showing that the accuracy of target prediction significantly increased by 21.5% in the reverse docking by Glide after score normalization, though there was no obvious change in the reverse docking by DOCK and AutoDock Vina. Our results demonstrate the effectiveness of score normalization to eliminate the scoring bias and improve the accuracy of target

  17. 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

  18. 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.

  19. A Self-Instructional Device for Conditioning Accurate Prosody.

    ERIC Educational Resources Information Center

    Buiten, Roger; Lane, Harlan

    1965-01-01

    A self-instructional device for conditioning accurate prosody in second-language learning is described in this article. The Speech Auto-Instructional Device (SAID) is electro-mechanical and performs three functions: SAID (1) presents to the student tape-recorded pattern sentences that are considered standards in prosodic performance; (2) processes…

  20. Comparison of the Wells score with the revised Geneva score for assessing suspected pulmonary embolism: a systematic review and meta-analysis.

    PubMed

    Shen, Jun-Hua; Chen, Hong-Lin; Chen, Jian-Rong; Xing, Jia-Li; Gu, Peng; Zhu, Bao-Feng

    2016-04-01

    The Wells score and the revised Geneva score are two most commonly used clinical rules for excluding pulmonary embolism (PE). In this study, we aimed to assess the diagnostic accuracy of these two rules; we also compared the diagnostic accuracy between them. We searched PubMed and Web of science up to April 2015. Studies assessed Wells score and revised Geneva score for diagnosis suspected PE were included. The summary area under the curve (AUC) and the 95 % confidence interval (CI) were calculated. Eleven studies were included in this meta-analysis. For Wells score, the sensitivity ranged from 63.8 to 79.3 %, and the specificity ranged from 48.8 to 90.0 %. The overall weighted AUC was 0.778 (95 % CI 0.740-0.818; Z = 9.88, P < 0.001). For revised Geneva score, the sensitivity ranged from 55.3 to 73.6 %. The overall weighted AUC was 0.693 (95 % CI 0.653-0.736; Z = 11.96, P < 0.001). 95 % CIs of two AUCs were not overlapped, which indicated Wells score was more accurate than revised Geneva score for predicting PE in suspected patients. Meta-regression showed diagnostic accuracy of these two rules was not related with PE prevalence. Sensitivity analysis by only included prospective studies showed the results were robust. Our results showed the Wells score was more effective than the revised Geneva score in discriminate PE in suspected patients.

  1. Accurate Biomass Estimation via Bayesian Adaptive Sampling

    NASA Astrophysics Data System (ADS)

    Wheeler, K.; Knuth, K.; Castle, P.

    2005-12-01

    Typical estimates of standing wood derived from remote sensing sources take advantage of aggregate measurements of canopy heights (e.g. LIDAR) and canopy diameters (segmentation of IKONOS imagery) to obtain a wood volume estimate by assuming homogeneous species and a fixed function that returns volume. The validation of such techniques use manually measured diameter at breast height records (DBH). Our goal is to improve the accuracy and applicability of biomass estimation methods to heterogeneous forests and transitional areas. We are developing estimates with quantifiable uncertainty using a new form of estimation function, active sampling, and volumetric reconstruction image rendering for species specific mass truth. Initially we are developing a Bayesian adaptive sampling method for BRDF associated with the MISR Rahman model with respect to categorical biomes. This involves characterizing the probability distributions of the 3 free parameters of the Rahman model for the 6 categories of biomes used by MISR. Subsequently, these distributions can be used to determine the optimal sampling methodology to distinguish biomes during acquisition. We have a remotely controlled semi-autonomous helicopter that has stereo imaging, lidar, differential GPS, and spectrometers covering wavelengths from visible to NIR. We intend to automatically vary the way points of the flight path via the Bayesian adaptive sampling method. The second critical part of this work is in automating the validation of biomass estimates via using machine vision techniques. This involves taking 2-D pictures of trees of known species, and then via Bayesian techniques, reconstructing 3-D models of the trees to estimate the distribution moments associated with wood volume. Similar techniques have been developed by the medical imaging community. This then provides probability distributions conditional upon species. The final part of this work is in relating the BRDF actively sampled measurements to species

  2. 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.

  3. 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.

  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.

  5. Mangled extremity severity score in children.

    PubMed

    Fagelman, Mitchell F; Epps, Howard R; Rang, Mercer

    2002-01-01

    Treatment of the severely traumatized or mangled lower extremity poses significant challenges. The Mangled Extremity Severity Score (MESS) is a scale that uses objective criteria to assist with acute management decisions. Most research on the MESS has been in adults or combined series with few children. The study was performed to investigate the MESS in children exclusively. The MESS was applied retrospectively to 36 patients with grades IIIB and IIIC open lower extremity fractures collected from two level 1 pediatric trauma centers. Patients were divided into limb salvage and primary amputation groups based on the decision of the treating surgeon. In the salvage group there were 18 grade IIIB fractures and 10 grade IIIC fractures. The MESS prediction was accurate in 93% of the injured limbs. In the amputation group eight limbs met the inclusion criteria; the MESS agreed with the treating surgeon in 63% of cases. These findings suggest the MESS should be considered when managing a child with severe lower extremity trauma.

  6. 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.

  7. Propensity Score Matching: Retrospective Randomization?

    PubMed

    Jupiter, Daniel C

    Randomized controlled trials are viewed as the optimal study design. In this commentary, we explore the strength of this design and its complexity. We also discuss some situations in which these trials are not possible, or not ethical, or not economical. In such situations, specifically, in retrospective studies, we should make every effort to recapitulate the rigor and strength of the randomized trial. However, we could be faced with an inherent indication bias in such a setting. Thus, we consider the tools available to address that bias. Specifically, we examine matching and introduce and explore a new tool: propensity score matching. This tool allows us to group subjects according to their propensity to be in a particular treatment group and, in so doing, to account for the indication bias.

  8. 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…

  9. Docking into knowledge-based potential fields: a comparative evaluation of DrugScore.

    PubMed

    Sotriffer, Christoph A; Gohlke, Holger; Klebe, Gerhard

    2002-05-09

    A new application of DrugScore is reported in which the knowledge-based pair potentials serve as objective function in docking optimizations. The Lamarckian genetic algorithm of AutoDock is used to search for favorable ligand binding modes guided by DrugScore grids as representations of the protein binding site. The approach is found to be successful in many cases where DrugScore-based re-ranking of already docked ligand conformations does not yield satisfactory results. Compared to the AutoDock scoring function, DrugScore yields slightly superior results in flexible docking.

  10. Exact Score Distribution Computation for Similarity Searches in Ontologies

    NASA Astrophysics Data System (ADS)

    Schulz, Marcel H.; Köhler, Sebastian; Bauer, Sebastian; Vingron, Martin; Robinson, Peter N.

    Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., protein function prediction with the Gene Ontology. In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik’s definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the Human Phenotype Ontology.

  11. 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.

  12. 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.

  13. 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.

  14. Detection of Differential Item Functioning for More than Two Groups: A Monte Carlo Comparison of Methods

    ERIC Educational Resources Information Center

    Finch, W. Holmes

    2016-01-01

    Differential item functioning (DIF) assessment is a crucial component in test construction, serving as the primary way in which instrument developers ensure that measures perform in the same way for multiple groups within the population. When such is not the case, scores may not accurately reflect the trait of interest for all individuals in the…

  15. 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

  16. 42 CFR 414.1260 - Composite scores.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 3 2014-10-01 2014-10-01 false Composite scores. 414.1260 Section 414.1260 Public... Modifier Under the Physician Fee Schedule § 414.1260 Composite scores. (a)(1) The standardized score for... determine the quality composite: (i) Patient safety. (ii) Patient experience. (iii) Care coordination....

  17. 42 CFR 414.1260 - Composite scores.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 3 2013-10-01 2013-10-01 false Composite scores. 414.1260 Section 414.1260 Public... Modifier Under the Physician Fee Schedule § 414.1260 Composite scores. (a)(1) The standardized score for... determine the quality composite: (i) Patient safety. (ii) Patient experience. (iii) Care coordination....

  18. Aptitude Test Score Trends: 1959-1984.

    ERIC Educational Resources Information Center

    Brown, Dianne C.

    The decline in standardized test scores during the 1960s and 1970s is well documented and is seen in both aptitude and achievement test scores. This paper describes and analyzes the test score trends over the 1960s, 1970s and early 1980s for five aptitude tests: (1) the Scholastic Aptitude Test; (2) the American College Test; (3) the Preliminary…

  19. 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…

  20. 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…

  1. On the Reliability of Categorically Scored Examinations

    ERIC Educational Resources Information Center

    Kupermintz, Haggai

    2004-01-01

    A decision-theoretic approach to the question of reliability in categorically scored examinations is explored. The concepts of true scores and errors are discussed as they deviate from conventional psychometric definitions and measurement error in categorical scores is cast in terms of misclassifications. A reliability measure based on…

  2. "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…

  3. 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…

  4. 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/.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. CSAR scoring challenge reveals the need for new concepts in estimating protein-ligand binding affinity.

    PubMed

    Novikov, Fedor N; Zeifman, Alexey A; Stroganov, Oleg V; Stroylov, Viktor S; Kulkov, Val; Chilov, Ghermes G

    2011-09-26

    The dG prediction accuracy by the Lead Finder docking software on the CSAR test set was characterized by R(2)=0.62 and rmsd=1.93 kcal/mol, and the method of preparation of the full-atom structures of the test set did not significantly affect the resulting accuracy of predictions. The primary factors determining the correlation between the predicted and experimental values were the van der Waals interactions and solvation effects. Those two factors alone accounted for R(2)=0.50. The other factors that affected the accuracy of predictions, listed in the order of decreasing importance, were the change of ligand's internal energy upon binding with protein, the electrostatic interactions, and the hydrogen bonds. It appears that those latter factors contributed to the independence of the prediction results from the method of full-atom structure preparation. Then, we turned our attention to the other factors that could potentially improve the scoring function in order to raise the accuracy of the dG prediction. It turned out that the ligand-centric factors, including Mw, cLogP, PSA, etc. or protein-centric factors, such as the functional class of protein, did not improve the prediction accuracy. Following that, we explored if the weak molecular interactions such as X-H...Ar, X-H...Hal, CO...Hal, C-H...X, stacking and π-cationic interactions (where X is N or O), that are generally of interest to the medicinal chemists despite their lack of proper molecular mechanical parametrization, could improve dG prediction. Our analysis revealed that out of these new interactions only CO...Hal is statistically significant for dG predictions using Lead FInder scoring function. Accounting for the CO...Hal interaction resulted in the reduction of the rmsd from 2.19 to 0.69 kcal/mol for the corresponding structures. The other weak interaction factors were not statistically significant and therefore irrelevant to the accuracy of dG prediction. On the basis of our findings from our

  11. 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

  12. Automatic sleep scoring in normals and in individuals with neurodegenerative disorders according to new international sleep scoring criteria.

    PubMed

    Jensen, Peter S; Sorensen, Helge B D; Leonthin, Helle L; Jennum, Poul

    2010-08-01

    The aim of this study was to develop a fully automatic sleep scoring algorithm on the basis of a reproduction of new international sleep scoring criteria from the American Academy of Sleep Medicine. A biomedical signal processing algorithm was developed, allowing for automatic sleep depth quantification of routine polysomnographic recordings through feature extraction, supervised probabilistic Bayesian classification, and heuristic rule-based smoothing. The performance of the algorithm was tested using 28 manually classified day-night polysomnograms from 18 normal subjects and 10 patients with Parkinson disease or multiple system atrophy. This led to quantification of automatic versus manual epoch-by-epoch agreement rates for both normals and abnormals. Resulting average agreement rates were 87.7% (Cohen's Kappa: 0.79) and 68.2% (Cohen's Kappa: 0.26) in the normal and abnormal group, respectively. Based on an observed reliability of the manual scorer of 92.5% (Cohen's Kappa: 0.87) in the normal group and 85.3% (Cohen's Kappa: 0.73) in the abnormal group, this study concluded that although the developed algorithm was capable of scoring normal sleep with an accuracy around the manual interscorer reliability, it failed in accurately scoring abnormal sleep as encountered for the Parkinson disease/multiple system atrophy patients.

  13. A robust and accurate formulation of molecular and colloidal electrostatics.

    PubMed

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y C

    2016-08-07

    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.

  14. 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.

  15. Accurate Scientific Visualization in Research and Physics Teaching

    NASA Astrophysics Data System (ADS)

    Wendler, Tim

    2011-10-01

    Accurate visualization is key in the expression and comprehension of physical principles. Many 3D animation software packages come with built-in numerical methods for a variety of fundamental classical systems. Scripting languages give access to low-level computational functionality, thereby revealing a virtual physics laboratory for teaching and research. Specific examples will be presented: Galilean relativistic hair, energy conservation in complex systems, scattering from a central force, and energy transfer in bi-molecular reactions.

  16. 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

  17. Observed-Score Equating as a Test Assembly Problem.

    ERIC Educational Resources Information Center

    van der Linden, Wim J.; Luecht, Richard M.

    1998-01-01

    Derives a set of linear conditions of item-response functions that guarantees identical observed-score distributions on two test forms. The conditions can be added as constraints to a linear programming model for test assembly. An example illustrates the use of the model for an item pool from the Law School Admissions Test (LSAT). (SLD)

  18. Norms and Performance Standards for Work Sample Scores.

    ERIC Educational Resources Information Center

    Wisconsin Univ. - Stout, Menomonie. Dept. of Rehabilitation and Manpower Services. Materials Development Center.

    Work samples are commonly used to aid in the assessment of a client's potential for functioning in various competitive occupations. To determine an individual's position relative to a particular reference group the most commonly used norms are those based on scores of other clients who have performed a specific work sample, and performance scores…

  19. Model Building of Antibody-Antigen Complex Structures Using GBSA Scores.

    PubMed

    Shimba, Noriko; Kamiya, Narutoshi; Nakamura, Haruki

    2016-10-24

    Structure prediction of antibody-antigen complexes, which involves molecular docking to generate decoys that are ranked using a scoring function, is an important approach in the design of antibody drugs and biosensors. However, it is not easy to evaluate the stability of protein-protein complexes, using a single scoring function. Here, we developed a prediction method of antibody-antigen complex structures using the docking engine "surFit" and a scoring function (GBSA score) that combined the generalized Born (GB) energy and the hydration energy based on the solvent-accessible surface area (SA). We chose 95 antibody-antigen structural datasets for self-docking and generated many decoy structures using the surFit program. The GBSA scores were computed for all of the decoys, and the area under the curve (AUC) of the GBSA scores yielded a higher value (0.972) than the values obtained by the original surFit scores (0.873) and the ZRANK scores (0.953). To improve the accuracy of prediction, molecular dynamics (MD) simulations were performed for several decoy structures that had good GBSA scores. Consequently, average GBSA scores from MD trajectories can reduce the number of non-native decoys that have GBSA scores competitive with the near-native ones.

  20. Measurement of COPD Severity Using a Survey-Based Score

    PubMed Central

    Omachi, Theodore A.; Katz, Patricia P.; Yelin, Edward H.; Iribarren, Carlos; Blanc, Paul D.

    2010-01-01

    Background: A comprehensive survey-based COPD severity score has usefulness for epidemiologic and health outcomes research. We previously developed and validated the survey-based COPD Severity Score without using lung function or other physiologic measurements. In this study, we aimed to further validate the severity score in a different COPD cohort and using a combination of patient-reported and objective physiologic measurements. Methods: Using data from the Function, Living, Outcomes, and Work cohort study of COPD, we evaluated the concurrent and predictive validity of the COPD Severity Score among 1,202 subjects. The survey instrument is a 35-point score based on symptoms, medication and oxygen use, and prior hospitalization or intubation for COPD. Subjects were systemically assessed using structured telephone survey, spirometry, and 6-min walk testing. Results: We found evidence to support concurrent validity of the score. Higher COPD Severity Score values were associated with poorer FEV1 (r = −0.38), FEV1% predicted (r = −0.40), Body mass, Obstruction, Dyspnea, Exercise Index (r = 0.57), and distance walked in 6 min (r = −0.43) (P < .0001 in all cases). Greater COPD severity was also related to poorer generic physical health status (r = −0.49) and disease-specific health-related quality of life (r = 0.57) (P < .0001). The score also demonstrated predictive validity. It was also associated with a greater prospective risk of acute exacerbation of COPD defined as ED visits (hazard ratio [HR], 1.31; 95% CI, 1.24-1.39), hospitalizations (HR, 1.59; 95% CI, 1.44-1.75), and either measure of hospital-based care for COPD (HR, 1.34; 95% CI, 1.26-1.41) (P < .0001 in all cases). Conclusion: The COPD Severity Score is a valid survey-based measure of disease-specific severity, both in terms of concurrent and predictive validity. The score is a psychometrically sound instrument for use in epidemiologic and outcomes research in COPD. PMID:20040611

  1. 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.

  2. 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…

  3. Development of Dengue Infection Severity Score

    PubMed Central

    Pongpan, Surangrat; Tawichasri, Chamaiporn; 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 /μL, and platelet ≤50000 /μL. 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. PMID:24324896

  4. 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…

  5. The Mystery of the Z-Score.

    PubMed

    Curtis, Alexander E; Smith, Tanya A; Ziganshin, Bulat A; Elefteriades, John A

    2016-08-01

    Reliable methods for measuring the thoracic aorta are critical for determining treatment strategies in aneurysmal disease. Z-scores are a pragmatic alternative to raw diameter sizes commonly used in adult medicine. They are particularly valuable in the pediatric population, who undergo rapid changes in physical development. The advantage of the Z-score is its inclusion of body surface area (BSA) in determining whether an aorta is within normal size limits. Therefore, Z-scores allow us to determine whether true pathology exists, which can be challenging in growing children. In addition, Z-scores allow for thoughtful interpretation of aortic size in different genders, ethnicities, and geographical regions. Despite the advantages of using Z-scores, there are limitations. These include intra- and inter-observer bias, measurement error, and variations between alternative Z-score nomograms and BSA equations. Furthermore, it is unclear how Z-scores change in the normal population over time, which is essential when interpreting serial values. Guidelines for measuring aortic parameters have been developed by the American Society of Echocardiography Pediatric and Congenital Heart Disease Council, which may reduce measurement bias when calculating Z-scores for the aortic root. In addition, web-based Z-score calculators have been developed to aid in efficient Z-score calculations. Despite these advances, clinicians must be mindful of the limitations of Z-scores, especially when used to demonstrate beneficial treatment effect. This review looks to unravel the mystery of the Z-score, with a focus on the thoracic aorta. Here, we will discuss how Z-scores are calculated and the limitations of their use.

  6. The Mystery of the Z-Score

    PubMed Central

    Curtis, Alexander E.; Smith, Tanya A.; Ziganshin, Bulat A.; Elefteriades, John A.

    2016-01-01

    Reliable methods for measuring the thoracic aorta are critical for determining treatment strategies in aneurysmal disease. Z-scores are a pragmatic alternative to raw diameter sizes commonly used in adult medicine. They are particularly valuable in the pediatric population, who undergo rapid changes in physical development. The advantage of the Z-score is its inclusion of body surface area (BSA) in determining whether an aorta is within normal size limits. Therefore, Z-scores allow us to determine whether true pathology exists, which can be challenging in growing children. In addition, Z-scores allow for thoughtful interpretation of aortic size in different genders, ethnicities, and geographical regions. Despite the advantages of using Z-scores, there are limitations. These include intra- and inter-observer bias, measurement error, and variations between alternative Z-score nomograms and BSA equations. Furthermore, it is unclear how Z-scores change in the normal population over time, which is essential when interpreting serial values. Guidelines for measuring aortic parameters have been developed by the American Society of Echocardiography Pediatric and Congenital Heart Disease Council, which may reduce measurement bias when calculating Z-scores for the aortic root. In addition, web-based Z-score calculators have been developed to aid in efficient Z-score calculations. Despite these advances, clinicians must be mindful of the limitations of Z-scores, especially when used to demonstrate beneficial treatment effect. This review looks to unravel the mystery of the Z-score, with a focus on the thoracic aorta. Here, we will discuss how Z-scores are calculated and the limitations of their use. PMID:28097194

  7. A general formula for computing maximum proportion correct scores in various psychophysical paradigms with arbitrary probability distributions of stimulus observations.