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

    2018-01-01

    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. GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

    NASA Astrophysics Data System (ADS)

    Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok

    2017-07-01

    Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

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

    PubMed

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

    2012-09-11

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

  4. ASTRAL, DRAGON and SEDAN scores predict stroke outcome more accurately than physicians.

    PubMed

    Ntaios, G; Gioulekas, F; Papavasileiou, V; Strbian, D; Michel, P

    2016-11-01

    ASTRAL, SEDAN and DRAGON scores are three well-validated scores for stroke outcome prediction. Whether these scores predict stroke outcome more accurately compared with physicians interested in stroke was investigated. Physicians interested in stroke were invited to an online anonymous survey to provide outcome estimates in randomly allocated structured scenarios of recent real-life stroke patients. Their estimates were compared to scores' predictions in the same scenarios. An estimate was considered accurate if it was within 95% confidence intervals of actual outcome. In all, 244 participants from 32 different countries responded assessing 720 real scenarios and 2636 outcomes. The majority of physicians' estimates were inaccurate (1422/2636, 53.9%). 400 (56.8%) of physicians' estimates about the percentage probability of 3-month modified Rankin score (mRS) > 2 were accurate compared with 609 (86.5%) of ASTRAL score estimates (P < 0.0001). 394 (61.2%) of physicians' estimates about the percentage probability of post-thrombolysis symptomatic intracranial haemorrhage were accurate compared with 583 (90.5%) of SEDAN score estimates (P < 0.0001). 160 (24.8%) of physicians' estimates about post-thrombolysis 3-month percentage probability of mRS 0-2 were accurate compared with 240 (37.3%) DRAGON score estimates (P < 0.0001). 260 (40.4%) of physicians' estimates about the percentage probability of post-thrombolysis mRS 5-6 were accurate compared with 518 (80.4%) DRAGON score estimates (P < 0.0001). ASTRAL, DRAGON and SEDAN scores predict outcome of acute ischaemic stroke patients with higher accuracy compared to physicians interested in stroke. © 2016 EAN.

  5. A collaborative filtering approach for protein-protein docking scoring functions.

    PubMed

    Bourquard, Thomas; Bernauer, Julie; Azé, Jérôme; Poupon, Anne

    2011-04-22

    A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions. In this work, we introduce a new procedure for conformation ranking. We previously developed a set of scoring functions where learning was performed using a genetic algorithm. These functions were used to assign a rank to each possible conformation. We now have a refined rank using different classifiers (decision trees, rules and support vector machines) in a collaborative filtering scheme. The scoring function newly obtained is evaluated using 10 fold cross-validation, and compared to the functions obtained using either genetic algorithms or collaborative filtering taken separately. This new approach was successfully applied to the CAPRI scoring ensembles. We show that for 10 targets out of 12, we are able to find a near-native conformation in the 10 best ranked solutions. Moreover, for 6 of them, the near-native conformation selected is of high accuracy. Finally, we show that this function dramatically enriches the 100 best-ranking conformations in near-native structures.

  6. A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

    PubMed Central

    Bourquard, Thomas; Bernauer, Julie; Azé, Jérôme; Poupon, Anne

    2011-01-01

    A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions. In this work, we introduce a new procedure for conformation ranking. We previously developed a set of scoring functions where learning was performed using a genetic algorithm. These functions were used to assign a rank to each possible conformation. We now have a refined rank using different classifiers (decision trees, rules and support vector machines) in a collaborative filtering scheme. The scoring function newly obtained is evaluated using 10 fold cross-validation, and compared to the functions obtained using either genetic algorithms or collaborative filtering taken separately. This new approach was successfully applied to the CAPRI scoring ensembles. We show that for 10 targets out of 12, we are able to find a near-native conformation in the 10 best ranked solutions. Moreover, for 6 of them, the near-native conformation selected is of high accuracy. Finally, we show that this function dramatically enriches the 100 best-ranking conformations in near-native structures. PMID:21526112

  7. Simple prediction scores predict good and devastating outcomes after stroke more accurately than physicians.

    PubMed

    Reid, John Michael; Dai, Dingwei; Delmonte, Susanna; Counsell, Carl; Phillips, Stephen J; MacLeod, Mary Joan

    2017-05-01

    physicians are often asked to prognosticate soon after a patient presents with stroke. This study aimed to compare two outcome prediction scores (Five Simple Variables [FSV] score and the PLAN [Preadmission comorbidities, Level of consciousness, Age, and focal Neurologic deficit]) with informal prediction by physicians. demographic and clinical variables were prospectively collected from consecutive patients hospitalised with acute ischaemic or haemorrhagic stroke (2012-13). In-person or telephone follow-up at 6 months established vital and functional status (modified Rankin score [mRS]). Area under the receiver operating curves (AUC) was used to establish prediction score performance. five hundred and seventy-five patients were included; 46% female, median age 76 years, 88% ischaemic stroke. Six months after stroke, 47% of patients had a good outcome (alive and independent, mRS 0-2) and 26% a devastating outcome (dead or severely dependent, mRS 5-6). The FSV and PLAN scores were superior to physician prediction (AUCs of 0.823-0.863 versus 0.773-0.805, P < 0.0001) for good and devastating outcomes. The FSV score was superior to the PLAN score for predicting good outcomes and vice versa for devastating outcomes (P < 0.001). Outcome prediction was more accurate for those with later presentations (>24 hours from onset). the FSV and PLAN scores are validated in this population for outcome prediction after both ischaemic and haemorrhagic stroke. The FSV score is the least complex of all developed scores and can assist outcome prediction by physicians. © The Author 2016. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved. For permissions, please email: journals.permissions@oup.com

  8. Pediatric siMS score: A new, simple and accurate continuous metabolic syndrome score for everyday use in pediatrics.

    PubMed

    Vukovic, Rade; Milenkovic, Tatjana; Stojan, George; Vukovic, Ana; Mitrovic, Katarina; Todorovic, Sladjana; Soldatovic, Ivan

    2017-01-01

    The dichotomous nature of the current definition of metabolic syndrome (MS) in youth results in loss of information. On the other hand, the calculation of continuous MS scores using standardized residuals in linear regression (Z scores) or factor scores of principal component analysis (PCA) is highly impractical for clinical use. Recently, a novel, easily calculated continuous MS score called siMS score was developed based on the IDF MS criteria for the adult population. To develop a Pediatric siMS score (PsiMS), a modified continuous MS score for use in the obese youth, based on the original siMS score, while keeping the score as simple as possible and retaining high correlation with more complex scores. The database consisted of clinical data on 153 obese (BMI ≥95th percentile) children and adolescents. Continuous MS scores were calculated using Z scores and PCA, as well as the original siMS score. Four variants of PsiMS score were developed in accordance with IDF criteria for MS in youth and correlation of these scores with PCA and Z score derived MS continuous scores was assessed. PsiMS score calculated using formula: (2xWaist/Height) + (Glucose(mmol/l)/5.6) + (triglycerides(mmol/l)/1.7) + (Systolic BP/130)-(HDL(mmol/l)/1.02) showed the highest correlation with most of the complex continuous scores (0.792-0.901). The original siMS score also showed high correlation with continuous MS scores. PsiMS score represents a practical and accurate score for the evaluation of MS in the obese youth. The original siMS score should be used when evaluating large cohorts consisting of both adults and children.

  9. 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.

  10. Allele-sharing models: LOD scores and accurate linkage tests.

    PubMed

    Kong, A; Cox, N J

    1997-11-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

  11. Allele-sharing models: LOD scores and accurate linkage tests.

    PubMed Central

    Kong, A; Cox, N J

    1997-01-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested. PMID:9345087

  12. Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery.

    PubMed

    Catana, Cornel; Stouten, Pieter F W

    2007-01-01

    The ability to accurately predict biological affinity on the basis of in silico docking to a protein target remains a challenging goal in the CADD arena. Typically, "standard" scoring functions have been employed that use the calculated docking result and a set of empirical parameters to calculate a predicted binding affinity. To improve on this, we are exploring novel strategies for rapidly developing and tuning "customized" scoring functions tailored to a specific need. In the present work, three such customized scoring functions were developed using a set of 129 high-resolution protein-ligand crystal structures with measured Ki values. The functions were parametrized using N-PLS (N-way partial least squares), a multivariate technique well-known in the 3D quantitative structure-activity relationship field. A modest correlation between observed and calculated pKi values using a standard scoring function (r2 = 0.5) could be improved to 0.8 when a customized scoring function was applied. To mimic a more realistic scenario, a second scoring function was developed, not based on crystal structures but exclusively on several binding poses generated with the Flo+ docking program. Finally, a validation study was conducted by generating a third scoring function with 99 randomly selected complexes from the 129 as a training set and predicting pKi values for a test set that comprised the remaining 30 complexes. Training and test set r2 values were 0.77 and 0.78, respectively. These results indicate that, even without direct structural information, predictive customized scoring functions can be developed using N-PLS, and this approach holds significant potential as a general procedure for predicting binding affinity on the basis of in silico docking.

  13. RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics

    PubMed Central

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

    2010-01-01

    Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an -value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic -value reported by any method into the textbook-defined -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 -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 -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. PMID:21103371

  14. Does the emergency surgery score accurately predict outcomes in emergent laparotomies?

    PubMed

    Peponis, Thomas; Bohnen, Jordan D; Sangji, Naveen F; Nandan, Anirudh R; Han, Kelsey; Lee, Jarone; Yeh, D Dante; de Moya, Marc A; Velmahos, George C; Chang, David C; Kaafarani, Haytham M A

    2017-08-01

    The emergency surgery score is a mortality-risk calculator for emergency general operation patients. We sought to examine whether the emergency surgery score predicts 30-day morbidity and mortality in a high-risk group of patients undergoing emergent laparotomy. Using the 2011-2012 American College of Surgeons National Surgical Quality Improvement Program database, we identified all patients who underwent emergent laparotomy using (1) the American College of Surgeons National Surgical Quality Improvement Program definition of "emergent," and (2) all Current Procedural Terminology codes denoting a laparotomy, excluding aortic aneurysm rupture. Multivariable logistic regression analyses were performed to measure the correlation (c-statistic) between the emergency surgery score and (1) 30-day mortality, and (2) 30-day morbidity after emergent laparotomy. As sensitivity analyses, the correlation between the emergency surgery score and 30-day mortality was also evaluated in prespecified subgroups based on Current Procedural Terminology codes. A total of 26,410 emergent laparotomy patients were included. Thirty-day mortality and morbidity were 10.2% and 43.8%, respectively. The emergency surgery score correlated well with mortality (c-statistic = 0.84); scores of 1, 11, and 22 correlated with mortalities of 0.4%, 39%, and 100%, respectively. Similarly, the emergency surgery score correlated well with morbidity (c-statistic = 0.74); scores of 0, 7, and 11 correlated with complication rates of 13%, 58%, and 79%, respectively. The morbidity rates plateaued for scores higher than 11. Sensitivity analyses demonstrated that the emergency surgery score effectively predicts mortality in patients undergoing emergent (1) splenic, (2) gastroduodenal, (3) intestinal, (4) hepatobiliary, or (5) incarcerated ventral hernia operation. The emergency surgery score accurately predicts outcomes in all types of emergent laparotomy patients and may prove valuable as a bedside decision

  15. 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

  16. How Accurate Is a Test Score?

    ERIC Educational Resources Information Center

    Doppelt, Jerome E.

    1956-01-01

    The standard error of measurement as a means for estimating the margin of error that should be allowed for in test scores is discussed. The true score measures the performance that is characteristic of the person tested; the variations, plus and minus, around the true score describe a characteristic of the test. When the standard deviation is used…

  17. Are medical students assigning proper global assessment of functioning scores?

    PubMed

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

    2007-01-01

    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 assessed by the psychiatry residents and staff psychiatrists. The authors designed a cross-sectional confidential survey of medical students, psychiatry residents, and staff psychiatrists. Consenting participants were asked to provide demographic information and then complete the accompanying questionnaire after reading two vignettes. One of the vignettes described a depressed patient and the other a psychotic patient. The subjects were asked to estimate the GAF scores for the patients in both vignettes. Then the subjects were given the GAF scoring guide to review and were asked to re-assess their initial GAF scores for the patients in the vignettes. Medical students assigned much higher GAF scores for the patient in the vignette with less severe symptoms than the psychiatry residents and staff psychiatrists. The GAF scores of all three groups for the patient in the vignette with more severe symptoms were comparable. The ability of medical students to assign proper GAF scores needs to be studied further. Our study suggests that current 1-month rotations in psychiatry, without specific training on assigning GAF scores, may not provide medical students with enough information to assess GAF scores accurately. This might need to be addressed in psychiatry clerkships.

  18. 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…

  19. A Critical Assessment of the Performance of Protein-ligand Scoring Functions Based on NMR Chemical Shift Perturbations

    PubMed Central

    Wang, Bing; Westerhoff, Lance M.; Merz, Kenneth M.

    2008-01-01

    We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby, providing a new tool facilitating the structure-based drug discovery process. PMID:17867664

  20. Validity Assessment of Low-risk SCORE Function and SCORE Function Calibrated to the Spanish Population in the FRESCO Cohorts.

    PubMed

    Baena-Díez, José Miguel; Subirana, Isaac; Ramos, Rafael; Gómez de la Cámara, Agustín; Elosua, Roberto; Vila, Joan; Marín-Ibáñez, Alejandro; Guembe, María Jesús; Rigo, Fernando; Tormo-Díaz, María José; Moreno-Iribas, Conchi; Cabré, Joan Josep; Segura, Antonio; Lapetra, José; Quesada, Miquel; Medrano, María José; González-Diego, Paulino; Frontera, Guillem; Gavrila, Diana; Ardanaz, Eva; Basora, Josep; García, José María; García-Lareo, Manel; Gutiérrez-Fuentes, José Antonio; Mayoral, Eduardo; Sala, Joan; Dégano, Irene R; Francès, Albert; Castell, Conxa; Grau, María; Marrugat, Jaume

    2018-04-01

    To assess the validity of the original low-risk SCORE function without and with high-density lipoprotein cholesterol and SCORE calibrated to the Spanish population. Pooled analysis with individual data from 12 Spanish population-based cohort studies. We included 30 919 individuals aged 40 to 64 years with no history of cardiovascular disease at baseline, who were followed up for 10 years for the causes of death included in the SCORE project. The validity of the risk functions was analyzed with the area under the ROC curve (discrimination) and the Hosmer-Lemeshow test (calibration), respectively. Follow-up comprised 286 105 persons/y. Ten-year cardiovascular mortality was 0.6%. The ratio between estimated/observed cases ranged from 9.1, 6.5, and 9.1 in men and 3.3, 1.3, and 1.9 in women with original low-risk SCORE risk function without and with high-density lipoprotein cholesterol and calibrated SCORE, respectively; differences were statistically significant with the Hosmer-Lemeshow test between predicted and observed mortality with SCORE (P < .001 in both sexes and with all functions). The area under the ROC curve with the original SCORE was 0.68 in men and 0.69 in women. All versions of the SCORE functions available in Spain significantly overestimate the cardiovascular mortality observed in the Spanish population. Despite the acceptable discrimination capacity, prediction of the number of fatal cardiovascular events (calibration) was significantly inaccurate. Copyright © 2017 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

  1. Fast and accurate computation of projected two-point functions

    NASA Astrophysics Data System (ADS)

    Grasshorn Gebhardt, Henry S.; Jeong, Donghui

    2018-01-01

    We present the two-point function from the fast and accurate spherical Bessel transformation (2-FAST) algorithmOur code is available at https://github.com/hsgg/twoFAST. for a fast and accurate computation of integrals involving one or two spherical Bessel functions. These types of integrals occur when projecting the galaxy power spectrum P (k ) onto the configuration space, ξℓν(r ), or spherical harmonic space, Cℓ(χ ,χ'). First, we employ the FFTLog transformation of the power spectrum to divide the calculation into P (k )-dependent coefficients and P (k )-independent integrations of basis functions multiplied by spherical Bessel functions. We find analytical expressions for the latter integrals in terms of special functions, for which recursion provides a fast and accurate evaluation. The algorithm, therefore, circumvents direct integration of highly oscillating spherical Bessel functions.

  2. TS-Chemscore, a Target-Specific Scoring Function, Significantly Improves the Performance of Scoring in Virtual Screening.

    PubMed

    Wang, Wen-Jing; Huang, Qi; Zou, Jun; Li, Lin-Li; Yang, Sheng-Yong

    2015-07-01

    Most of the scoring functions currently used in structure-based drug design belong to 'universal' scoring functions, which often give a poor correlation between the calculated scores and experimental binding affinities. In this investigation, we proposed a simple strategy to construct target-specific scoring functions based on known 'universal' scoring functions. This strategy was applied to Chemscore, a widely used empirical scoring function, which led to a new scoring function, termed TS-Chemscore. TS-Chemscore was validated on 14 protein targets, which cover a wide range of biological target categories. The results showed that TS-Chemscore significantly improved the correlation between the calculated scores and experimental binding affinities compared with the original Chemscore. TS-Chemscore was then applied in virtual screening to retrieve novel JAK3 and YopH inhibitors. Top 30 compounds for each target were selected for experimental validation. Six active compounds for JAK3 and four for YopH were obtained. These compounds were out of the lists of top 30 compounds sorted by Chemscore. Collectively, TS-Chemscore established in this study showed a better performance in virtual screening than its counterpart Chemscore. © 2014 John Wiley & Sons A/S.

  3. 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

  4. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets.

    PubMed

    Xu, Weijun; Lucke, Andrew J; Fairlie, David P

    2015-04-01

    Accurately predicting relative binding affinities and biological potencies for ligands that interact with proteins remains a significant challenge for computational chemists. Most evaluations of docking and scoring algorithms have focused on enhancing ligand affinity for a protein by optimizing docking poses and enrichment factors during virtual screening. However, there is still relatively limited information on the accuracy of commercially available docking and scoring software programs for correctly predicting binding affinities and biological activities of structurally related inhibitors of different enzyme classes. Presented here is a comparative evaluation of eight molecular docking programs (Autodock Vina, Fitted, FlexX, Fred, Glide, GOLD, LibDock, MolDock) using sixteen docking and scoring functions to predict the rank-order activity of different ligand series for six pharmacologically important protein and enzyme targets (Factor Xa, Cdk2 kinase, Aurora A kinase, COX-2, pla2g2a, β Estrogen receptor). Use of Fitted gave an excellent correlation (Pearson 0.86, Spearman 0.91) between predicted and experimental binding only for Cdk2 kinase inhibitors. FlexX and GOLDScore produced good correlations (Pearson>0.6) for hydrophilic targets such as Factor Xa, Cdk2 kinase and Aurora A kinase. By contrast, pla2g2a and COX-2 emerged as difficult targets for scoring functions to predict ligand activities. Although possessing a high hydrophobicity in its binding site, β Estrogen receptor produced reasonable correlations using LibDock (Pearson 0.75, Spearman 0.68). These findings can assist medicinal chemists to better match scoring functions with ligand-target systems for hit-to-lead optimization using computer-aided drug design approaches. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Lower NIH stroke scale scores are required to accurately predict a good prognosis in posterior circulation stroke.

    PubMed

    Inoa, Violiza; Aron, Abraham W; Staff, Ilene; Fortunato, Gilbert; Sansing, Lauren H

    2014-01-01

    The NIH stroke scale (NIHSS) is an indispensable tool that aids in the determination of acute stroke prognosis and decision making. Patients with posterior circulation (PC) strokes often present with lower NIHSS scores, which may result in the withholding of thrombolytic treatment from these patients. However, whether these lower initial NIHSS scores predict better long-term prognoses is uncertain. We aimed to assess the utility of the NIHSS at presentation for predicting the functional outcome at 3 months in anterior circulation (AC) versus PC strokes. This was a retrospective analysis of a large prospectively collected database of adults with acute ischemic stroke. Univariate and multivariate analyses were conducted to identify factors associated with outcome. Additional analyses were performed to determine the receiver operating characteristic (ROC) curves for NIHSS scores and outcomes in AC and PC infarctions. Both the optimal cutoffs for maximal diagnostic accuracy and the cutoffs to obtain >80% sensitivity for poor outcomes were determined in AC and PC strokes. The analysis included 1,197 patients with AC stroke and 372 with PC stroke. The median initial NIHSS score for patients with AC strokes was 7 and for PC strokes it was 2. The majority (71%) of PC stroke patients had baseline NIHSS scores ≤4, and 15% of these 'minor' stroke patients had a poor outcome at 3 months. ROC analysis identified that the optimal NIHSS cutoff for outcome prediction after infarction in the AC was 8 and for infarction in the PC it was 4. To achieve >80% sensitivity for detecting patients with a subsequent poor outcome, the NIHSS cutoff for infarctions in the AC was 4 and for infarctions in the PC it was 2. The NIHSS cutoff that most accurately predicts outcomes is 4 points higher in AC compared to PC infarctions. There is potential for poor outcomes in patients with PC strokes and low NIHSS scores, suggesting that thrombolytic treatment should not be withheld from these patients

  6. A scoring function based on solvation thermodynamics for protein structure prediction

    PubMed Central

    Du, Shiqiao; Harano, Yuichi; Kinoshita, Masahiro; Sakurai, Minoru

    2012-01-01

    We predict protein structure using our recently developed free energy function for describing protein stability, which is focused on solvation thermodynamics. The function is combined with the current most reliable sampling methods, i.e., fragment assembly (FA) and comparative modeling (CM). The prediction is tested using 11 small proteins for which high-resolution crystal structures are available. For 8 of these proteins, sequence similarities are found in the database, and the prediction is performed with CM. Fairly accurate models with average Cα root mean square deviation (RMSD) ∼ 2.0 Å are successfully obtained for all cases. For the rest of the target proteins, we perform the prediction following FA protocols. For 2 cases, we obtain predicted models with an RMSD ∼ 3.0 Å as the best-scored structures. For the other case, the RMSD remains larger than 7 Å. For all the 11 target proteins, our scoring function identifies the experimentally determined native structure as the best structure. Starting from the predicted structure, replica exchange molecular dynamics is performed to further refine the structures. However, we are unable to improve its RMSD toward the experimental structure. The exhaustive sampling by coarse-grained normal mode analysis around the native structures reveals that our function has a linear correlation with RMSDs < 3.0 Å. These results suggest that the function is quite reliable for the protein structure prediction while the sampling method remains one of the major limiting factors in it. The aspects through which the methodology could further be improved are discussed. PMID:27493529

  7. Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.

    PubMed

    Yan, Yumeng; Wen, Zeyu; Zhang, Di; Huang, Sheng-You

    2018-05-18

    RNA-RNA interactions play fundamental roles in gene and cell regulation. Therefore, accurate prediction of RNA-RNA interactions is critical to determine their complex structures and understand the molecular mechanism of the interactions. Here, we have developed a physics-based double-iterative strategy to determine the effective potentials for RNA-RNA interactions based on a training set of 97 diverse RNA-RNA complexes. The double-iterative strategy circumvented the reference state problem in knowledge-based scoring functions by updating the potentials through iteration and also overcame the decoy-dependent limitation in previous iterative methods by constructing the decoys iteratively. The derived scoring function, which is referred to as DITScoreRR, was evaluated on an RNA-RNA docking benchmark of 60 test cases and compared with three other scoring functions. It was shown that for bound docking, our scoring function DITScoreRR obtained the excellent success rates of 90% and 98.3% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 63.3% and 71.7% for van der Waals interactions, 45.0% and 65.0% for ITScorePP, and 11.7% and 26.7% for ZDOCK 2.1, respectively. For unbound docking, DITScoreRR achieved the good success rates of 53.3% and 71.7% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 13.3% and 28.3% for van der Waals interactions, 11.7% and 26.7% for our ITScorePP, and 3.3% and 6.7% for ZDOCK 2.1, respectively. DITScoreRR also performed significantly better in ranking decoys and obtained significantly higher score-RMSD correlations than the other three scoring functions. DITScoreRR will be of great value for the prediction and design of RNA structures and RNA-RNA complexes.

  8. A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

    PubMed Central

    Hayik, Seth A.; Dunbrack, Roland; Merz, Kenneth M.

    2010-01-01

    Computational methods for predicting protein-ligand binding free energy continue to be popular as a potential cost-cutting method in the drug discovery process. However, accurate predictions are often difficult to make as estimates must be made for certain electronic and entropic terms in conventional force field based scoring functions. Mixed quantum mechanics/molecular mechanics (QM/MM) methods allow electronic effects for a small region of the protein to be calculated, treating the remaining atoms as a fixed charge background for the active site. Such a semi-empirical QM/MM scoring function has been implemented in AMBER using DivCon and tested on a set of 23 metalloprotein-ligand complexes, where QM/MM methods provide a particular advantage in the modeling of the metal ion. The binding affinity of this set of proteins can be calculated with an R2 of 0.64 and a standard deviation of 1.88 kcal/mol without fitting and 0.71 and a standard deviation of 1.69 kcal/mol with fitted weighting of the individual scoring terms. In this study we explore using various methods to calculate terms in the binding free energy equation, including entropy estimates and minimization standards. From these studies we found that using the rotational bond estimate to ligand entropy results in a reasonable R2 of 0.63 without fitting. We also found that using the ESCF energy of the proteins without minimization resulted in an R2 of 0.57, when using the rotatable bond entropy estimate. PMID:21221417

  9. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

    PubMed

    Benkert, Pascal; Schwede, Torsten; Tosatto, Silvio Ce

    2009-05-20

    The selection of the most accurate protein model from a set of alternatives is a crucial step in protein structure prediction both in template-based and ab initio approaches. Scoring functions have been developed which can either return a quality estimate for a single model or derive a score from the information contained in the ensemble of models for a given sequence. Local structural features occurring more frequently in the ensemble have a greater probability of being correct. Within the context of the CASP experiment, these so called consensus methods have been shown to perform considerably better in selecting good candidate models, but tend to fail if the best models are far from the dominant structural cluster. In this paper we show that model selection can be improved if both approaches are combined by pre-filtering the models used during the calculation of the structural consensus. Our recently published QMEAN composite scoring function has been improved by including an all-atom interaction potential term. The preliminary model ranking based on the new QMEAN score is used to select a subset of reliable models against which the structural consensus score is calculated. This scoring function called QMEANclust achieves a correlation coefficient of predicted quality score and GDT_TS of 0.9 averaged over the 98 CASP7 targets and perform significantly better in selecting good models from the ensemble of server models than any other groups participating in the quality estimation category of CASP7. Both scoring functions are also benchmarked on the MOULDER test set consisting of 20 target proteins each with 300 alternatives models generated by MODELLER. QMEAN outperforms all other tested scoring functions operating on individual models, while the consensus method QMEANclust only works properly on decoy sets containing a certain fraction of near-native conformations. We also present a local version of QMEAN for the per-residue estimation of model quality (QMEANlocal

  10. Force fields and scoring functions for carbohydrate simulation.

    PubMed

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

    2015-01-12

    Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Accurate prediction of pregnancy viability by means of a simple scoring system.

    PubMed

    Bottomley, Cecilia; Van Belle, Vanya; Kirk, Emma; Van Huffel, Sabine; Timmerman, Dirk; Bourne, Tom

    2013-01-01

    What is the performance of a simple scoring system to predict whether women will have an ongoing viable intrauterine pregnancy beyond the first trimester? A simple scoring system using demographic and initial ultrasound variables accurately predicts pregnancy viability beyond the first trimester with an area under the curve (AUC) in a receiver operating characteristic curve of 0.924 [95% confidence interval (CI) 0.900-0.947] on an independent test set. Individual demographic and ultrasound factors, such as maternal age, vaginal bleeding and gestational sac size, are strong predictors of miscarriage. Previous mathematical models have combined individual risk factors with reasonable performance. A simple scoring system derived from a mathematical model that can be easily implemented in clinical practice has not previously been described for the prediction of ongoing viability. This was a prospective observational study in a single early pregnancy assessment centre during a 9-month period. A cohort of 1881 consecutive women undergoing transvaginal ultrasound scan at a gestational age <84 days were included. Women were excluded if the first trimester outcome was not known. Demographic features, symptoms and ultrasound variables were tested for their influence on ongoing viability. Logistic regression was used to determine the influence on first trimester viability from demographics and symptoms alone, ultrasound findings alone and then from all the variables combined. Each model was developed on a training data set, and a simple scoring system was derived from this. This scoring system was tested on an independent test data set. The final outcome based on a total of 1435 participants was an ongoing viable pregnancy in 885 (61.7%) and early pregnancy loss in 550 (38.3%) women. The scoring system using significant demographic variables alone (maternal age and amount of bleeding) to predict ongoing viability gave an AUC of 0.724 (95% CI = 0.692-0.756) in the training set

  12. Performance of machine-learning scoring functions in structure-based virtual screening.

    PubMed

    Wójcikowski, Maciej; Ballester, Pedro J; Siedlecki, Pawel

    2017-04-25

    Classical scoring functions have reached a plateau in their performance in virtual screening and binding affinity prediction. Recently, machine-learning scoring functions trained on protein-ligand complexes have shown great promise in small tailored studies. They have also raised controversy, specifically concerning model overfitting and applicability to novel targets. Here we provide a new ready-to-use scoring function (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets. We use the full DUD-E data sets along with three docking tools, five classical and three machine-learning scoring functions for model building and performance assessment. Our results show RF-Score-VS can substantially improve virtual screening performance: RF-Score-VS top 1% provides 55.6% hit rate, whereas that of Vina only 16.2% (for smaller percent the difference is even more encouraging: RF-Score-VS top 0.1% achieves 88.6% hit rate for 27.5% using Vina). In addition, RF-Score-VS provides much better prediction of measured binding affinity than Vina (Pearson correlation of 0.56 and -0.18, respectively). Lastly, we test RF-Score-VS on an independent test set from the DEKOIS benchmark and observed comparable results. We provide full data sets to facilitate further research in this area (http://github.com/oddt/rfscorevs) as well as ready-to-use RF-Score-VS (http://github.com/oddt/rfscorevs_binary).

  13. Performance of machine-learning scoring functions in structure-based virtual screening

    PubMed Central

    Wójcikowski, Maciej; Ballester, Pedro J.; Siedlecki, Pawel

    2017-01-01

    Classical scoring functions have reached a plateau in their performance in virtual screening and binding affinity prediction. Recently, machine-learning scoring functions trained on protein-ligand complexes have shown great promise in small tailored studies. They have also raised controversy, specifically concerning model overfitting and applicability to novel targets. Here we provide a new ready-to-use scoring function (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets. We use the full DUD-E data sets along with three docking tools, five classical and three machine-learning scoring functions for model building and performance assessment. Our results show RF-Score-VS can substantially improve virtual screening performance: RF-Score-VS top 1% provides 55.6% hit rate, whereas that of Vina only 16.2% (for smaller percent the difference is even more encouraging: RF-Score-VS top 0.1% achieves 88.6% hit rate for 27.5% using Vina). In addition, RF-Score-VS provides much better prediction of measured binding affinity than Vina (Pearson correlation of 0.56 and −0.18, respectively). Lastly, we test RF-Score-VS on an independent test set from the DEKOIS benchmark and observed comparable results. We provide full data sets to facilitate further research in this area (http://github.com/oddt/rfscorevs) as well as ready-to-use RF-Score-VS (http://github.com/oddt/rfscorevs_binary). PMID:28440302

  14. Daily FOUR score assessment provides accurate prognosis of long-term outcome in out-of-hospital cardiac arrest.

    PubMed

    Weiss, N; Venot, M; Verdonk, F; Chardon, A; Le Guennec, L; Llerena, M C; Raimbourg, Q; Taldir, G; Luque, Y; Fagon, J-Y; Guerot, E; Diehl, J-L

    2015-05-01

    The accurate prediction of outcome after out-of-hospital cardiac arrest (OHCA) is of major importance. The recently described Full Outline of UnResponsiveness (FOUR) is well adapted to mechanically ventilated patients and does not depend on verbal response. To evaluate the ability of FOUR assessed by intensivists to accurately predict outcome in OHCA. We prospectively identified patients admitted for OHCA with a Glasgow Coma Scale below 8. Neurological assessment was performed daily. Outcome was evaluated at 6 months using Glasgow-Pittsburgh Cerebral Performance Categories (GP-CPC). Eighty-five patients were included. At 6 months, 19 patients (22%) had a favorable outcome, GP-CPC 1-2, and 66 (78%) had an unfavorable outcome, GP-CPC 3-5. Compared to both brainstem responses at day 3 and evolution of Glasgow Coma Scale, evolution of FOUR score over the three first days was able to predict unfavorable outcome more precisely. Thus, absence of improvement or worsening from day 1 to day 3 of FOUR had 0.88 (0.79-0.97) specificity, 0.71 (0.66-0.76) sensitivity, 0.94 (0.84-1.00) PPV and 0.54 (0.49-0.59) NPV to predict unfavorable outcome. Similarly, the brainstem response of FOUR score at 0 evaluated at day 3 had 0.94 (0.89-0.99) specificity, 0.60 (0.50-0.70) sensitivity, 0.96 (0.92-1.00) PPV and 0.47 (0.37-0.57) NPV to predict unfavorable outcome. The absence of improvement or worsening from day 1 to day 3 of FOUR evaluated by intensivists provides an accurate prognosis of poor neurological outcome in OHCA. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  15. 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. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Glasgow Coma Scale score, mortality, and functional outcome in head-injured patients.

    PubMed

    Udekwu, Pascal; Kromhout-Schiro, Sharon; Vaslef, Steven; Baker, Christopher; Oller, Dale

    2004-05-01

    Preresuscitation Glasgow Coma Scale (P-GCS) score is frequently obtained in injured patients and incorporated into mortality prediction. Data on functional outcome in head injury is sparse. A large group of patients with head injuries was analyzed to assess relationships between P-GCS score, mortality, and functional outcome as measured by the Functional Independence Measure (FIM). Records for patients with International Classification of Diseases, Ninth Revision diagnosis codes indicating head injury in a statewide trauma registry between 1994 and 2002 were selected. P-GCS score, mortality, and FIM score at hospital discharge were integrated and analyzed. Of 138,750 patients, 22,924 patients were used for the mortality study and 7,150 patients for the FIM study. A good correlation exists between P-GCS score and FIM, as determined by rank correlation coefficients, whereas mortality falls steeply between a P-GCS score of 3 and a P-GCS score of 7 followed by a shallow fall. Although P-GCS score is related to mortality in head-injured patients, its relationship is nonlinear, which casts doubt on its use as a continuous measure or an equivalent set of categorical measures incorporated into outcome prediction models. The average FIM scores indicate substantial likelihood of good outcomes in survivors with low P-GCS scores, further complicating the use of the P-GCS score in the prediction of poor outcome at the time of initial patient evaluation. Although the P-GCS score is related to functional outcome as measured by the FIM score and mortality in head injury, current mortality prediction models may need to be modified to account for the nonlinear relationship between P-GCS score and mortality. The P-GCS score is not a good clinical tool for outcome prediction in individual head-injured patients, given the variability in mortality rates and functional outcomes at all scores.

  17. Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning.

    PubMed

    Mirzaei, Shokoufeh; Sidi, Tomer; Keasar, Chen; Crivelli, Silvia

    2016-08-24

    The function of a protein is determined by its structure, which creates a need for efficient methods of protein structure determination to advance scientific and medical research. Because current experimental structure determination methods carry a high price tag, computational predictions are highly desirable. Given a protein sequence, computational methods produce numerous 3D structures known as decoys. However, selection of the best quality decoys is challenging as the end users can handle only a few ones. Therefore, scoring functions are central to decoy selection. They combine measurable features into a single number indicator of decoy quality. Unfortunately, current scoring functions do not consistently select the best decoys. Machine learning techniques offer great potential to improve decoy scoring. This paper presents two machine-learning based scoring functions to predict the quality of proteins structures, i.e., the similarity between the predicted structure and the experimental one without knowing the latter. We use different metrics to compare these scoring functions against three state-of-the-art scores. This is a first attempt at comparing different scoring functions using the same non-redundant dataset for training and testing and the same features. The results show that adding informative features may be more significant than the method used.

  18. 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.

  19. Peritumoral Artery Scoring System: a Novel Scoring System to Predict Renal Function Outcome after Laparoscopic Partial Nephrectomy.

    PubMed

    Zhang, Ruiyun; Wu, Guangyu; Huang, Jiwei; Shi, Oumin; Kong, Wen; Chen, Yonghui; Xu, Jianrong; Xue, Wei; Zhang, Jin; Huang, Yiran

    2017-06-06

    The present study aimed to assess the impact of peritumoral artery characteristics on renal function outcome prediction using a novel Peritumoral Artery Scoring System based on computed tomography arteriography. Peritumoral artery characteristics and renal function were evaluated in 220 patients who underwent laparoscopic partial nephrectomy and then validate in 51 patients with split and total glomerular filtration rate (GFR). In particular, peritumoral artery classification and diameter were measured to assign arteries into low, moderate, and high Peritumoral Artery Scoring System risk categories. Univariable and multivariable logistic regression analyses were then used to determine risk factors for major renal functional decline. The Peritumoral Artery Scoring System and four other nephrometry systems were compared using receiver operating characteristic curve analysis. The Peritumoral Artery Scoring System was significantly superior to the other systems for predicting postoperative renal function decline (p < 0.001). In receiver operating characteristic analysis, our category system was a superior independent predictor of estimated glomerular filtration rate (eGFR) decline (area-under-the-curve = 0.865, p < 0.001) and total GFR decline (area-under-the-curve = 0.796, p < 0.001), and split GFR decline (area-under-the-curve = 0.841, p < 0.001). Peritumoral artery characteristics were independent predictors of renal function outcome after laparoscopic partial nephrectomy.

  20. English Cross-Cultural Translation and Validation of the Neuromuscular Score: A System for Motor Function Classification in Patients With Neuromuscular Diseases

    PubMed Central

    Vuillerot, Carole; Meilleur, Katherine G.; Jain, Minal; Waite, Melissa; Wu, Tianxia; Linton, Melody; Datsgir, Jahannaz; Donkervoort, Sandra; Leach, Meganne E.; Rutkowski, Anne; Rippert, Pascal; Payan, Christine; Iwaz, Jean; Hamroun, Dalil; Bérard, Carole; Poirot, Isabelle; Bönnemann, Carsten G.

    2016-01-01

    Objective To develop and validate an English version of the Neuromuscular (NM)-Score, a classification for patients with NM diseases in each of the 3 motor function domains: D1, standing and transfers; D2, axial and proximal motor function; and D3, distal motor function. Design Validation survey. Setting Patients seen at a medical research center between June and September 2013. Participants Consecutive patients (N = 42) aged 5 to 19 years with a confirmed or suspected diagnosis of congenital muscular dystrophy. Interventions Not applicable. Main Outcome Measures An English version of the NM-Score was developed by a 9-person expert panel that assessed its content validity and semantic equivalence. Its concurrent validity was tested against criterion standards (Brooke Scale, Motor Function Measure [MFM], activity limitations for patients with upper and/or lower limb impairments [ACTIVLIM], Jebsen Test, and myometry measurements). Informant agreement between patient/caregiver (P/C)-reported and medical doctor (MD)-reported NM scores was measured by weighted kappa. Results Significant correlation coefficients were found between NM scores and criterion standards. The highest correlations were found between NM-score D1 and MFM score D1 (ρ = −.944, P<.0001), ACTIVLIM (ρ = −.895, P<.0001), and hip abduction strength by myometry (ρ = −.811, P<.0001). Informant agreement between P/C-reported and MD-reported NM scores was high for D1 (κ = .801; 95% confidence interval [CI], .701–.914) but moderate for D2 (κ = .592; 95% CI, .412–.773) and D3 (κ = .485; 95% CI, .290–.680). Correlation coefficients between the NM scores and the criterion standards did not significantly differ between P/C-reported and MD-reported NM scores. Conclusions Patients and physicians completed the English NM-Score easily and accurately. The English version is a reliable and valid instrument that can be used in clinical practice and research to describe the functional abilities of

  1. Validity of the Cambridge Cognitive Examination-Revised new Executive Function Scores in the diagnosis of dementia: some early findings.

    PubMed

    Heinik, Jeremia; Solomesh, Isaac

    2007-03-01

    The Cambridge Cognitive Examination-Revised introduces 2 new executive items (Ideational Fluency and Visual Reasoning), which separately or combined with 2 executive items in the former version (word list generation and similarities) might constitute an Executive Function Score (EFS). The authors studied the validity of these new EFSs in 51 demented (dementia of the Alzheimer's type, vascular dementia) and nondemented individuals (depressives and normals). The new EFSs were found valid to accurately differentiate between demented and nondemented subjects; however, they were considerably less so when specific diagnoses were considered. Correlations between the variously combined executive scores and the cognitive scales and subscales studied were prevalently low to moderate, and ranged from high and significant to low and nonsignificant when the 4 executive items were correlated to each other. The ability of the executive scores to discriminate demented from nondemented individuals was lower compared with the Cambridge Cognitive Examination-Revised scores. EFS was found internally consistent.

  2. Physical Function Does Not Predict Care Assessment Need Score in Older Veterans.

    PubMed

    Serra, Monica C; Addison, Odessa; Giffuni, Jamie; Paden, Lydia; Morey, Miriam C; Katzel, Leslie

    2017-01-01

    The Veterans Health Administration's Care Assessment Need (CAN) score is a statistical model, aimed to predict high-risk patients. We were interested in determining if a relationship existed between physical function and CAN scores. Seventy-four older (71 ± 1 years) male Veterans underwent assessment of CAN score and subjective (Short Form-36 [SF-36]) and objective (self-selected walking speed, four square step test, short physical performance battery) assessment of physical function. Approximately 25% of participants self-reported limitations performing lower intensity activities, while 70% to 90% reported limitations with more strenuous activities. When compared with cut points indicative of functional limitations, 35% to 65% of participants had limitations for each of the objective measures. Any measure of subjective or objective physical function did not predict CAN score. These data indicate that the addition of a physical function assessment may complement the CAN score in the identification of high-risk patients.

  3. Tangent function transformation of the Abbreviated Injury Scale improves accuracy and simplifies scoring.

    PubMed

    Wang, Muding; Qiu, Wusi; Qiu, Fang; Mo, Yinan; Fan, Wenhui

    2015-03-16

    The Injury Severity Score (ISS) and the New Injury Severity Score (NISS) are widely used for anatomic severity assessments after trauma. We present here the Tangent Injury Severity Score (TISS), which transforms the Abbreviated Injury Scale (AIS) as a predictor of mortality. The TISS is defined as the sum of the tangent function of AIS/6 to the power 3.04 multiplied by 18.67 of a patient's three most severe AIS injuries regardless of body regions. TISS values were calculated for every patient in two large independent data sets: 3,908 and 4,171 patients treated during a 6-year period at level-3 first-class comprehensive hospitals: the Affiliated Hospital of Hangzhou Normal University and Fengtian Hospital Affiliated to Shenyang Medical College, China. The power of TISS to predict mortality was compared with previously calculated NISS values for the same patients in each data set. The TISS is more predictive of survival than NISS (Hangzhou: receiver operating characteristic (ROC): NISS = 0.929, TISS = 0.949; p = 0.002; Shenyang: ROC: NISS = 0.924, TISS = 0.942; p = 0.008). Moreover, TISS provides a better fit throughout its entire range of prediction (Hosmer Lemeshow statistic for Hangzhou NISS = 29.71; p < 0.001, TISS = 19.59; p = 0.003; Hosmer Lemeshow statistic for Shenyang NISS = 33.49; p < 0.001, TISS = 21.19; p = 0.002). The TISS shows more accurate prediction of prognosis and a linear relation to mortality. The TISS might be a better injury scoring tool with simple computation.

  4. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

    PubMed

    Olson, Mark A; Feig, Michael; Brooks, Charles L

    2008-04-15

    This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy

  5. Correlates of cognitive function scores in elderly outpatients.

    PubMed

    Mangione, C M; Seddon, J M; Cook, E F; Krug, J H; Sahagian, C R; Campion, E W; Glynn, R J

    1993-05-01

    To determine medical, ophthalmologic, and demographic predictors of cognitive function scores as measured by the Telephone Interview for Cognitive Status (TICS), an adaptation of the Folstein Mini-Mental Status Exam. A secondary objective was to perform an item-by-item analysis of the TICS scores to determine which items correlated most highly with the overall scores. Cross-sectional cohort study. The Glaucoma Consultation Service of the Massachusetts Eye and Ear Infirmary. 472 of 565 consecutive patients age 65 and older who were seen at the Glaucoma Consultation Service between November 1, 1987 and October 31, 1988. Each subject had a standard visual examination and review of medical history at entry, followed by a telephone interview that collected information on demographic characteristics, cognitive status, health status, accidents, falls, symptoms of depression, and alcohol intake. A multivariate linear regression model of correlates of TICS score found the strongest correlates to be education, age, occupation, and the presence of depressive symptoms. The only significant ocular condition that correlated with lower TICS score was the presence of surgical aphakia (model R2 = .46). Forty-six percent (216/472) of patients fell below the established definition of normal on the mental status scale. In a logistic regression analysis, the strongest correlates of an abnormal cognitive function score were age, diabetes, educational status, and occupational status. An item analysis using step-wise linear regression showed that 85 percent of the variance in the TICS score was explained by the ability to perform serial sevens and to repeat 10 items immediately after hearing them. Educational status correlated most highly with both of these items (Kendall Tau R = .43 and Kendall Tau R = .30, respectively). Education, occupation, depression, and age were the strongest correlates of the score on this new screening test for assessing cognitive status. These factors were

  6. Evaluation and application of multiple scoring functions for a virtual screening experiment

    NASA Astrophysics Data System (ADS)

    Xing, Li; Hodgkin, Edward; Liu, Qian; Sedlock, David

    2004-05-01

    In order to identify novel chemical classes of factor Xa inhibitors, five scoring functions (FlexX, DOCK, GOLD, ChemScore and PMF) were engaged to evaluate the multiple docking poses generated by FlexX. The compound collection was composed of confirmed potent factor Xa inhibitors and a subset of the LeadQuest® screening compound library. Except for PMF the other four scoring functions succeeded in reproducing the crystal complex (PDB code: 1FAX). During virtual screening the highest hit rate (80%) was demonstrated by FlexX at an energy cutoff of -40 kJ/mol, which is about 40-fold over random screening (2.06%). Limited results suggest that presenting more poses of a single molecule to the scoring functions could deteriorate their enrichment factors. A series of promising scaffolds with favorable binding scores was retrieved from LeadQuest. Consensus scoring by pair-wise intersection failed to enrich the hit rate yielded by single scorings (i.e. FlexX). We note that reported successes of consensus scoring in hit rate enrichment could be artificial because their comparisons were based on a selected subset of single scoring and a markedly reduced subset of double or triple scoring. The findings presented in this report are based upon a single biological system and support further studies.

  7. The Cut-Score Operating Function: A New Tool to Aid in Standard Setting

    ERIC Educational Resources Information Center

    Grabovsky, Irina; Wainer, Howard

    2017-01-01

    In this essay, we describe the construction and use of the Cut-Score Operating Function in aiding standard setting decisions. The Cut-Score Operating Function shows the relation between the cut-score chosen and the consequent error rate. It allows error rates to be defined by multiple loss functions and will show the behavior of each loss…

  8. 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…

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

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

    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

  10. 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. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. 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

  12. A study of accurate exchange-correlation functionals through adiabatic connection

    NASA Astrophysics Data System (ADS)

    Singh, Rabeet; Harbola, Manoj K.

    2017-10-01

    A systematic way of improving exchange-correlation energy functionals of density functional theory has been to make them satisfy more and more exact relations. Starting from the initial generalized gradient approximation (GGA) functionals, this has culminated into the recently proposed SCAN (strongly constrained and appropriately normed) functional that satisfies several known constraints and is appropriately normed. The ultimate test for the functionals developed is the accuracy of energy calculated by employing them. In this paper, we test these exchange-correlation functionals—the GGA hybrid functionals B3LYP and PBE0 and the meta-GGA functional SCAN—from a different perspective. We study how accurately these functionals reproduce the exchange-correlation energy when electron-electron interaction is scaled as αVee with α varying between 0 and 1. Our study reveals interesting comparison between these functionals and the associated difference Tc between the interacting and the non-interacting kinetic energy for the same density.

  13. Combining Spot Sign and Intracerebral Hemorrhage Score to Estimate Functional Outcome: Analysis From the PREDICT Cohort.

    PubMed

    Schneider, Hauke; Huynh, Thien J; Demchuk, Andrew M; Dowlatshahi, Dar; Rodriguez-Luna, David; Silva, Yolanda; Aviv, Richard; Dzialowski, Imanuel

    2018-06-01

    The intracerebral hemorrhage (ICH) score is the most commonly used grading scale for stratifying functional outcome in patients with acute ICH. We sought to determine whether a combination of the ICH score and the computed tomographic angiography spot sign may improve outcome prediction in the cohort of a prospective multicenter hemorrhage trial. Prospectively collected data from 241 patients from the observational PREDICT study (Prediction of Hematoma Growth and Outcome in Patients With Intracerebral Hemorrhage Using the CT-Angiography Spot Sign) were analyzed. Functional outcome at 3 months was dichotomized using the modified Rankin Scale (0-3 versus 4-6). Performance of (1) the ICH score and (2) the spot sign ICH score-a scoring scale combining ICH score and spot sign number-was tested. Multivariable analysis demonstrated that ICH score (odds ratio, 3.2; 95% confidence interval, 2.2-4.8) and spot sign number (n=1: odds ratio, 2.7; 95% confidence interval, 1.1-7.4; n>1: odds ratio, 3.8; 95% confidence interval, 1.2-17.1) were independently predictive of functional outcome at 3 months with similar odds ratios. Prediction of functional outcome was not significantly different using the spot sign ICH score compared with the ICH score alone (spot sign ICH score area under curve versus ICH score area under curve: P =0.14). In the PREDICT cohort, a prognostic score adding the computed tomographic angiography-based spot sign to the established ICH score did not improve functional outcome prediction compared with the ICH score. © 2018 American Heart Association, Inc.

  14. Pneumococcal pneumonia - Are the new severity scores more accurate in predicting adverse outcomes?

    PubMed

    Ribeiro, C; Ladeira, I; Gaio, A R; Brito, M C

    2013-01-01

    The site-of-care decision is one of the most important factors in the management of patients with community-acquired pneumonia. The severity scores are validated prognostic tools for community-acquired pneumonia mortality and treatment site decision. The aim of this paper was to compare the discriminatory power of four scores - the classic PSI and CURB65 ant the most recent SCAP and SMART-COP - in predicting major adverse events: death, ICU admission, need for invasive mechanical ventilation or vasopressor support in patients admitted with pneumococcal pneumonia. A five year retrospective study of patients admitted for pneumococcal pneumonia. Patients were stratified based on admission data and assigned to low-, intermediate-, and high-risk classes for each score. Results were obtained comparing low versus non-low risk classes. We studied 142 episodes of hospitalization with 2 deaths and 10 patients needing mechanical ventilation and vasopressor support. The majority of patients were classified as low risk by all scores - we found high negative predictive values for all adverse events studied, the most negative value corresponding to the SCAP score. The more recent scores showed better accuracy for predicting ICU admission and need for ventilation or vasopressor support (mostly for the SCAP score with higher AUC values for all adverse events). The rate of all adverse outcomes increased directly with increasing risk class in all scores. The new gravity scores appear to have a higher discriminatory power in all adverse events in our study, particularly, the SCAP score. Copyright © 2012 Sociedade Portuguesa de Pneumologia. Published by Elsevier España. All rights reserved.

  15. Physiologic Dysfunction Scores and Cognitive Function Test Performance in United States Adults

    PubMed Central

    Kobrosly, Roni W; Seplaki, Christopher L; Jones, Courtney M; van Wijngaarden, Edwin

    2013-01-01

    Objective To investigate the relationship between a measure of cumulative physiologic dysfunction and specific domains of cognitive function. Methods We examined a summary score measuring physiological dysfunction, a multisystem measure of the body’s ability to effectively adapt to physical and psychological demands, in relation to cognitive function deficits in a population of 4511 adults aged 20 to 59 who participated in the third National Health and Nutrition Examination Survey (1988–1994). Measures of cognitive function comprised three domains: working memory, visuomotor speed, and perceptual-motor speed. ‘Physiologic dysfunction’ scores summarizing measures of cardiovascular, immunologic, kidney, and liver function were explored. We used multiple linear regression models to estimate associations between cognitive function measures and physiological dysfunction scores, adjusting for socioeconomic factors, test conditions, and self-reported health factors. Results We noted a dose-response relationship between physiologic dysfunction and working memory (coefficient = 0.207, 95% CI = (0.066, 0.348), p < 0.0001) that persisted after adjustment for all covariates (p = 0.03). We did not observe any significant relationships between dysfunction scores and visuomotor (p = 0.37) or perceptual-motor ability (p = 0.33). Conclusions Our findings suggest that multisystem physiologic dysfunction is associated with working memory. Future longitudinal studies are needed to clarify the underlying mechanisms and explore the persistency of this association into later life. We suggest that such studies should incorporate physiologic data, neuroendocrine parameters, and a wide range of specific cognitive domains. PMID:22155941

  16. 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).

  17. Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.

    PubMed

    Dutagaci, Bercem; Wittayanarakul, Kitiyaporn; Mori, Takaharu; Feig, Michael

    2017-06-13

    A scoring protocol based on implicit membrane-based scoring functions and a new protocol for optimizing the positioning of proteins inside the membrane was evaluated for its capacity to discriminate native-like states from misfolded decoys. A decoy set previously established by the Baker lab (Proteins: Struct., Funct., Genet. 2006, 62, 1010-1025) was used along with a second set that was generated to cover higher resolution models. The Implicit Membrane Model 1 (IMM1), IMM1 model with CHARMM 36 parameters (IMM1-p36), generalized Born with simple switching (GBSW), and heterogeneous dielectric generalized Born versions 2 (HDGBv2) and 3 (HDGBv3) were tested along with the new HDGB van der Waals (HDGBvdW) model that adds implicit van der Waals contributions to the solvation free energy. For comparison, scores were also calculated with the distance-scaled finite ideal-gas reference (DFIRE) scoring function. Z-scores for native state discrimination, energy vs root-mean-square deviation (RMSD) correlations, and the ability to select the most native-like structures as top-scoring decoys were evaluated to assess the performance of the scoring functions. Ranking of the decoys in the Baker set that were relatively far from the native state was challenging and dominated largely by packing interactions that were captured best by DFIRE with less benefit of the implicit membrane-based models. Accounting for the membrane environment was much more important in the second decoy set where especially the HDGB-based scoring functions performed very well in ranking decoys and providing significant correlations between scores and RMSD, which shows promise for improving membrane protein structure prediction and refinement applications. The new membrane structure scoring protocol was implemented in the MEMScore web server ( http://feiglab.org/memscore ).

  18. Accurate mass and velocity functions of dark matter haloes

    NASA Astrophysics Data System (ADS)

    Comparat, Johan; Prada, Francisco; Yepes, Gustavo; Klypin, Anatoly

    2017-08-01

    N-body cosmological simulations are an essential tool to understand the observed distribution of galaxies. We use the MultiDark simulation suite, run with the Planck cosmological parameters, to revisit the mass and velocity functions. At redshift z = 0, the simulations cover four orders of magnitude in halo mass from ˜1011M⊙ with 8783 874 distinct haloes and 532 533 subhaloes. The total volume used is ˜515 Gpc3, more than eight times larger than in previous studies. We measure and model the halo mass function, its covariance matrix w.r.t halo mass and the large-scale halo bias. With the formalism of the excursion-set mass function, we explicit the tight interconnection between the covariance matrix, bias and halo mass function. We obtain a very accurate (<2 per cent level) model of the distinct halo mass function. We also model the subhalo mass function and its relation to the distinct halo mass function. The set of models obtained provides a complete and precise framework for the description of haloes in the concordance Planck cosmology. Finally, we provide precise analytical fits of the Vmax maximum velocity function up to redshift z < 2.3 to push for the development of halo occupation distribution using Vmax. The data and the analysis code are made publicly available in the Skies and Universes data base.

  19. Is there a relation between priapism occurring after penile doppler ultrasonography and international erectile function index score and erection hardness score levels?

    PubMed Central

    Sönmez, Mehmet Giray; Öztürk, Ahmet

    2017-01-01

    Objective The relation between Erection Hardness Score (EHS) and The International Erectile Function Index (IIEF) Questionnaire- Erectile Function Domain Score (IIEF-EF score) used in erectile dysfunction (ED) evaluation and the prevalence of priapism after penile Doppler ultrasonography (PDU) was examined in this study. Material and methods A total of 62 patients who had PDU were included in the study. Patients were divided into two groups; there were 33 patients in IIEF-EF score ≤10, EHS <2 group (Group 1) and 29 patients in IIEF-EF score >10, EHS ≥2 group (Group 2). The two groups separated according to their scores were compared for age, body mass index (BMI), prevalence of priapism, vascular comorbidities and duration of erection. Results When compared to Group 2, median age, rate of vascular comorbidities rate and BMI were detected to be higher in Group 1 with IIEF-EF score ≤10 and EHS <2. But contrary to age and rate of vascular comorbidities (p=0.035, p=0.049 respectively), higher BMI was detected to be statistically insignificant (p=0.093). Duration of erection, IIEF-EF score and number of cases with priapism were significantly higher in Group 2 with IIEF-EF score >10 and EHS ≥2 (p<0.001, p=0.027, p=0.049 respectively). Conclusion High IIEF-EF and EHS scores, younger ages and lower rates of vascular comorbidities in patients from whom PDU was demanded increase the prevalence of priapism. PMID:29201505

  20. Is there a relation between priapism occurring after penile doppler ultrasonography and international erectile function index score and erection hardness score levels?

    PubMed

    Sönmez, Mehmet Giray; Öztürk, Ahmet

    2017-12-01

    The relation between Erection Hardness Score (EHS) and The International Erectile Function Index (IIEF) Questionnaire- Erectile Function Domain Score (IIEF-EF score) used in erectile dysfunction (ED) evaluation and the prevalence of priapism after penile Doppler ultrasonography (PDU) was examined in this study. A total of 62 patients who had PDU were included in the study. Patients were divided into two groups; there were 33 patients in IIEF-EF score ≤10, EHS <2 group (Group 1) and 29 patients in IIEF-EF score >10, EHS ≥2 group (Group 2). The two groups separated according to their scores were compared for age, body mass index (BMI), prevalence of priapism, vascular comorbidities and duration of erection. When compared to Group 2, median age, rate of vascular comorbidities rate and BMI were detected to be higher in Group 1 with IIEF-EF score ≤10 and EHS <2. But contrary to age and rate of vascular comorbidities (p=0.035, p=0.049 respectively), higher BMI was detected to be statistically insignificant (p=0.093). Duration of erection, IIEF-EF score and number of cases with priapism were significantly higher in Group 2 with IIEF-EF score >10 and EHS ≥2 (p<0.001, p=0.027, p=0.049 respectively). High IIEF-EF and EHS scores, younger ages and lower rates of vascular comorbidities in patients from whom PDU was demanded increase the prevalence of priapism.

  1. Same But Different: FIM Summary Scores May Mask Variability in Physical Functioning Profiles.

    PubMed

    Fisher, Steve R; Middleton, Addie; Graham, James E; Ottenbacher, Kenneth J

    2018-02-08

    To examine how similar summary scores of physical functioning using the FIM can represent different patient clinical profiles. Retrospective cohort study. Inpatient rehabilitation facilities. Medicare fee-for-service beneficiaries (N=765,441) discharged from inpatient rehabilitation. Not applicable. We used patients' scores on items of the FIM to quantify their level of independence on both self-care and mobility domains. We then identified patients as requiring "no physical assistance" at discharge from inpatient rehabilitation by using a rule and score-based approach. In those patients with FIM self-care and mobility summary scores suggesting no physical assistance needed, we found that physical assistance was in fact needed frequently in bathroom-related activities (eg, continence, toilet and tub transfers, hygiene, clothes management) and with stairs. It was not uncommon for actual performance to be lower than what may be suggested by a summary score of those domains. Further research is needed to create clinically meaningful descriptions of summary scores from combined performances on individual items of physical functioning. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  2. 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

  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

    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

  4. Accurate analytical modeling of junctionless DG-MOSFET by green's function approach

    NASA Astrophysics Data System (ADS)

    Nandi, Ashutosh; Pandey, Nilesh

    2017-11-01

    An accurate analytical model of Junctionless double gate MOSFET (JL-DG-MOSFET) in the subthreshold regime of operation is developed in this work using green's function approach. The approach considers 2-D mixed boundary conditions and multi-zone techniques to provide an exact analytical solution to 2-D Poisson's equation. The Fourier coefficients are calculated correctly to derive the potential equations that are further used to model the channel current and subthreshold slope of the device. The threshold voltage roll-off is computed from parallel shifts of Ids-Vgs curves between the long channel and short-channel devices. It is observed that the green's function approach of solving 2-D Poisson's equation in both oxide and silicon region can accurately predict channel potential, subthreshold current (Isub), threshold voltage (Vt) roll-off and subthreshold slope (SS) of both long & short channel devices designed with different doping concentrations and higher as well as lower tsi/tox ratio. All the analytical model results are verified through comparisons with TCAD Sentaurus simulation results. It is observed that the model matches quite well with TCAD device simulations.

  5. Late-Onset Alzheimer's Disease Polygenic Risk Profile Score Predicts Hippocampal Function.

    PubMed

    Xiao, Ena; Chen, Qiang; Goldman, Aaron L; Tan, Hao Yang; Healy, Kaitlin; Zoltick, Brad; Das, Saumitra; Kolachana, Bhaskar; Callicott, Joseph H; Dickinson, Dwight; Berman, Karen F; Weinberger, Daniel R; Mattay, Venkata S

    2017-11-01

    We explored the cumulative effect of several late-onset Alzheimer's disease (LOAD) risk loci using a polygenic risk profile score (RPS) approach on measures of hippocampal function, cognition, and brain morphometry. In a sample of 231 healthy control subjects (19-55 years of age), we used an RPS to study the effect of several LOAD risk loci reported in a recent meta-analysis on hippocampal function (determined by its engagement with blood oxygen level-dependent functional magnetic resonance imaging during episodic memory) and several cognitive metrics. We also studied effects on brain morphometry in an overlapping sample of 280 subjects. There was almost no significant association of LOAD-RPS with cognitive or morphometric measures. However, there was a significant negative relationship between LOAD-RPS and hippocampal function (familywise error [small volume correction-hippocampal region of interest] p < .05). There were also similar associations for risk score based on APOE haplotype, and for a combined LOAD-RPS + APOE haplotype risk profile score (p < .05 familywise error [small volume correction-hippocampal region of interest]). Of the 29 individual single nucleotide polymorphisms used in calculating LOAD-RPS, variants in CLU, PICALM, BCL3, PVRL2, and RELB showed strong effects (p < .05 familywise error [small volume correction-hippocampal region of interest]) on hippocampal function, though none survived further correction for the number of single nucleotide polymorphisms tested. There is a cumulative deleterious effect of LOAD risk genes on hippocampal function even in healthy volunteers. The effect of LOAD-RPS on hippocampal function in the relative absence of any effect on cognitive and morphometric measures is consistent with the reported temporal characteristics of LOAD biomarkers with the earlier manifestation of synaptic dysfunction before morphometric and cognitive changes. Copyright © 2017 Society of Biological Psychiatry. All rights reserved.

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

    PubMed

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

    2009-01-01

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

  7. Accurate evaluation and analysis of functional genomics data and methods

    PubMed Central

    Greene, Casey S.; Troyanskaya, Olga G.

    2016-01-01

    The development of technology capable of inexpensively performing large-scale measurements of biological systems has generated a wealth of data. Integrative analysis of these data holds the promise of uncovering gene function, regulation, and, in the longer run, understanding complex disease. However, their analysis has proved very challenging, as it is difficult to quickly and effectively assess the relevance and accuracy of these data for individual biological questions. Here, we identify biases that present challenges for the assessment of functional genomics data and methods. We then discuss evaluation methods that, taken together, begin to address these issues. We also argue that the funding of systematic data-driven experiments and of high-quality curation efforts will further improve evaluation metrics so that they more-accurately assess functional genomics data and methods. Such metrics will allow researchers in the field of functional genomics to continue to answer important biological questions in a data-driven manner. PMID:22268703

  8. A New Glaucoma Severity Score Combining Structural and Functional Defects.

    PubMed

    Wachtl, J; Töteberg-Harms, M; Frimmel, S; Kniestedt, C

    2017-04-01

    Background In order to assess glaucoma severity and to compare the success of surgical and medical therapy and study outcomes, an objective and independent staging tool is necessary. A combination of information from both structural and functional testing is probably the best approach to stage glaucomatous damage. There has been no universally accepted standard for glaucoma staging. The aim of this study was to develop a Glaucoma Severity Score (GSS) for objective assessment of a patient's glaucoma severity, combining both functional and structural information. Materials and methods The Glaucoma Severity Score includes the following 3 criteria: superior and inferior Retinal Nerve Fibre Layer (RNFL) thickness, perimetric mean defect (MD), and agreement of anatomical and perimetric defects, as assessed by two glaucoma specialists. The specialists defined a staging tool for each of the 3 criteria in a consensus process, assigning specific characteristics to a scale value between 0 and 2 or 0 and 3, respectively. The GSS ranges between 0 and 10 points. In a prospective observational study, the data of 112 glaucoma patients were assessed independently by the two specialists according to this staging tool. Results The GSS was applied to 112 eyes and patients (59.8 % female) with a mean age of 66.3 ± 13.1 years. Mean GSS was 4.73 points. Cohen's kappa coefficient was determined to measure inter-rater agreement between glaucoma specialists for the third criterion. With κ = 0.83, the agreement was very good. Thus, all 3 criteria of the GSS may be regarded as objective. Conclusions The Glaucoma Severity Score is an objective tool, combining both structural and functional characteristics, and permitting comparison of different patients, populations and studies. The Glaucoma Severity Score has proven effective in the objective assessment of 112 glaucoma patients and is relatively user-friendly in clinical practice. A comparative study of the GSS with the results of

  9. Scoring systems for the Clock Drawing Test: A historical review

    PubMed Central

    Spenciere, Bárbara; Alves, Heloisa; Charchat-Fichman, Helenice

    2017-01-01

    The Clock Drawing Test (CDT) is a simple neuropsychological screening instrument that is well accepted by patients and has solid psychometric properties. Several different CDT scoring methods have been developed, but no consensus has been reached regarding which scoring method is the most accurate. This article reviews the literature on these scoring systems and the changes they have undergone over the years. Historically, different types of scoring systems emerged. Initially, the focus was on screening for dementia, and the methods were both quantitative and semi-quantitative. Later, the need for an early diagnosis called for a scoring system that can detect subtle errors, especially those related to executive function. Therefore, qualitative analyses began to be used for both differential and early diagnoses of dementia. A widely used qualitative method was proposed by Rouleau et al. (1992). Tracing the historical path of these scoring methods is important for developing additional scoring systems and furthering dementia prevention research. PMID:29213488

  10. Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function.

    PubMed

    Lizunov, A Y; Gonchar, A L; Zaitseva, N I; Zosimov, V V

    2015-10-26

    We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

  11. HIV-associated cognitive disorders in perinatally infected children and adolescents: a novel composite cognitive domains score.

    PubMed

    Phillips, Nicole J; Hoare, Jacqueline; Stein, Dan J; Myer, Landon; Zar, Heather J; Thomas, Kevin G F

    2018-04-22

    Accurate assessment of HIV-associated cognitive disorders in perinatally infected children and adolescents is challenging. Assessments of general intellectual functioning, or global cognition, may not provide information regarding domain-specific strengths and weaknesses, and may therefore fail to detect, impaired trajectories of development within particular cognitive domains. We compare the efficacy of global cognitive scores to that of composite cognitive domain scores in detecting cognitive disorders in a sample of perinatally HIV-infected children, and a demographically matched HIV negative control group, drawn from the Cape Town Adolescent Antiretroviral Cohort (CTAAC) study. All children were administered a comprehensive neuropsychological test battery. Using data from that test battery, we created ten separate composite cognitive domains: general intellectual functioning, attention, working memory, visual memory, verbal memory, language, visual spatial ability, motor coordination, processing speed and executive function. Within each domain, each test bore a high level of association with each of the other tests in that domain (Cronbach's α ≥ .70 for all domains). We found that composite domain scores calculated on whole-sample data were significantly higher than those calculated using control-sample data. Our comparison of a global cognitive score to composite domain scores suggested that the latter provided more detailed information (regarding strengths, weaknesses, areas of impairment), and when compared to global scores, were more sensitive in detecting HIV-associated cognitive disorders, and were able to distinguish HIV-infected patients from uninfected controls. Hence, we recommend using this method of composite cognitive domains scores, rather than global aggregate scores, when assessing cognitive function in paediatric HIV. This method provides a convenient and relatively accurate assessment that might help with cross-cultural and cross

  12. 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.

  13. 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.

  14. Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints.

    PubMed

    Liu, Jie; Su, Minyi; Liu, Zhihai; Li, Jie; Li, Yan; Wang, Renxiao

    2017-07-18

    In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively. In this study, we have developed an upgraded version, i.e. KGS2, by employing 3D protein-ligand interaction fingerprints in reference selection. KGS2 was evaluated in combination with four scoring functions (X-Score, ChemPLP, ASP, and GoldScore) on five drug targets (HIV-1 protease, carbonic anhydrase 2, beta-secretase 1, beta-trypsin, and checkpoint kinase 1). In the in situ scoring test, considerable improvements were observed in most cases after application of KGS2. Besides, the performance of KGS2 was always better than KGS in all cases. In the more challenging molecular docking test, application of KGS2 also led to improved structure-activity relationship in some cases. KGS2 can be applied as a convenient "add-on" to current scoring functions without the need to re-engineer them, and its application is not limited to certain target proteins as customized scoring functions. As an interpolation method, its accuracy in principle can be improved further with the increasing knowledge of protein-ligand complex structures and binding affinity data. We expect that KGS2 will become a practical tool for enhancing the performance of current scoring functions in binding affinity prediction. The KGS2 software is available upon contacting the authors.

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

    PubMed Central

    Wu, Chia-Chou; Lin, Che

    2015-01-01

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

  16. Extension of the lod score: the mod score.

    PubMed

    Clerget-Darpoux, F

    2001-01-01

    In 1955 Morton proposed the lod score method both for testing linkage between loci and for estimating the recombination fraction between them. If a disease is controlled by a gene at one of these loci, the lod score computation requires the prior specification of an underlying model that assigns the probabilities of genotypes from the observed phenotypes. To address the case of linkage studies for diseases with unknown mode of inheritance, we suggested (Clerget-Darpoux et al., 1986) extending the lod score function to a so-called mod score function. In this function, the variables are both the recombination fraction and the disease model parameters. Maximizing the mod score function over all these parameters amounts to maximizing the probability of marker data conditional on the disease status. Under the absence of linkage, the mod score conforms to a chi-square distribution, with extra degrees of freedom in comparison to the lod score function (MacLean et al., 1993). The mod score is asymptotically maximum for the true disease model (Clerget-Darpoux and Bonaïti-Pellié, 1992; Hodge and Elston, 1994). Consequently, the power to detect linkage through mod score will be highest when the space of models where the maximization is performed includes the true model. On the other hand, one must avoid overparametrization of the model space. For example, when the approach is applied to affected sibpairs, only two constrained disease model parameters should be used (Knapp et al., 1994) for the mod score maximization. It is also important to emphasize the existence of a strong correlation between the disease gene location and the disease model. Consequently, there is poor resolution of the location of the susceptibility locus when the disease model at this locus is unknown. Of course, this is true regardless of the statistics used. The mod score may also be applied in a candidate gene strategy to model the potential effect of this gene in the disease. Since, however, it

  17. Functional Movement Screen: Pain versus composite score and injury risk.

    PubMed

    Alemany, Joseph A; Bushman, Timothy T; Grier, Tyson; Anderson, Morgan K; Canham-Chervak, Michelle; North, William J; Jones, Bruce H

    2017-11-01

    The Functional Movement Screen (FMS™) has been used as a screening tool to determine musculoskeletal injury risk using composite scores based on movement quality and/or pain. However, no direct comparisons between movement quality and pain have been quantified. Retrospective injury data analysis. Male Soldiers (n=2154, 25.0±1.3years; 26.2±.7kg/m 2 ) completed the FMS (scored from 0 points (pain) to 3 points (no pain and perfect movement quality)) with injury data over the following six months. The FMS is seven movements. Injury data were collected six months after FMS completion. Sensitivity, specificity, receiver operator characteristics and positive and negative predictive values were calculated for pain occurrence and low (≤14 points) composite score. Risk, risk ratios (RR) and 95% confidence intervals were calculated for injury risk. Pain was associated with slightly higher injury risk (RR=1.62) than a composite score of ≤14 points (RR=1.58). When comparing injury risk between those who scored a 1, 2 or 3 on each individual movement, no differences were found (except deep squat). However, Soldiers who experienced pain on any movement had a greater injury risk than those who scored 3 points for that movement (p<0.05). A progressive increase in the relative risk occurred as the number of movements in which pain occurrence increased, so did injury risk (p<0.01). Pain occurrence may be a stronger indicator of injury risk than a low composite score and provides a simpler method of evaluating injury risk compared to the full FMS. Published by Elsevier Ltd.

  18. Optimal protein library design using recombination or point mutations based on sequence-based scoring functions.

    PubMed

    Pantazes, Robert J; Saraf, Manish C; Maranas, Costas D

    2007-08-01

    In this paper, we introduce and test two new sequence-based protein scoring systems (i.e. S1, S2) for assessing the likelihood that a given protein hybrid will be functional. By binning together amino acids with similar properties (i.e. volume, hydrophobicity and charge) the scoring systems S1 and S2 allow for the quantification of the severity of mismatched interactions in the hybrids. The S2 scoring system is found to be able to significantly functionally enrich a cytochrome P450 library over other scoring methods. Given this scoring base, we subsequently constructed two separate optimization formulations (i.e. OPTCOMB and OPTOLIGO) for optimally designing protein combinatorial libraries involving recombination or mutations, respectively. Notably, two separate versions of OPTCOMB are generated (i.e. model M1, M2) with the latter allowing for position-dependent parental fragment skipping. Computational benchmarking results demonstrate the efficacy of models OPTCOMB and OPTOLIGO to generate high scoring libraries of a prespecified size.

  19. Assessment of Musculoskeletal Function and its Correlation with Radiological Joint Score in Children with Hemophilia A.

    PubMed

    Gupta, Samriti; Garg, Kapil; Singh, Jagdish

    2015-12-01

    To evaluate the functional independence of children with hemophilia A and its correlation to radiological joint score. The present cross sectional study was conducted at SPMCHI, SMS Medical College, Jaipur, India. Children in the age group of 4-18 y affected with severe, moderate and mild hemophilia A and with a history of hemarthrosis who attended the OPD, emergency or got admitted in wards of SPMCHI, SMS Medical College were examined. Musculoskeletal function was measured in 98 patients using Functional Independence Score in Hemophilia (FISH) and index joints (joints most commonly affected with repeated bleeding) were assessed radiologically with plain X rays using Pettersson score. The mean FISH score was 28.07 ± 3.90 (range 17-32) with squatting, running and step climbing as most affected tasks. The mean Pettersson score was 3.8 ± 3.2. A significant correlation was found between mean Pettersson score and FISH (r = -0.875, P < 0.001) with knee and elbow having r = -0.810 and -0.861 respectively, but not in case of ankle with r = -0.420 (P 0.174). The FISH and radiological joint (Pettersson's) scores may be extremely useful in the clinical practice in the absence of magnetic resonance imaging (MRI), which is considered very sensitive to detect early joint damage, but at a cost that makes it relatively inaccessible. FISH seems to be a reliable tool for assessment of functional independence in patients with hemophilia A.

  20. 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.

  1. 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

  2. Advanced clinical interpretation of the Delis-Kaplan Executive Function System: multivariate base rates of low scores.

    PubMed

    Karr, Justin E; Garcia-Barrera, Mauricio A; Holdnack, James A; Iverson, Grant L

    2018-01-01

    Multivariate base rates allow for the simultaneous statistical interpretation of multiple test scores, quantifying the normal frequency of low scores on a test battery. This study provides multivariate base rates for the Delis-Kaplan Executive Function System (D-KEFS). The D-KEFS consists of 9 tests with 16 Total Achievement scores (i.e. primary indicators of executive function ability). Stratified by education and intelligence, multivariate base rates were derived for the full D-KEFS and an abbreviated four-test battery (i.e. Trail Making, Color-Word Interference, Verbal Fluency, and Tower Test) using the adult portion of the normative sample (ages 16-89). Multivariate base rates are provided for the full and four-test D-KEFS batteries, calculated using five low score cutoffs (i.e. ≤25th, 16th, 9th, 5th, and 2nd percentiles). Low scores occurred commonly among the D-KEFS normative sample, with 82.6 and 71.8% of participants obtaining at least one score ≤16th percentile for the full and four-test batteries, respectively. Intelligence and education were inversely related to low score frequency. The base rates provided herein allow clinicians to interpret multiple D-KEFS scores simultaneously for the full D-KEFS and an abbreviated battery of commonly administered tests. The use of these base rates will support clinicians when differentiating between normal variations in cognitive performance and true executive function deficits.

  3. The mortality risk score and the ADG score: two points-based scoring systems for the Johns Hopkins aggregated diagnosis groups to predict mortality in a general adult population cohort in Ontario, Canada.

    PubMed

    Austin, Peter C; Walraven, Carl van

    2011-10-01

    Logistic regression models that incorporated age, sex, and indicator variables for the Johns Hopkins' Aggregated Diagnosis Groups (ADGs) categories have been shown to accurately predict all-cause mortality in adults. To develop 2 different point-scoring systems using the ADGs. The Mortality Risk Score (MRS) collapses age, sex, and the ADGs to a single summary score that predicts the annual risk of all-cause death in adults. The ADG Score derives weights for the individual ADG diagnosis groups. : Retrospective cohort constructed using population-based administrative data. All 10,498,413 residents of Ontario, Canada, between the age of 20 and 100 years who were alive on their birthday in 2007, participated in this study. Participants were randomly divided into derivation and validation samples. : Death within 1 year. In the derivation cohort, the MRS ranged from -21 to 139 (median value 29, IQR 17 to 44). In the validation group, a logistic regression model with the MRS as the sole predictor significantly predicted the risk of 1-year mortality with a c-statistic of 0.917. A regression model with age, sex, and the ADG Score has similar performance. Both methods accurately predicted the risk of 1-year mortality across the 20 vigintiles of risk. The MRS combined values for a person's age, sex, and the John Hopkins ADGs to accurately predict 1-year mortality in adults. The ADG Score is a weighted score representing the presence or absence of the 32 ADG diagnosis groups. These scores will facilitate health services researchers conducting risk adjustment using administrative health care databases.

  4. Chi-square-based scoring function for categorization of MEDLINE citations.

    PubMed

    Kastrin, A; Peterlin, B; Hristovski, D

    2010-01-01

    Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine-learning algorithms (support vector machines, decision trees, naïve Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine-learning algorithms. We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.

  5. Branch and bound algorithm for accurate estimation of analytical isotropic bidirectional reflectance distribution function models.

    PubMed

    Yu, Chanki; Lee, Sang Wook

    2016-05-20

    We present a reliable and accurate global optimization framework for estimating parameters of isotropic analytical bidirectional reflectance distribution function (BRDF) models. This approach is based on a branch and bound strategy with linear programming and interval analysis. Conventional local optimization is often very inefficient for BRDF estimation since its fitting quality is highly dependent on initial guesses due to the nonlinearity of analytical BRDF models. The algorithm presented in this paper employs L1-norm error minimization to estimate BRDF parameters in a globally optimal way and interval arithmetic to derive our feasibility problem and lower bounding function. Our method is developed for the Cook-Torrance model but with several normal distribution functions such as the Beckmann, Berry, and GGX functions. Experiments have been carried out to validate the presented method using 100 isotropic materials from the MERL BRDF database, and our experimental results demonstrate that the L1-norm minimization provides a more accurate and reliable solution than the L2-norm minimization.

  6. 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.…

  7. Understanding the Relationship Between 3-Month and 2-Year Pain and Function Scores After Total Knee Arthroplasty for Osteoarthritis.

    PubMed

    Gandhi, Rajiv; Mahomed, Nizar N; Cram, Peter; Perruccio, Anthony V

    2018-05-01

    Research to understand predictors of poor outcomes after total knee arthroplasty (TKA) has largely focused on presurgery factors. We examined whether pain and function 3-month postsurgery were predictive of longer-term outcomes ascertained 2 years after TKA. Western Ontario McMaster University Osteoarthritis Index pain and physical function scores (scaled 0-20 and 0-68; higher = worse) were recorded pre-TKA and 3, 12, and 24 months post-TKA. A sequential series of regression models was used to examine the relative contribution of baseline score and baseline to 3-month and 3 to 12-month change score to explaining variability (R 2 ) in 2-year pain and function scores, with consideration for presurgery covariates. Data from 560 patients were analyzed. Mean pain and function scores improved significantly presurgery to 2 years postsurgery; 10-4 and 33-16 (P < .001), respectively. Considerable variability in 2-year scores was observed. Overall, 80.3% and 79.9% of changes in pain and function scores over the 2 years occurred within the first 3 months. Change over these 3 months explained the greatest proportion of variability in 2-year scores, 16% and 23% for pain and function, respectively. The influences of these early changes were similar to those of baseline status. Changes in patient-reported pain and function occurring within the first 3 months post-TKA strongly determine pain and function status at 2 years. Research to identify pre-/intra-/early postoperative factors associated with change in this early postoperative period that may be amenable to modification or used to better inform education and decision-making is warranted. Copyright © 2017 Elsevier Inc. All rights reserved.

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

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

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

    2016-06-13

    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 vanmore » 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.« less

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

    PubMed

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

    2016-09-01

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

  10. Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening.

    PubMed

    Hsieh, Jui-Hua; Yin, Shuangye; Wang, Xiang S; Liu, Shubin; Dokholyan, Nikolay V; Tropsha, Alexander

    2012-01-23

    Poor performance of scoring functions is a well-known bottleneck in structure-based virtual screening (VS), which is most frequently manifested in the scoring functions' inability to discriminate between true ligands vs known nonbinders (therefore designated as binding decoys). This deficiency leads to a large number of false positive hits resulting from VS. We have hypothesized that filtering out or penalizing docking poses recognized as non-native (i.e., pose decoys) should improve the performance of VS in terms of improved identification of true binders. Using several concepts from the field of cheminformatics, we have developed a novel approach to identifying pose decoys from an ensemble of poses generated by computational docking procedures. We demonstrate that the use of target-specific pose (scoring) filter in combination with a physical force field-based scoring function (MedusaScore) leads to significant improvement of hit rates in VS studies for 12 of the 13 benchmark sets from the clustered version of the Database of Useful Decoys (DUD). This new hybrid scoring function outperforms several conventional structure-based scoring functions, including XSCORE::HMSCORE, ChemScore, PLP, and Chemgauss3, in 6 out of 13 data sets at early stage of VS (up 1% decoys of the screening database). We compare our hybrid method with several novel VS methods that were recently reported to have good performances on the same DUD data sets. We find that the retrieved ligands using our method are chemically more diverse in comparison with two ligand-based methods (FieldScreen and FLAP::LBX). We also compare our method with FLAP::RBLB, a high-performance VS method that also utilizes both the receptor and the cognate ligand structures. Interestingly, we find that the top ligands retrieved using our method are highly complementary to those retrieved using FLAP::RBLB, hinting effective directions for best VS applications. We suggest that this integrative VS approach combining

  11. The FOUR score and GCS as predictors of outcome after traumatic brain injury.

    PubMed

    McNett, Molly; Amato, Shelly; Gianakis, Anastasia; Grimm, Dawn; Philippbar, Sue Ann; Belle, Josie; Moran, Cristina

    2014-08-01

    The Glasgow Coma Scale (GCS) is a routine component of a neurological exam for critically ill traumatic brain injury (TBI) patients, yet has been criticized for not accurately depicting verbal status among intubated patients or including brain stem reflexes. Preliminary research on the Full Outline of UnResponsiveness (FOUR) Scale suggests it overcomes these limitations. Research is needed to determine correlations with patient outcomes. The aims of this study were to: (1) examine correlations between 24 and 72 h FOUR and GCS scores and functional/cognitive outcomes; (2) determine relationship between 24 and 72 h FOUR scores and mortality. Prospective cohort study. Data gathered on adult TBI patients at a Level I trauma center. FOUR scores assigned at 24, 72 h. Functional outcome measured by functional independence measure scores at rehabilitation discharge; cognitive status measured by Weschler Memory Scale scores 3 months post-injury. n = 136. Mean age 53.1. 72 h FOUR and GCS scores correlated with functional outcome (r s = 0.34, p = 0.05; r s = 0.39, p = 0.02), but not cognitive status. Receiver operating characteristic curves were comparable for FOUR and GCS at 24 and 72 h for functional status (24 h FOUR, GCS = 0.625, 0.602, respectively; 72 h FOUR, GCS = 0.640, 0.688), cognitive status (24 h FOUR, GCS = 0.703, 0.731; 72 h FOUR, GCS = 0.837, 0.674), and mortality (24 h FOUR, GCS = 0.913, 0.935; 72 h FOUR, GCS = 0.837, 0.884). FOUR is comparable to GCS in terms of predictive ability for functional status, cognitive outcome 3 months post-injury, and in-hospital mortality.

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

    PubMed

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

    2016-07-15

    Neuroimaging holds the promise that it may one day aid the clinical assessment. However, the vast majority of studies using resting-state functional magnetic resonance imaging (fMRI) have reported average differences between Parkinson's disease (PD) patients and healthy controls, which do not permit inferences at the level of individuals. This study was to develop a model for the prediction of PD illness severity ratings from individual fMRI brain scan. The resting-state fMRI scans were obtained from 84 patients with PD and the Unified Parkinson's Disease Rating Scale-III (UPDRS-III) scores were obtained before scanning. The RVR method was used to predict clinical scores (UPDRS-III) from fMRI scans. The application of RVR to whole-brain resting-state fMRI data allowed prediction of UPDRS-III scores with statistically significant accuracy (correlation=0.35, P-value=0.001; mean sum of squares=222.17, P-value=0.002). This prediction was informed strongly by negative weight areas including prefrontal lobe and medial occipital lobe, and positive weight areas including medial parietal lobe. It was suggested that fMRI scans contained sufficient information about neurobiological change in patients with PD to permit accurate prediction about illness severity, on an individual subject basis. Our results provided preliminary evidence, as proof-of-concept, to support that fMRI might be possible to be a clinically useful quantitative assessment aid in PD at individual level. This may enable clinicians to target those uncooperative patients and machines to replace human for a more efficient use of health care resources. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Application of prognostic scores in the STOPAH trial: Discriminant function is no longer the optimal scoring system in alcoholic hepatitis.

    PubMed

    Forrest, Ewan H; Atkinson, Stephen R; Richardson, Paul; Masson, Steven; Ryder, Stephen; Thursz, Mark R; Allison, Michael

    2018-03-01

    'Static' prognostic models in alcoholic hepatitis, using data from a single time point, include the discriminant function (DF), Glasgow alcoholic hepatitis score (GAHS), the age, serum bilirubin, international normalized ratio and serum creatinine (ABIC) score and the model of end-stage liver disease (MELD). 'Dynamic' scores, incorporating evolution of bilirubin at seven days, include the Lille score. The aim of this study was to assess these scores' performance in patients from the STOPAH trial. Predictive performance of scores was assessed by area under the receiver operating curve (AUC). The effect of different therapeutic strategies upon survival was assessed by Kaplan-Meier analysis and tested using the log-rank test. A total of 1,068 patients were studied. The AUCs for the DF were significantly lower than for MELD, ABIC and GAHS for both 28- and 90-day outcomes: 90-day values were 0.670, 0.704, 0.726 and 0.713, respectively. 'Dynamic' scores and change in 'static' scores by Day 7 had similar AUCs. Patients with consistently low 'static' scores had low 28-day mortalities that were not improved with prednisolone (MELD <25: 8.6%; ABIC <6.71: 6.6%; GAHS <9: 5.9%). In patients with high 'static' scores without gastrointestinal bleeding or sepsis, prednisolone reduced 28-day mortality (MELD: 22.2% vs. 28.9%, p = 0.13; ABIC 14.6% vs. 21%, p = 0.02; GAHS 21% vs. 29.3%, p = 0.04). Overall mortality from treating all patients with a DF ≥32 and Lille assessment (90-day mortality 26.8%) was greater than combining newer 'static' and 'dynamic' scores (90-day mortality: MELD/Lille 21.8%; ABIC/Lille 23.7%; GAHS/Lille 20.6%). MELD, ABIC and GAHS are superior to the DF in alcoholic hepatitis. Consistently low scores have a favourable outcome not improved with prednisolone. Combined baseline 'static' and Day 7 scores reduce the number of patients exposed to corticosteroids and improve 90-day outcome. Alcoholic hepatitis is a life-threatening condition. Several

  14. External Validation of the ASTRAL and DRAGON Scores for Prediction of Functional Outcome in Stroke.

    PubMed

    Cooray, Charith; Mazya, Michael; Bottai, Matteo; Dorado, Laura; Skoda, Ondrej; Toni, Danilo; Ford, Gary A; Wahlgren, Nils; Ahmed, Niaz

    2016-06-01

    ASTRAL (Acute Stroke Registry and Analysis of Lausanne) and DRAGON (includes dense middle cerebral artery sign, prestroke modified Rankin Scale score, age, glucose, onset to treatment, National Institutes of Health Stroke Scale score) are 2 recently developed scores for predicting functional outcome after acute stroke in unselected acute ischemic stroke patients and in patients treated with intravenous thrombolysis, respectively. We aimed to perform external validation of these scores to assess their predictive performance in the large multicentre Safe Implementation of Thrombolysis in Stroke-International Stroke Thrombolysis Register. We calculated the ASTRAL and DRAGON scores in 36 131 and 33 716 patients, respectively, registered in Safe Implementation of Thrombolysis in Stroke-International Stroke Thrombolysis Register between 2003 and 2013. The proportion of patients with 3-month modified Rankin Scale scores of 3 to 6 was observed for each score point and compared with the predicted proportion according to the risk scores. Calibration was assessed using calibration plots, and predictive performance was assessed using area under the curve of the receiver operating characteristic. Multivariate logistic regression coefficients for the variables in the 2 scores were compared with the original derivation cohorts. The ASTRAL showed an area under the curve of 0.790 (95% confidence interval, 0.786-0.795) and the DRAGON an area under the curve of 0.774 (95% confidence interval, 0.769-0.779). All ASTRAL parameters except range of visual fields and all DRAGON parameters were significantly associated with functional outcome in multivariate analysis. The ASTRAL and DRAGON scores show an acceptable predictive performance. ASTRAL does not require imaging-data and therefore may have an advantage for the use in prehospital patient assessment. Prospective studies of both scores evaluating the impact of their use on patient outcomes after intravenous thrombolysis and

  15. A combined pulmonary function and emphysema score prognostic index for staging in Chronic Obstructive Pulmonary Disease.

    PubMed

    Boutou, Afroditi K; Nair, Arjun; Douraghi-Zadeh, Dariush; Sandhu, Ranbir; Hansell, David M; Wells, Athol U; Polkey, Michael I; Hopkinson, Nicholas S

    2014-01-01

    Chronic Obstructive Pulmonary Disease (COPD) is characterized by high morbidity and mortality. Lung computed tomography parameters, individually or as part of a composite index, may provide more prognostic information than pulmonary function tests alone. To investigate the prognostic value of emphysema score and pulmonary artery measurements compared with lung function parameters in COPD and construct a prognostic index using a contingent staging approach. Predictors of mortality were assessed in COPD outpatients whose lung computed tomography, spirometry, lung volumes and gas transfer data were collected prospectively in a clinical database. Univariate and multivariate Cox proportional hazard analysis models with bootstrap techniques were used. 169 patients were included (59.8% male, 61.1 years old; Forced Expiratory Volume in 1 second % predicted: 40.5±19.2). 20.1% died; mean survival was 115.4 months. Age (HR = 1.098, 95% Cl = 1.04-1.252) and emphysema score (HR = 1.034, 95% CI = 1.007-1.07) were the only independent predictors of mortality. Pulmonary artery dimensions were not associated with survival. An emphysema score of 55% was chosen as the optimal threshold and 30% and 65% as suboptimals. Where emphysema score was between 30% and 65% (intermediate risk) the optimal lung volume threshold, a functional residual capacity of 210% predicted, was applied. This contingent staging approach separated patients with an intermediate risk based on emphysema score alone into high risk (Functional Residual Capacity ≥210% predicted) or low risk (Functional Residual Capacity <210% predicted). This approach was more discriminatory for survival (HR = 3.123; 95% CI = 1.094-10.412) than either individual component alone. Although to an extent limited by the small sample size, this preliminary study indicates that the composite Emphysema score-Functional Residual Capacity index might provide a better separation of high and low risk patients with COPD

  16. Cardiovascular Disease Risk Score: Results from the Filipino-American Women Cardiovascular Study.

    PubMed

    Ancheta, Irma B; Battie, Cynthia A; Volgman, Annabelle S; Ancheta, Christine V; Palaniappan, Latha

    2017-02-01

    Although cardiovascular disease (CVD) is a leading cause of morbidity and mortality of Filipino-Americans, conventional CVD risk calculators may not be accurate for this population. CVD risk scores of a group of Filipino-American women (FAW) were measured using the major risk calculators. Secondly, the sensitivity of the various calculators to obesity was determined. This is a cross-sectional descriptive study that enrolled 40-65-year-old FAW (n = 236), during a community-based health screening study. Ten-year CVD risk was calculated using the Framingham Risk Score (FRS), Reynolds Risk Score (RRS), and Atherosclerotic Cardiovascular Disease (ASCVD) calculators. The 30-year risk FRS and the lifetime ASCVD calculators were also determined. Levels of predicted CVD risk varied as a function of the calculator. The 10-year ASCVD calculator classified 12 % of participants with ≥10 % risk, but the 10-year FRS and RRS calculators classified all participants with ≤10 % risk. The 30-year "Hard" Lipid and BMI FRS calculators classified 32 and 43 % of participants with high (≥20 %) risk, respectively, while 95 % of participants were classified with ≥20 % risk by the lifetime ASCVD calculator. The percent of participants with elevated CVD risk increased as a function of waist circumference for most risk score calculators. Differences in risk score as a function of the risk score calculator indicate the need for outcome studies in this population. Increased waist circumference was associated with increased CVD risk scores underscoring the need for obesity control as a primary prevention of CVD in FAW.

  17. A Factor Analysis of Functional Independence and Functional Assessment Measure Scores Among Focal and Diffuse Brain Injury Patients: The Importance of Bifactor Models.

    PubMed

    Gunn, Sarah; Burgess, Gerald H; Maltby, John

    2018-04-30

    To explore the factor structure of the UK Functional Independence Measure and Functional Assessment Measure (FIM+FAM) among focal and diffuse acquired brain injury patients. Criterion standard. A National Health Service acute acquired brain injury inpatient rehabilitation hospital. Referred sample of N=447 adults admitted for inpatient treatment following an acquired brain injury significant enough to justify intensive inpatient neurorehabilitation INTERVENTION: Not applicable. Functional Independence Measure and Functional Assessment Measure. Exploratory factor analysis suggested a 2-factor structure to FIM+FAM scores, among both focal-proximate and diffuse-proximate acquired brain injury aetiologies. Confirmatory factor analysis suggested a 3-factor bifactor structure presented the best fit of the FIM+FAM score data across both aetiologies. However, across both analyses, a convergence was found towards a general factor, demonstrated by high correlations between factors in the exploratory factor analysis, and by a general factor explaining the majority of the variance in scores on confirmatory factor analysis. Our findings suggested that although factors describing specific functional domains can be derived from FIM+FAM item scores, there is a convergence towards a single factor describing overall functioning. This single factor informs the specific group factors (eg, motor, psychosocial, and communication function) after brain injury. Further research into the comparative value of the general and group factors as evaluative/prognostic measures is indicated. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  18. Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

    PubMed Central

    2009-01-01

    Background A central task in contemporary biosciences is the identification of biological processes showing response in genome-wide differential gene expression experiments. Two types of analysis are common. Either, one generates an ordered list based on the differential expression values of the probed genes and examines the tail areas of the list for over-representation of various functional classes. Alternatively, one monitors the average differential expression level of genes belonging to a given functional class. So far these two types of method have not been combined. Results We introduce a scoring function, Gene Set Z-score (GSZ), for the analysis of functional class over-representation that combines two previous analysis methods. GSZ encompasses popular functions such as correlation, hypergeometric test, Max-Mean and Random Sets as limiting cases. GSZ is stable against changes in class size as well as across different positions of the analysed gene list in tests with randomized data. GSZ shows the best overall performance in a detailed comparison to popular functions using artificial data. Likewise, GSZ stands out in a cross-validation of methods using split real data. A comparison of empirical p-values further shows a strong difference in favour of GSZ, which clearly reports better p-values for top classes than the other methods. Furthermore, GSZ detects relevant biological themes that are missed by the other methods. These observations also hold when comparing GSZ with popular program packages. Conclusion GSZ and improved versions of earlier methods are a useful contribution to the analysis of differential gene expression. The methods and supplementary material are available from the website http://ekhidna.biocenter.helsinki.fi/users/petri/public/GSZ/GSZscore.html. PMID:19775443

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

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

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

    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

  20. 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

  1. A physical function test for use in the intensive care unit: validity, responsiveness, and predictive utility of the physical function ICU test (scored).

    PubMed

    Denehy, Linda; de Morton, Natalie A; Skinner, Elizabeth H; Edbrooke, Lara; Haines, Kimberley; Warrillow, Stephen; Berney, Sue

    2013-12-01

    Several tests have recently been developed to measure changes in patient strength and functional outcomes in the intensive care unit (ICU). The original Physical Function ICU Test (PFIT) demonstrates reliability and sensitivity. The aims of this study were to further develop the original PFIT, to derive an interval score (the PFIT-s), and to test the clinimetric properties of the PFIT-s. A nested cohort study was conducted. One hundred forty-four and 116 participants performed the PFIT at ICU admission and discharge, respectively. Original test components were modified using principal component analysis. Rasch analysis examined the unidimensionality of the PFIT, and an interval score was derived. Correlations tested validity, and multiple regression analyses investigated predictive ability. Responsiveness was assessed using the effect size index (ESI), and the minimal clinically important difference (MCID) was calculated. The shoulder lift component was removed. Unidimensionality of combined admission and discharge PFIT-s scores was confirmed. The PFIT-s displayed moderate convergent validity with the Timed "Up & Go" Test (r=-.60), the Six-Minute Walk Test (r=.41), and the Medical Research Council (MRC) sum score (rho=.49). The ESI of the PFIT-s was 0.82, and the MCID was 1.5 points (interval scale range=0-10). A higher admission PFIT-s score was predictive of: an MRC score of ≥48, increased likelihood of discharge home, reduced likelihood of discharge to inpatient rehabilitation, and reduced acute care hospital length of stay. Scoring of sit-to-stand assistance required is subjective, and cadence cutpoints used may not be generalizable. The PFIT-s is a safe and inexpensive test of physical function with high clinical utility. It is valid, responsive to change, and predictive of key outcomes. It is recommended that the PFIT-s be adopted to test physical function in the ICU.

  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. 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

  4. The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

    PubMed Central

    Xu, Xin; Goddard, William A.

    2004-01-01

    We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee–Yang–Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA. PMID:14981235

  5. Accurate donor electron wave functions from a multivalley effective mass theory.

    NASA Astrophysics Data System (ADS)

    Pendo, Luke; Hu, Xuedong

    Multivalley effective mass (MEM) theories combine physical intuition with a marginal need for computational resources, but they tend to be insensitive to variations in the wavefunction. However, recent papers suggest full Bloch functions and suitable central cell donor potential corrections are essential to replicating qualitative and quantitative features of the wavefunction. In this talk, we consider a variational MEM method that can accurately predict both spectrum and wavefunction of isolated phosphorus donors. As per Gamble et. al, we employ a truncated series representation of the Bloch function with a tetrahedrally symmetric central cell correction. We use a dynamic dielectric constant, a feature commonly seen in tight-binding methods. Uniquely, we use a freely extensible basis of either all Slater- or all Gaussian-type functions. With a large basis able to capture the influence of higher energy eigenstates, this method is well positioned to consider the influence of external perturbations, such as electric field or applied strain, on the charge density. This work is supported by the US Army Research Office (W911NF1210609).

  6. Correlation of the VEMP score, ambulation and upper extremity function in clinically isolated syndrome.

    PubMed

    Crnošija, Luka; Krbot Skorić, Magdalena; Gabelić, Tereza; Adamec, Ivan; Brinar, Vesna; Habek, Mario

    2015-12-15

    To investigate the correlation of the vestibular evoked myogenic potential (VEMP) score with Timed 25-Foot Walk (T25FW), 9-Hole Peg Test (9HPT), Paced Auditory Serial Addition Test (PASAT) and EDSS in patients with multiple sclerosis (MS). This prospective, cross sectional study included 52 patients with clinically isolated syndrome (CIS). Cervical VEMP (cVEMP) and ocular VEMP (oVEMP), analyzed in the form of the cVEMP, oVEMP and VEMP scores, T25FW, 9HPT, PASAT and Expanded Disability Status Scale (EDSS) were performed. The only predictor of walking impairment in this study was general disability as measured by the EDSS, after controlling for age, gender, PASAT and EDSS the effect of VEMP score was non-significant (p=0.419). 9HPT of the dominant hand did not correlate with the oVEMP score (rs=0.258, p=0.065), however after controlling for age, gender, PASAT and EDSS, the effect of the oVEMP score on 9HPT of the dominant hand was statistically significant (p=0.017). After controlling for age, gender and oVEMP score, the effect of the PASAT on 9HPT variable for the non-dominant hand was statistically significant (p=0.001). We found possible effects of brainstem dysfunction on walking impairment, however they were not seen after correction for EDSS and cognitive dysfunction. On the other hand, dominant hand function seems to be influenced by upper brainstem dysfunction measured with oVEMP, while cognitive dysfunction is related to non-dominant hand function. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Correlation between radiographic parameters and functional scores in degenerative lumbar and thoracolumbar scoliosis.

    PubMed

    Simon, J; Longis, P-M; Passuti, N

    2017-04-01

    Adult scoliosis is a condition in which the spinal deformity occurs because of degeneration. Although various studies have agreed on the importance of restoring the sagittal balance, few have evaluated the relationship between functional scores and radiological parameters. The primary objective of this retrospective study was to demonstrate the correlation between radiographic parameters and functional outcomes in adult patients with lumbar or thoracolumbar degenerative scoliosis. The secondary objective was to assess the long-term effects of posterolateral fusion for treating this deformity. This single-centre retrospective study included 47 patients over 50years of age who had degenerative lumbar scoliosis treated with an instrumented posterolateral fusion; the mean follow-up was 6.4years (range 2 to 20). Radiographic analysis of A/P and lateral full spine standing radiographs was carried out with the KEOPS software. Three pelvic parameters (pelvic tilt, pelvic incidence, sacral slope), two spinal parameters (lumbar lordosis and thoracic kyphosis) and three sagittal balance parameters (C7 sagittal tilt, C7 Barrey's ratio and spinosacral angle) were calculated. The functional outcomes were evaluated through three self-assessment questionnaires: Oswestry Disability Index, SRS-30 and SF-36. The correlation between clinical and radiographic parameters was calculated with Spearman's correlation test. There was a significant correlation between the SF-36 (PCS) and the following three sagittal parameters: sacral slope (r=-0.31453; P=0.04), lumbar lordosis (r=-0.30198; P=0.0491) and spinosacral angle (r=-0.311967; P=0.0366). The mean ODI score was 33.61, which corresponds to minimal to moderate disability. The mean physical (PCS) and mental (MCS) component summary scores of the SF-36 were 37.70 and 38.40, respectively. The mean SRS-30 score was 3.07. It is essential that the sagittal balance be restored when treating degenerative lumbar scoliosis to generate better

  8. 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

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

    PubMed

    Li, Yang; Yang, Jianyi

    2017-04-24

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

  10. Higher mobility scores in patients with cystic fibrosis are associated with better lung function.

    PubMed

    Thobani, Aneesha; Alvarez, Jessica A; Blair, Shaina; Jackson, Kaila; Gottlieb, Eric R; Walker, Seth; Tangpricha, Vin

    2015-01-01

    The purpose of this study was to determine whether mobility and physical activity were associated with lung function in adults with cystic fibrosis (CF). This was a prospective cohort observational study in an urban, academic, specialized care center. Participants were ambulatory, nonhospitalized adults with CF. Mobility was assessed monthly by the Life-Space Assessment (LSA) questionnaire and quarterly by pedometer. Lung function was assessed by spirometry. Twenty-seven subjects participated. Subjects recorded mean pedometer steps of 20,213 ± 11,331 over three days and FEV1% predicted of 77.48% ± 22.60% over one year. The LSA score at enrollment was correlated with initial pedometer steps (r = 0.42 and P = 0.03), and mean LSA score over one year was correlated with mean number of steps (r = 0.51 and P = 0.007). LSA mobility and pedometer scores were correlated with FEV1% predicted at enrollment and throughout the study. Mobility and physical activity measured by LSA questionnaire and pedometer are positively associated with lung function in adults with CF. This study confirms the importance of mobility and physical activity and supports the utility of a simple office-based questionnaire as a measure of mobility in adults with CF.

  11. Can computer assistance improve the clinical and functional scores in total knee arthroplasty?

    PubMed

    Hernández-Vaquero, Daniel; Suarez-Vazquez, Abelardo; Iglesias-Fernandez, Susana

    2011-12-01

    Surgical navigation in TKA facilitates better alignment; however, it is unclear whether improved alignment alters clinical evolution and midterm and long-term complication rates. We determined the alignment differences between patients with standard, manual, jig-based TKAs and patients with navigation-based TKAs, and whether any differences would modify function, implant survival, and/or complications. We retrospectively reviewed 97 patients (100 TKAs) undergoing TKAs for minimal preoperative deformities. Fifty TKAs were performed with an image-free surgical navigation system and the other 50 with a standard technique. We compared femoral angle (FA), tibial angle (TA), and femorotibial angle (FTA) and determined whether any differences altered clinical or functional scores, as measured by the Knee Society Score (KSS), or complications. Seventy-three patients (75 TKAs) had a minimum followup of 8 years (mean, 8.3 years; range, 8-9.1 years). All patients included in the surgical navigation group had a FTA between 177° and 182º. We found no differences in the KSS or implant survival between the two groups and no differences in complication rates, although more complications occurred in the standard technique group (seven compared with two in the surgical navigation group). In the midterm, we found no difference in functional and clinical scores or implant survival between TKAs performed with and without the assistance of a navigation system. Level II, therapeutic study. See the Guidelines online for a complete description of levels of evidence.

  12. Automated Quantitative Computed Tomography Versus Visual Computed Tomography Scoring in Idiopathic Pulmonary Fibrosis: Validation Against Pulmonary Function.

    PubMed

    Jacob, Joseph; Bartholmai, Brian J; Rajagopalan, Srinivasan; Kokosi, Maria; Nair, Arjun; Karwoski, Ronald; Raghunath, Sushravya M; Walsh, Simon L F; Wells, Athol U; Hansell, David M

    2016-09-01

    The aim of the study was to determine whether a novel computed tomography (CT) postprocessing software technique (CALIPER) is superior to visual CT scoring as judged by functional correlations in idiopathic pulmonary fibrosis (IPF). A total of 283 consecutive patients with IPF had CT parenchymal patterns evaluated quantitatively with CALIPER and by visual scoring. These 2 techniques were evaluated against: forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), diffusing capacity for carbon monoxide (DLco), carbon monoxide transfer coefficient (Kco), and a composite physiological index (CPI), with regard to extent of interstitial lung disease (ILD), extent of emphysema, and pulmonary vascular abnormalities. CALIPER-derived estimates of ILD extent demonstrated stronger univariate correlations than visual scores for most pulmonary function tests (PFTs): (FEV1: CALIPER R=0.29, visual R=0.18; FVC: CALIPER R=0.41, visual R=0.27; DLco: CALIPER R=0.31, visual R=0.35; CPI: CALIPER R=0.48, visual R=0.44). Correlations between CT measures of emphysema extent and PFTs were weak and did not differ significantly between CALIPER and visual scoring. Intriguingly, the pulmonary vessel volume provided similar correlations to total ILD extent scored by CALIPER for FVC, DLco, and CPI (FVC: R=0.45; DLco: R=0.34; CPI: R=0.53). CALIPER was superior to visual scoring as validated by functional correlations with PFTs. The pulmonary vessel volume, a novel CALIPER CT parameter with no visual scoring equivalent, has the potential to be a CT feature in the assessment of patients with IPF and requires further exploration.

  13. Decreased Visual Function Scores on a Low Luminance Questionnaire Is Associated with Impaired Dark Adaptation.

    PubMed

    Yazdanie, Mohammad; Alvarez, Jason; Agrón, Elvira; Wong, Wai T; Wiley, Henry E; Ferris, Frederick L; Chew, Emily Y; Cukras, Catherine

    2017-09-01

    We investigate whether responses on a Low Luminance Questionnaire (LLQ) in patients with a range of age-related macular degeneration (AMD) severity are associated with their performance on focal dark adaptation (DA) testing and with choroidal thickness. Cross-sectional, single-center, observational study. A total of 113 participants older than 50 years of age with a range of AMD severity. Participants answered the LLQ on the same day they underwent DA testing using a focal dark adaptometer measuring rod intercept time (RIT). We performed univariable and multivariable analyses of the LLQ scores and age, RIT, AMD severity, subfoveal choroidal thickness [SFCT], phakic status, and best-corrected visual acuity. The primary outcome of this study was the score on the 32-question LLQ. Each item in the LLQ is designated to 1 of 6 subscales describing functional problems in low luminance: driving, emotional distress, mobility, extreme lighting, peripheral vision, and general dim lighting. Scores were computed for each subscale, in addition to a weighted total mean score. Responses from 113 participants (mean age, 76.2±9.3 years; 58.4% were female) and 113 study eyes were analyzed. Univariable analysis demonstrated that lower scores on all LLQ subscales were correlated with prolonged DA testing (longer RIT) and decreased choroidal thickness. All associations were statistically significant except for the association of choroidal thickness and "peripheral vision." The strongest association was the LLQ subscale of driving with RIT (r =-0.97, P < 0.001). Multivariable analysis for each of the LLQ subscale outcomes, adjusted for age, included RIT, with total LLQ score, "driving," "extreme lighting," and "mobility" also including choroidal thickness. In all multivariable analyses, RIT had a stronger association than choroidal thickness. This cross-sectional analysis demonstrates associations of patient-reported functional deficits, as assessed on the LLQ, with both reduced DA and

  14. Scoring from Contests

    PubMed Central

    Penn, Elizabeth Maggie

    2014-01-01

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

  15. Maturational effect on Functional Movement Screen™ score in adolescent soccer players.

    PubMed

    Portas, Matthew David; Parkin, Guy; Roberts, James; Batterham, Alan Mark

    2016-10-01

    The effect of maturity on Functional Movement Screen (FMS) scores in elite, adolescent soccer players was examined. A cross-sectional observational study was completed. Participants were 1163 male English Football League soccer players (age 8-18 years). Players were mid-foundation phase (MF) (U9); late foundation phase (LF) (U10 and U11); early youth development phase (EYD) (U12 and U13); mid-youth development (MYD) phase (U14-U15); Late Youth Development Phase (LYD) (U16) and early professional development phase (EPD) (U18). Age from peak height velocity was estimated and players were categorized as pre- or post-peak height velocity (PHV). To analyse where differences in FMStotal score existed we separated the screen into FMSmove (3 movement tests); FMSflex (2 mobility tests) and FMSstab (2 stability tests). FMStotal median score ranged from 11 at MF to 14 for EPD. There was a substantial increase (10%) in those able to achieve a score of ≥14 on FMStotal in those who were post-PHV compared to pre-PHV. This was explained by a substantial increase in those achieving a score of ≥4 on FMSstab (21%). There was a substantial increase in the proportion of players who achieved the FMStotal threshold of ≥14 with an increase of 47.5 (41.4-53.6)% from the MF phase to the EPD phase due to improvements in FMSmove and FMSstab. PHV and maturity have substantial effects on FMS performance. FMS assessment appears to be invalid for very young players. Findings are relevant to those analyzing movement in soccer players. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  16. Using Multivariate Base Rates to Interpret Low Scores on an Abbreviated Battery of the Delis-Kaplan Executive Function System.

    PubMed

    Karr, Justin E; Garcia-Barrera, Mauricio A; Holdnack, James A; Iverson, Grant L

    2017-05-01

    Executive function consists of multiple cognitive processes that operate as an interactive system to produce volitional goal-oriented behavior, governed in large part by frontal microstructural and physiological networks. Identification of deficits in executive function in those with neurological or psychiatric conditions can be difficult because the normal variation in executive function test scores, in healthy adults when multiple tests are used, is largely unknown. This study addresses that gap in the literature by examining the prevalence of low scores on a brief battery of executive function tests. The sample consisted of 1,050 healthy individuals (ages 16-89) from the standardization sample for the Delis-Kaplan Executive Function System (D-KEFS). Seven individual test scores from the Trail Making Test, Color-Word Interference Test, and Verbal Fluency Test were analyzed. Low test scores, as defined by commonly used clinical cut-offs (i.e., ≤25th, 16th, 9th, 5th, and 2nd percentiles), occurred commonly among the adult portion of the D-KEFS normative sample (e.g., 62.8% of the sample had one or more scores ≤16th percentile, 36.1% had one or more scores ≤5th percentile), and the prevalence of low scores increased with lower intelligence and fewer years of education. The multivariate base rates (BR) in this article allow clinicians to understand the normal frequency of low scores in the general population. By use of these BRs, clinicians and researchers can improve the accuracy with which they identify executive dysfunction in clinical groups, such as those with traumatic brain injury or neurodegenerative diseases. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  17. Measurement of hepatic functional mass by means of 13C-methacetin and 13C-phenylalanine breath tests in chronic liver disease: Comparison with Child-Pugh score and serum bile acid levels

    PubMed Central

    Festi, D.; Capodicasa, S.; Sandri, L.; Colaiocco-Ferrante, L.; Staniscia, T.; Vitacolonna, E.; Vestito, A.; Simoni, P.; Mazzella, G.; Portincasa, P.; Roda, E.; Colecchia, A.

    2005-01-01

    AIM: To evaluate and compare the clinical usefulness of 13C-phenylalanine and 13C-methacetin breath tests in quantitating functional hepatic mass in patients with chronic liver disease and to further compare these results with those of conventional tests, Child-Pugh score and serum bile acid levels. METHODS: One hundred and forty patients (50 HCV- related chronic hepatitis, 90 liver cirrhosis patients) and 40 matched healthy controls were studied. Both breath test and routine liver test, serum levels of cholic and chenodeoxycholic acid conjugates were evaluated. RESULTS: Methacetin breath test, expressed as 60 min cumulative percent of oxidation, discriminated the hepatic functional capacity not only between controls and liver disease patients, but also between different categories of chronic liver disease patients. Methacetin breath test was correlated with liver function tests and serum bile acids. Furthermore, methacetin breath test, as well as serum bile acids, were highly predictive of Child-Pugh scores. The diagnostic power of phenylalanine breath test was always less than that of methacetin breath test. CONCLUSION: Methacetin breath test represents a safe and accurate diagnostic tool in the evaluation of hepatic functional mass in chronic liver disease patients. PMID:15609414

  18. Fine-Tuning Cross-Battery Assessment Procedures: After Follow-Up Testing, Use All Valid Scores, Cohesive or Not

    ERIC Educational Resources Information Center

    Schneider, W. Joel; Roman, Zachary

    2018-01-01

    We used data simulations to test whether composites consisting of cohesive subtest scores are more accurate than composites consisting of divergent subtest scores. We demonstrate that when multivariate normality holds, divergent and cohesive scores are equally accurate. Furthermore, excluding divergent scores results in biased estimates of…

  19. Tracking functional status across the spinal cord injury lifespan: linking pediatric and adult patient-reported outcome scores.

    PubMed

    Tian, Feng; Ni, Pengsheng; Mulcahey, M J; Hambleton, Ronald K; Tulsky, David; Haley, Stephen M; Jette, Alan M

    2014-11-01

    To use item response theory (IRT) methods to link scores from 2 recently developed contemporary functional outcome measures, the adult Spinal Cord Injury-Functional Index (SCI-FI) and the Pedi SCI (both the parent version and the child version). Secondary data analysis of the physical functioning items of the adult SCI-FI and the Pedi SCI instruments. We used a nonequivalent group design with items common to both instruments and the Stocking-Lord method for the linking. Linking was conducted so that the adult SCI-FI and Pedi SCI scaled scores could be compared. Community. This study included a total sample of 1558 participants. Pedi SCI items were administered to a sample of children (n=381) with SCI aged 8 to 21 years, and of parents/caregivers (n=322) of children with SCI aged 4 to 21 years. Adult SCI-FI items were administered to a sample of adults (n=855) with SCI aged 18 to 92 years. Not applicable. Five scales common to both instruments were included in the analysis: Wheelchair, Daily Routine/Self-care, Daily Routine/Fine Motor, Ambulation, and General Mobility functioning. Confirmatory factor analysis and exploratory factor analysis results indicated that the 5 scales are unidimensional. A graded response model was used to calibrate the items. Misfitting items were identified and removed from the item banks. Items that function differently between the adult and child samples (ie, exhibit differential item functioning) were identified and removed from the common items used for linking. Domain scores from the Pedi SCI instruments were transformed onto the adult SCI-FI metric. This IRT linking allowed estimation of adult SCI-FI scale scores based on Pedi SCI scale scores and vice versa; therefore, it provides clinicians with a means of tracking long-term functional data for children with an SCI across their entire lifespan. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  20. DRAGON score predicts functional outcomes in acute ischemic stroke patients receiving both intravenous tissue plasminogen activator and endovascular therapy.

    PubMed

    Wang, Arthur; Pednekar, Noorie; Lehrer, Rachel; Todo, Akira; Sahni, Ramandeep; Marks, Stephen; Stiefel, Michael F

    2017-01-01

    The DRAGON score, which includes clinical and computed tomographic (CT) scan parameters, predicts functional outcomes in ischemic stroke patients treated with intravenous tissue plasminogen activator (IV tPA). We assessed the utility of the DRAGON score in predicting functional outcome in stroke patients receiving both IV tPA and endovascular therapy. A retrospective chart review of patients treated at our institution from February 2009 to October 2015 was conducted. All patients with computed tomography angiography (CTA) proven large vessel occlusions (LVO) who underwent intravenous thrombolysis and endovascular therapy were included. Baseline DRAGON scores and modified Rankin Score (mRS) at the time of hospital discharge was calculated. Good outcome was defined as mRS ≤3. Fifty-eight patients with LVO of the anterior circulation were studied. The mean DRAGON score of patients on admission was 5.3 (range, 3-8). All patients received IV tPA and endovascular therapy. Multivariate analysis demonstrated that DRAGON scores ≥7 was associated with higher mRS ( P < 0.006) and higher mortality ( P < 0.0001) compared with DRAGON scores ≤6. Patients with DRAGON scores of 7 and 8 on admission had a mortality rate of 3.8% and 40%, respectively. The DRAGON score can help predict better functional outcomes in ischemic stroke patients receiving both IV tPA and endovascular therapy. This data supports the use of the DRAGON score in selecting patients who could potentially benefit from more invasive therapies such as endovascular treatment. Larger prospective studies are warranted to further validate these results.

  1. A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

    PubMed

    Muegge, I; Martin, Y C

    1999-03-11

    A fast, simplified potential-based approach is presented that estimates the protein-ligand binding affinity based on the given 3D structure of a protein-ligand complex. This general, knowledge-based approach exploits structural information of known protein-ligand complexes extracted from the Brookhaven Protein Data Bank and converts it into distance-dependent Helmholtz free interaction energies of protein-ligand atom pairs (potentials of mean force, PMF). The definition of an appropriate reference state and the introduction of a correction term accounting for the volume taken by the ligand were found to be crucial for deriving the relevant interaction potentials that treat solvation and entropic contributions implicitly. A significant correlation between experimental binding affinities and computed score was found for sets of diverse protein-ligand complexes and for sets of different ligands bound to the same target. For 77 protein-ligand complexes taken from the Brookhaven Protein Data Bank, the calculated score showed a standard deviation from observed binding affinities of 1.8 log Ki units and an R2 value of 0.61. The best results were obtained for the subset of 16 serine protease complexes with a standard deviation of 1.0 log Ki unit and an R2 value of 0.86. A set of 33 inhibitors modeled into a crystal structure of HIV-1 protease yielded a standard deviation of 0.8 log Ki units from measured inhibition constants and an R2 value of 0.74. In contrast to empirical scoring functions that show similar or sometimes better correlation with observed binding affinities, our method does not involve deriving specific parameters that fit the observed binding affinities of protein-ligand complexes of a given training set. We compared the performance of the PMF score, Böhm's score (LUDI), and the SMOG score for eight different test sets of protein-ligand complexes. It was found that for the majority of test sets the PMF score performs best. The strength of the new approach

  2. Forecasting the value of credit scoring

    NASA Astrophysics Data System (ADS)

    Saad, Shakila; Ahmad, Noryati; Jaffar, Maheran Mohd

    2017-08-01

    Nowadays, credit scoring system plays an important role in banking sector. This process is important in assessing the creditworthiness of customers requesting credit from banks or other financial institutions. Usually, the credit scoring is used when customers send the application for credit facilities. Based on the score from credit scoring, bank will be able to segregate the "good" clients from "bad" clients. However, in most cases the score is useful at that specific time only and cannot be used to forecast the credit worthiness of the same applicant after that. Hence, bank will not know if "good" clients will always be good all the time or "bad" clients may become "good" clients after certain time. To fill up the gap, this study proposes an equation to forecast the credit scoring of the potential borrowers at a certain time by using the historical score related to the assumption. The Mean Absolute Percentage Error (MAPE) is used to measure the accuracy of the forecast scoring. Result shows the forecast scoring is highly accurate as compared to actual credit scoring.

  3. qFibrosis: A fully-quantitative innovative method incorporating histological features to facilitate accurate fibrosis scoring in animal model and chronic hepatitis B patients

    PubMed Central

    Tai, Dean C.S.; Wang, Shi; Cheng, Chee Leong; Peng, Qiwen; Yan, Jie; Chen, Yongpeng; Sun, Jian; Liang, Xieer; Zhu, Youfu; Rajapakse, Jagath C.; Welsch, Roy E.; So, Peter T.C.; Wee, Aileen; Hou, Jinlin; Yu, Hanry

    2014-01-01

    Background & Aims There is increasing need for accurate assessment of liver fibrosis/cirrhosis. We aimed to develop qFibrosis, a fully-automated assessment method combining quantification of histopathological architectural features, to address unmet needs in core biopsy evaluation of fibrosis in chronic hepatitis B (CHB) patients. Methods qFibrosis was established as a combined index based on 87 parameters of architectural features. Images acquired from 25 Thioacetamide-treated rat samples and 162 CHB core biopsies were used to train and test qFibrosis and to demonstrate its reproducibility. qFibrosis scoring was analyzed employing Metavir and Ishak fibrosis staging as standard references, and collagen proportionate area (CPA) measurement for comparison. Results qFibrosis faithfully and reliably recapitulates Metavir fibrosis scores, as it can identify differences between all stages in both animal samples (p <0.001) and human biopsies (p <0.05). It is robust to sampling size, allowing for discrimination of different stages in samples of different sizes (area under the curve (AUC): 0.93–0.99 for animal samples: 1–16 mm2; AUC: 0.84–0.97 for biopsies: 10–44 mm in length). qFibrosis can significantly predict staging underestimation in suboptimal biopsies (<15 mm) and under- and over-scoring by different pathologists (p <0.001). qFibrosis can also differentiate between Ishak stages 5 and 6 (AUC: 0.73, p = 0.008), suggesting the possibility of monitoring intra-stage cirrhosis changes. Best of all, qFibrosis demonstrates superior performance to CPA on all counts. Conclusions qFibrosis can improve fibrosis scoring accuracy and throughput, thus allowing for reproducible and reliable analysis of efficacies of anti-fibrotic therapies in clinical research and practice. PMID:24583249

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

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

    PubMed

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

    2014-09-01

    Charcot-Marie-Tooth Neuropathy Score second version (CMTNSv2) is a validated clinical outcome measure developed for use in clinical trials to monitor disease impairment and progression in affected CMT patients. Currently, all items of CMTNSv2 have identical contribution to the total score. We used Rasch analysis to further explore psychometric properties of CMTNSv2, and in particular, category response functioning, and their weight on the overall disease progression. Weighted category responses represent a more accurate estimate of actual values measuring disease severity and therefore could potentially be used in improving the current version. © 2014 Peripheral Nerve Society.

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

    PubMed Central

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

    2012-01-01

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

  7. The UK-PBC risk scores: Derivation and validation of a scoring system for long-term prediction of end-stage liver disease in primary biliary cholangitis.

    PubMed

    Carbone, Marco; Sharp, Stephen J; Flack, Steve; Paximadas, Dimitrios; Spiess, Kelly; Adgey, Carolyn; Griffiths, Laura; Lim, Reyna; Trembling, Paul; Williamson, Kate; Wareham, Nick J; Aldersley, Mark; Bathgate, Andrew; Burroughs, Andrew K; Heneghan, Michael A; Neuberger, James M; Thorburn, Douglas; Hirschfield, Gideon M; Cordell, Heather J; Alexander, Graeme J; Jones, David E J; Sandford, Richard N; Mells, George F

    2016-03-01

    The biochemical response to ursodeoxycholic acid (UDCA)--so-called "treatment response"--strongly predicts long-term outcome in primary biliary cholangitis (PBC). Several long-term prognostic models based solely on the treatment response have been developed that are widely used to risk stratify PBC patients and guide their management. However, they do not take other prognostic variables into account, such as the stage of the liver disease. We sought to improve existing long-term prognostic models of PBC using data from the UK-PBC Research Cohort. We performed Cox's proportional hazards regression analysis of diverse explanatory variables in a derivation cohort of 1,916 UDCA-treated participants. We used nonautomatic backward selection to derive the best-fitting Cox model, from which we derived a multivariable fractional polynomial model. We combined linear predictors and baseline survivor functions in equations to score the risk of a liver transplant or liver-related death occurring within 5, 10, or 15 years. We validated these risk scores in an independent cohort of 1,249 UDCA-treated participants. The best-fitting model consisted of the baseline albumin and platelet count, as well as the bilirubin, transaminases, and alkaline phosphatase, after 12 months of UDCA. In the validation cohort, the 5-, 10-, and 15-year risk scores were highly accurate (areas under the curve: >0.90). The prognosis of PBC patients can be accurately evaluated using the UK-PBC risk scores. They may be used to identify high-risk patients for closer monitoring and second-line therapies, as well as low-risk patients who could potentially be followed up in primary care. © 2015 by the American Association for the Study of Liver Diseases.

  8. A novel risk score for mortality in renal transplant recipients beyond the first posttransplant year.

    PubMed

    Hernández, Domingo; Sánchez-Fructuoso, Ana; González-Posada, José Manuel; Arias, Manuel; Campistol, Josep María; Rufino, Margarita; Morales, José María; Moreso, Francesc; Pérez, Germán; Torres, Armando; Serón, Daniel

    2009-09-27

    All-cause mortality is high after kidney transplantation (KT), but no prognostic index has focused on predicting mortality in KT using baseline and emergent comorbidity after KT. A total of 4928 KT recipients were used to derive a risk score predicting mortality. Patients were randomly assigned to two groups: a modeling population (n=2452), used to create a new index, and a testing population (n=2476), used to test this index. Multivariate Cox regression model coefficients of baseline (age, weight, time on dialysis, diabetes, hepatitis C, and delayed graft function) and emergent comorbidity within the first posttransplant year (diabetes, proteinuria, renal function, and immunosuppressants) were used to weigh each variable in the calculation of the score and allocated into risk quartiles. The probability of death at 3 years, estimated by baseline cumulative hazard function from the Cox model [P (death)=1-0.993592764 (exp(score/100)], increased from 0.9% in the lowest-risk quartile (score=40) to 4.7% in the highest risk-quartile (score=200). The observed incidence of death increased with increasing risk quartiles in testing population (log-rank analysis, P<0.0001). The overall C-index was 0.75 (95% confidence interval: 0.72-0.78) and 0.74 (95% confidence interval: 0.70-0.77) in both populations, respectively. This new index is an accurate tool to identify high-risk patients for mortality after KT.

  9. Mediterranean diet score and left ventricular structure and function: the Multi-Ethnic Study of Atherosclerosis.

    PubMed

    Levitan, Emily B; Ahmed, Ali; Arnett, Donna K; Polak, Joseph F; Hundley, W Gregory; Bluemke, David A; Heckbert, Susan R; Jacobs, David R; Nettleton, Jennifer A

    2016-09-01

    Data are limited on the relation between dietary patterns and left ventricular (LV) structure and function. We examined cross-sectional associations of a diet-score assessment of a Mediterranean dietary pattern with LV mass, volume, mass-to-volume ratio, stroke volume, and ejection fraction. We measured LV variables with the use of cardiac MRI in 4497 participants in the Multi-Ethnic Study of Atherosclerosis study who were aged 45-84 y and without clinical cardiovascular disease. We calculated a Mediterranean diet score from intakes of fruit, vegetables, nuts, legumes, whole grains, fish, red meat, the monounsaturated fat:saturated fat ratio, and alcohol that were self-reported with the use of a food-frequency questionnaire. We used linear regression with adjustment for body size, physical activity, and cardiovascular disease risk factors to model associations and assess the shape of these associations (linear or quadratic). The Mediterranean diet score had a slight U-shaped association with LV mass (adjusted means: 146, 145, 146, and 147 g across quartiles of diet score, respectively; P-quadratic trend = 0.04). The score was linearly associated with LV volume, stroke volume, and ejection fraction: for each +1-U difference in score, LV volume was 0.4 mL higher (95% CI: 0.0, 0.8 mL higher), the stroke volume was 0.5 mL higher (95% CI: 0.2, 0.8 mL higher), and the ejection fraction was 0.2 percentage points higher (95% CI: 0.1, 0.3 percentage points higher). The score was not associated with the mass-to-volume ratio. A higher Mediterranean diet score is cross-sectionally associated with a higher LV mass, which is balanced by a higher LV volume as well as a higher ejection fraction and stroke volume. Participants in this healthy, multiethnic sample whose dietary patterns most closely conformed to a Mediterranean-type pattern had a modestly better LV structure and function than did participants with less-Mediterranean-like dietary patterns. This trial was registered at

  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. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

  11. Ambulatory cancer and US general population reference values and cutoff scores for the functional assessment of cancer therapy.

    PubMed

    Pearman, Timothy; Yanez, Betina; Peipert, John; Wortman, Katy; Beaumont, Jennifer; Cella, David

    2014-09-15

    Health-related quality of life (HRQOL) measures are commonly used in oncology research. Interest in their use for monitoring or screening is increasing. The Functional Assessment of Cancer Therapy (FACT) is one of the most widely used HRQOL instruments. Consequently, oncology researchers and practitioners have an increasing need for reference values for the Functional Assessment of Cancer Therapy-General (FACT-G) and its 7-item rapid version, the Functional Assessment of Cancer Therapy-General 7 (FACT-G7), to compare FACT scores across specific subgroups of patients in research trials and practice. The objectives of this study are to provide 1) reference values from a sample of the general US adult population and a sample of adults diagnosed with cancer and 2) cutoff scores for quality of life. A sample of the general US population (N = 1075) and a sample of patients with cancer from 12 studies (N = 5065) were analyzed. Cutoff scores were established using distribution- and anchor-based methods. Mean values for the cancer sample were analyzed by performance status, cancer type, and disease status. Also, t tests and established criteria for meaningful differences were used to compare values. FACT-G and FACT-G7 scores in the general US population sample and cancer sample were generally comparable. Among the sample of patients with cancer, FACT-G and FACT-G7 scores worsened with declining performance status and increasing disease status. These data will aid interpretation of the magnitude and meaning of FACT scores, and allow for comparisons of scores across studies. © 2014 American Cancer Society.

  12. Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification.

    PubMed

    Khatun, Jainab; Hamlett, Eric; Giddings, Morgan C

    2008-03-01

    The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms remains limited. To improve the accuracy of identification we applied a machine-learning approach using a hidden Markov model (HMM) to capture the complex and often subtle links between a peptide sequence and its MS/MS spectrum. Our model, HMM_Score, represents ion types as HMM states and calculates the maximum joint probability for a peptide/spectrum pair using emission probabilities from three factors: the amino acids adjacent to each fragmentation site, the mass dependence of ion types and the intensity dependence of ion types. The Viterbi algorithm is used to calculate the most probable assignment between ion types in a spectrum and a peptide sequence, then a correction factor is added to account for the propensity of the model to favor longer peptides. An expectation value is calculated based on the model score to assess the significance of each peptide/spectrum match. We trained and tested HMM_Score on three data sets generated by two different mass spectrometer types. For a reference data set recently reported in the literature and validated using seven identification algorithms, HMM_Score produced 43% more positive identification results at a 1% false positive rate than the best of two other commonly used algorithms, Mascot and X!Tandem. HMM_Score is a highly accurate platform for peptide identification that works well for a variety of mass spectrometer and biological sample types. The program is freely available on ProteomeCommons via an OpenSource license. See http://bioinfo.unc.edu/downloads/ for the download link.

  13. The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

    PubMed

    Cerný, Jirí; Hobza, Pavel

    2005-04-21

    The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

  14. Nursing activities score.

    PubMed

    Miranda, Dinis Reis; Nap, Raoul; de Rijk, Angelique; Schaufeli, Wilmar; Iapichino, Gaetano

    2003-02-01

    The instruments used for measuring nursing workload in the intensive care unit (e.g., Therapeutic Intervention Scoring System-28) are based on therapeutic interventions related to severity of illness. Many nursing activities are not necessarily related to severity of illness, and cost-effectiveness studies require the accurate evaluation of nursing activities. The aim of the study was to determine the nursing activities that best describe workload in the intensive care unit and to attribute weights to these activities so that the score describes average time consumption instead of severity of illness. To define by consensus a list of nursing activities, to determine the average time consumption of these activities by use of a 1-wk observational cross-sectional study, and to compare these results with those of the Therapeutic Intervention Scoring System-28. A total of 99 intensive care units in 15 countries. Consecutive admissions to the intensive care units. Daily recording of nursing activities at a patient level and random multimoment recording of these activities. A total of five new items and 14 subitems describing nursing activities in the intensive care unit (e.g., monitoring, care of relatives, administrative tasks) were added to the list of therapeutic interventions in Therapeutic Intervention Scoring System-28. Data from 2,041 patients (6,451 nursing days and 127,951 multimoment recordings) were analyzed. The new activities accounted for 60% of the average nursing time; the new scoring system (Nursing Activities Score) explained 81% of the nursing time (vs. 43% in Therapeutic Intervention Scoring System-28). The weights in the Therapeutic Intervention Scoring System-28 are not derived from the use of nursing time. Our study suggests that the Nursing Activities Score measures the consumption of nursing time in the intensive care unit. These results should be validated in independent databases.

  15. How often is the office visit needed? Predicting total knee arthroplasty revision risk using pain/function scores.

    PubMed

    Hightower, Charles D; Hightower, Lisa S; Tatman, Penny J; Morgan, Patrick M; Gioe, Terence; Singh, Jasvinder A

    2016-08-24

    Most patients have favorable outcomes after primary total knee arthroplasty (TKA). Well-validated methods to predict the risk of poor outcomes have not been developed or implemented. Several patients have annual clinic visits despite well-funcitoning TKA, as a routine practice, to detect early failure requiring revision surgery. It is not known whether assessment of pain and function can be used as a predictive tool for early failure and revision to guide practice. Our objective was to determine whether pain and function can predict revision after TKA. We retrospectively studied data from a large prospectively gathered TKA registry to examine changes in outcome scores for primary TKAs undergoing revision compared to those not requiring revision to determine the factors that are predictive for revision. Of the 1,012 patients, 721 had had a single-sided primary TKA and had American Knee Society (AKS) Scores for three or more visits. 46 patients underwent revision, 23 acutely (fracture, traumatic component failure or acute infection) and 23 for latent causes (late implant loosening, progressive osteolysis, or pain and indolent infection). Mean age was 70 years for the non-revision patients, and 64 years for those revised. Both AKS Clinical and AKS Function Scores for non-revised patients were higher than in revision patients, higher in acute revision compared to latent revision patients. Significant predictors of revision surgery were preoperative, 3- and 15-month postoperative AKS Clinical Scores and 3-month AKS Function Scores. At 15-month post-TKA, a patient with a low calculated probability of revision, 32 % or less, was unlikely to require revision surgery with a negative predictive value of 99 %. Time dependent interval evaluation post-TKA with the AKS outcome scores may provide the ability to assign risk of revision to patients at the 15-month follow-up visit. If these findings can be replicated using a patient-reported measure, a virtual follow-up with

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

    ERIC Educational Resources Information Center

    Moses, Tim; Liu, Jinghua

    2011-01-01

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

  17. Assessment Tools for Identifying Functional Limitations Associated With Functional Ankle Instability

    PubMed Central

    Ross, Scott E; Guskiewicz, Kevin M; Gross, Michael T; Yu, Bing

    2008-01-01

    Context: Assessment tools should identify functional limitations associated with functional ankle instability (FAI) by discriminating unstable from stable ankles. Objective: To identify assessment tools that discriminated FAI from stable ankles and determine the most accurate assessment tool for discriminating between FAI and stable ankles. Design: Case-control study. Setting: Research laboratory. Patients or Other Participants: Fifteen individuals with FAI and 15 healthy individuals; participants with unilateral FAI reported “giving-way” sensations and ankle sprains, whereas healthy participants did not. Intervention(s): Participants answered 12 questions on the Ankle Joint Functional Assessment Tool (AJFAT). They also performed a single-leg jump landing, which required them to jump to half their maximum jump height, land on a single leg, and stabilize quickly on a force plate. Main Outcome Measure(s): Receiver operating characteristic curves determined cutoff scores for discriminating between ankle groups for AJFAT total score and resultant vector (RV) time to stabilization. Accuracy values for discriminating between groups were determined by calculating the area under the receiver operating characteristic curves. Results: The cutoff score for discriminating between FAI and stable ankles was ≥26 (sensitivity  =  1, specificity  =  1) and ≥1.58 seconds (sensitivity  =  0.67, specificity  =  0.73) for the AJFAT total score and RV time to stabilization, respectively. The area under the curve for the AJFAT was 1.0 (asymptotic significance <.05), whereas the RV time to stabilization had an area under the curve of 0.72 (asymptotic significance <.05). Conclusions: The AJFAT was an excellent assessment tool for discriminating between ankle groups, whereas RV time to stabilization was a fair assessment tool. Although both assessments discriminated between ankle groups, the AJFAT more accurately discriminated between groups than the RV time to

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

    PubMed

    Muthukrishnan, Shobitha; Jain, Reena; Kohli, Sangeeta; Batra, Swaraj

    2016-04-01

    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. To evaluate the effect of Mindfulness meditation on perceived stress scores and autonomic function tests of pregnant Indian women. 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. 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. 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.

  19. SCORE user's manual

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

    Brown, S.A.

    SABrE is a set of tools to facilitate the development of portable scientific software and to visualize scientific data. As with most constructs, SABRE has a foundation. In this case that foundation is SCORE. SCORE (SABRE CORE) has two main functions. The first and perhaps most important is to smooth over the differences between different C implementations and define the parameters which drive most of the conditional compilations in the rest of SABRE. Secondly, it contains several groups of functionality that are used extensively throughout SABRE. Although C is highly standardized now, that has not always been the case. Roughlymore » speaking C compilers fall into three categories: ANSI standard; derivative of the Portable C Compiler (Kernighan and Ritchie); and the rest. SABRE has been successfully ported to many ANSI and PCC systems. It has never been successfully ported to a system in the last category. The reason is mainly that the standard'' C library supplied with such implementations is so far from true ANSI or PCC standard that SABRE would have to include its own version of the standard C library in order to work at all. Even with standardized compilers life is not dead simple. The ANSI standard leaves several crucial points ambiguous as implementation defined.'' Under these conditions one can find significant differences in going from one ANSI standard compiler to another. SCORE's job is to include the requisite standard headers and ensure that certain key standard library functions exist and function correctly (there are bugs in the standard library functions supplied with some compilers) so that, to applications which include the SCORE header(s) and load with SCORE, all C implementations look the same.« less

  20. From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties.

    PubMed

    Xu, Xin; Goddard, William A

    2004-03-02

    We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

  1. From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

    NASA Astrophysics Data System (ADS)

    Xu, Xin; Goddard, William A., III

    2004-03-01

    We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

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

    PubMed

    Johnson, Erin R; Contreras-García, Julia

    2011-08-28

    We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)] and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems. © 2011 American Institute of Physics

  3. Comparison of libido, Female Sexual Function Index, and Arizona scores in women who underwent laparoscopic or conventional abdominal hysterectomy

    PubMed Central

    Kayataş, Semra; Özkaya, Enis; Api, Murat; Çıkman, Seyhan; Gürbüz, Ayşen; Eser, Ahmet

    2017-01-01

    Objective: The aim of the present study was to compare female sexual function between women who underwent conventional abdominal or laparoscopic hysterectomy. Materials and Methods: Seventy-seven women who were scheduled to undergo hysterectomy without oophorectomy for benign gynecologic conditions were included in the study. The women were assigned to laparoscopic or open abdominal hysterectomy according to the surgeons preference. Women with endometriosis and symptomatic prolapsus were excluded. Female sexual function scores were obtained before and six months after the operation from each participant by using validated questionnaires. Results: Pre- and postoperative scores of three different quationnaires were found as comparable in the group that underwent laparoscopic hysterectomy (p>0.05). Scores were also found as comparable in the group that underwent laparotomic hysterectomy (p>0.05). Pre- and postoperative values were compared between the two groups and revealed similar results with regard to all three scores (p>0.05). Conclusion: Our data showed comparable pre- and the postoperative scores for the two different hysterectomy techniques. The two groups were also found to have similar pre- and postoperative score values. PMID:28913149

  4. 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

  5. DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

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

    Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin

    In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

  6. DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

    DOE PAGES

    Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin; ...

    2017-01-26

    In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

  7. 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.

  8. [Upper gastrointestinal bleeding: usefulness of prognostic scores].

    PubMed

    Badel, S; Dorta, G; Carron, P-N

    2011-08-24

    Upper gastrointestinal bleeding is a potentially serious event, usually requiring urgent endoscopic treatment. Better stratification of the risk of complication or death could optimize management and improve patient outcomes, while ensuring adequate resource allocation. Several prognostic scores have been developed, in order to identify high risk patients, who require immediate treatment, and patients at low risk for whom endoscopy may be delayed. An ideal prognostic score should be accurate, simple, reproducible, and prospectively validated in different populations. Published scores meet these requirements only partially, and thus can only be used as part of an integrative diagnostic and therapeutic process.

  9. Function scores of different surgeries in the treatment of knee osteoarthritis: A PRISMA-compliant systematic review and network-meta analysis.

    PubMed

    Liu, Cheng-Yao; Li, Chuan-Dong; Wang, Liang; Ren, Shan; Yu, Fu-Bin; Li, Jin-Guang; Ma, Jiang-Xiong; Ma, Xing-Long

    2018-05-01

    Osteoarthritis (OA) is the third most common diagnosis made by general practitioners in older patients. The aim of this study was to compare the function scores of different surgeries in the treatment of knee osteoarthritis (KOA). Cohort studies about different surgical treatments for KOA were included with a comprehensive search in PubMed, Cochrane Library, and Embase. The standard mean difference (SMD) value was evaluated and the surface under the cumulative ranking (SUCRA) curve was drawn with a combination of direct and indirect evidence. A total of 265 eligible patients were enrolled and served as the nonoperative treatment group, osteotomy group, unicompartmental knee arthroplasty (UKA) group, total knee arthroplasty (TKA) group, and arthroscopic surgery group. Before surgery, 6 months after surgery, 1 year after surgery and 5 years after surgery, the hospital for special surgery (HSS) knee score, Lysholm score, Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score, and American knee society score (KSS) were recorded. A total of 9 cohort studies including 954 patients with KOA were finally enrolled into the study. The network-meta analysis revealed that osteotomy and UKA treatments showed a better efficacy on improving the function score. Our cohort study further confirmed that, a higher HSS knee score after 1 year and higher Lysholm score after 6 months and 1 year were observed in the osteotomy and UKA groups, while better HSS knee score and KSS after 6 months and 1 year were showed in the osteotomy and TKA groups. In the TKA group, Lysholm score and KSS were higher and WOMAC score was lower after 5 years than other groups. WOMAC score was lowest in the UKA group after 6 months, 1 year and 5 years of surgery. These results provide evidence that function scores of patients with KOA were improved by osteotomy, UKA, TKA, and arthroscopic surgery. And osteotomy and UKA showed better short-term efficacy, while TKA appeared better long

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

    PubMed

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

    2017-01-01

    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. 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. 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. 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 measurement.

  11. 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

  12. Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions.

    PubMed

    Ruvinsky, Anatoly M

    2007-06-01

    We present results of testing the ability of eleven popular scoring functions to predict native docked positions using a recently developed method (Ruvinsky and Kozintsev, J Comput Chem 2005, 26, 1089) for estimation the entropy contributions of relative motions to protein-ligand binding affinity. The method is based on the integration of the configurational integral over clusters obtained from multiple docked positions. We use a test set of 100 PDB protein-ligand complexes and ensembles of 101 docked positions generated by (Wang et al. J Med Chem 2003, 46, 2287) for each ligand in the test set. To test the suggested method we compared the averaged root-mean square deviations (RMSD) of the top-scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10-21% when used in conjunction with the AutoDock scoring function, by 2-25% with G-Score, by 7-41% with D-Score, by 0-8% with LigScore, by 1-6% with PLP, by 0-12% with LUDI, by 2-8% with F-Score, by 7-29% with ChemScore, by 0-9% with X-Score, by 2-19% with PMF, and by 1-7% with DrugScore. We also compared the performance of the suggested method with the method based on ranking by cluster occupancy only. We analyze how the choice of a clustering-RMSD and a low bound of dense clusters impacts on docking accuracy of the scoring methods. We derive optimal intervals of the clustering-RMSD for 11 scoring functions.

  13. Rapid and accurate prediction and scoring of water molecules in protein binding sites.

    PubMed

    Ross, Gregory A; Morris, Garrett M; Biggin, Philip C

    2012-01-01

    Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

  14. SCORE user`s manual

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

    Brown, S.A.

    SABrE is a set of tools to facilitate the development of portable scientific software and to visualize scientific data. As with most constructs, SABRE has a foundation. In this case that foundation is SCORE. SCORE (SABRE CORE) has two main functions. The first and perhaps most important is to smooth over the differences between different C implementations and define the parameters which drive most of the conditional compilations in the rest of SABRE. Secondly, it contains several groups of functionality that are used extensively throughout SABRE. Although C is highly standardized now, that has not always been the case. Roughlymore » speaking C compilers fall into three categories: ANSI standard; derivative of the Portable C Compiler (Kernighan and Ritchie); and the rest. SABRE has been successfully ported to many ANSI and PCC systems. It has never been successfully ported to a system in the last category. The reason is mainly that the ``standard`` C library supplied with such implementations is so far from true ANSI or PCC standard that SABRE would have to include its own version of the standard C library in order to work at all. Even with standardized compilers life is not dead simple. The ANSI standard leaves several crucial points ambiguous as ``implementation defined.`` Under these conditions one can find significant differences in going from one ANSI standard compiler to another. SCORE`s job is to include the requisite standard headers and ensure that certain key standard library functions exist and function correctly (there are bugs in the standard library functions supplied with some compilers) so that, to applications which include the SCORE header(s) and load with SCORE, all C implementations look the same.« less

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

    PubMed Central

    Atlas, Alvin; Grimmer, Karen; Kennedy, Kate

    2015-01-01

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

  16. [Carotid intima-media thickness distribution according to the stratification of cardiovascular risk by means of Framingham-REGICOR and score function charts].

    PubMed

    Hermida-Ameijeiras, Á; López-Paz, J E; Riveiro-Cruz, M A; Calvo-Gómez, C

    2016-01-01

    Carotid intima-media thickness (cIMT) has been suggested as a further tool for risk function charts. The aim of this study was to describethe relationship between cIMT and cardiovascular risk (CVR) estimation according to Framingham-REGICOR and SCORE equations. Observational, cross-sectional cohort study from 362 hypertensive subjects. Demographic and clinical information were collected as well as laboratory, ultrasonographic and CVR estimation by the Framingham-REGICOR and SCORE functions. Statistical analysis was performed using SPSS software (version 20,0). To analyze the data, statistical tests such as Chi-square, T-test, ANOVA, and Pearson correlation coefficient were used. According to both functions, differences on mean cIMT were found between low CVR group and intermediate to high groups. No differences were found between intermediate and high risk groups (cIMT: 0,73mm low risk patients vs. 0,89 or 0,88mm respectively according to SCORE function and cIMT: 0,73 vs. 0,85 or 0,87mm respectively according to Framingham-REGICOR function). cIMT correlated positively with CVR estimation according to both SCORE (r=0,421; P<.01), and Framingham-REGICOR functions (r=0,363; P<.01). cIMT correlates positively with CVR estimated by SCORE and Framingham-REGICOR functions. cIMT in those subjects at intermediate risk is similar to those at high risk. Our findings highlight the importance of carotid ultrasound in identifying silent target-organ damage in those patients at intermediate CVR. Copyright © 2015 SEHLELHA. Published by Elsevier España, S.L.U. All rights reserved.

  17. 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. © 2016 Wiley Periodicals, Inc.

  18. Individual Differences in Accurately Judging Personality From Text.

    PubMed

    Hall, Judith A; Goh, Jin X; Mast, Marianne Schmid; Hagedorn, Christian

    2016-08-01

    This research examines correlates of accuracy in judging Big Five traits from first-person text excerpts. Participants in six studies were recruited from psychology courses or online. In each study, participants performed a task of judging personality from text and performed other ability tasks and/or filled out questionnaires. Participants who were more accurate in judging personality from text were more likely to be female; had personalities that were more agreeable, conscientious, and feminine, and less neurotic and dominant (all controlling for participant gender); scored higher on empathic concern; self-reported more interest in, and attentiveness to, people's personalities in their daily lives; and reported reading more for pleasure, especially fiction. Accuracy was not associated with SAT scores but had a significant relation to vocabulary knowledge. Accuracy did not correlate with tests of judging personality and emotion based on audiovisual cues. This research is the first to address individual differences in accurate judgment of personality from text, thus adding to the literature on correlates of the good judge of personality. © 2015 Wiley Periodicals, Inc.

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

    PubMed

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

    2011-06-01

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

  20. The ERICE-score: the new native cardiovascular score for the low-risk and aged Mediterranean population of Spain.

    PubMed

    Gabriel, Rafael; Brotons, Carlos; Tormo, M José; Segura, Antonio; Rigo, Fernando; Elosua, Roberto; Carbayo, Julio A; Gavrila, Diana; Moral, Irene; Tuomilehto, Jaakko; Muñiz, Javier

    2015-03-01

    In Spain, data based on large population-based cohorts adequate to provide an accurate prediction of cardiovascular risk have been scarce. Thus, calibration of the EuroSCORE and Framingham scores has been proposed and done for our population. The aim was to develop a native risk prediction score to accurately estimate the individual cardiovascular risk in the Spanish population. Seven Spanish population-based cohorts including middle-aged and elderly participants were assembled. There were 11800 people (6387 women) representing 107915 person-years of follow-up. A total of 1214 cardiovascular events were identified, of which 633 were fatal. Cox regression analyses were conducted to examine the contributions of the different variables to the 10-year total cardiovascular risk. Age was the strongest cardiovascular risk factor. High systolic blood pressure, diabetes mellitus and smoking were strong predictive factors. The contribution of serum total cholesterol was small. Antihypertensive treatment also had a significant impact on cardiovascular risk, greater in men than in women. The model showed a good discriminative power (C-statistic=0.789 in men and C=0.816 in women). Ten-year risk estimations are displayed graphically in risk charts separately for men and women. The ERICE is a new native cardiovascular risk score for the Spanish population derived from the background and contemporaneous risk of several Spanish cohorts. The ERICE score offers the direct and reliable estimation of total cardiovascular risk, taking in consideration the effect of diabetes mellitus and cardiovascular risk factor management. The ERICE score is a practical and useful tool for clinicians to estimate the total individual cardiovascular risk in Spain. Copyright © 2014 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

  1. Association Between Montreal Cognitive Assessment Scores and Measures of Functional Mobility in Lower Extremity Amputees After Inpatient Rehabilitation.

    PubMed

    Frengopoulos, Courtney; Burley, Joshua; Viana, Ricardo; Payne, Michael W; Hunter, Susan W

    2017-03-01

    To determine whether scores on a cognitive measure are associated with walking endurance and functional mobility of individuals with transfemoral or transtibial amputations at discharge from inpatient prosthetic rehabilitation. Retrospective cohort study. Rehabilitation hospital. Consecutive admissions (N=176; mean age ± SD, 64.27±13.23y) with transfemoral or transtibial amputation that had data at admission and discharge from an inpatient prosthetic rehabilitation program. Not applicable. Cognitive status was assessed using the Montreal Cognitive Assessment (MoCA). The L Test and the 2-minute walk test (2MWT) were used to estimate functional mobility and walking endurance. The mean ± SD MoCA score was 24.05±4.09 (range, 6-30), and 56.3% of patients had scores <26. MoCA scores had a small positive correlation with the 2MWT (r=.29, P<.01), and a small negative correlation to the L Test (r=-.24, P<.01). In multivariable linear regression, compared with people with the highest MoCA score quartile, there was no difference on the 2MWT, but people in the lowest 2 quartiles took longer to complete the L Test. Cognitive impairment was very prevalent. The association between MoCA and functional mobility was statistically significant. These results highlight the potential for differences on complex motor tasks for individuals with cognitive impairment but does not indicate a need to exclude them from rehabilitation on the basis of cognitive impairment alone. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  2. Mediterranean diet score and left ventricular structure and function: the Multi-Ethnic Study of Atherosclerosis12

    PubMed Central

    Levitan, Emily B; Ahmed, Ali; Arnett, Donna K; Polak, Joseph F; Hundley, W Gregory; Bluemke, David A; Heckbert, Susan R; Jacobs, David R; Nettleton, Jennifer A

    2016-01-01

    Background: Data are limited on the relation between dietary patterns and left ventricular (LV) structure and function. Objective: We examined cross-sectional associations of a diet-score assessment of a Mediterranean dietary pattern with LV mass, volume, mass-to-volume ratio, stroke volume, and ejection fraction. Design: We measured LV variables with the use of cardiac MRI in 4497 participants in the Multi-Ethnic Study of Atherosclerosis study who were aged 45–84 y and without clinical cardiovascular disease. We calculated a Mediterranean diet score from intakes of fruit, vegetables, nuts, legumes, whole grains, fish, red meat, the monounsaturated fat:saturated fat ratio, and alcohol that were self-reported with the use of a food-frequency questionnaire. We used linear regression with adjustment for body size, physical activity, and cardiovascular disease risk factors to model associations and assess the shape of these associations (linear or quadratic). Results: The Mediterranean diet score had a slight U-shaped association with LV mass (adjusted means: 146, 145, 146, and 147 g across quartiles of diet score, respectively; P-quadratic trend = 0.04). The score was linearly associated with LV volume, stroke volume, and ejection fraction: for each +1-U difference in score, LV volume was 0.4 mL higher (95% CI: 0.0, 0.8 mL higher), the stroke volume was 0.5 mL higher (95% CI: 0.2, 0.8 mL higher), and the ejection fraction was 0.2 percentage points higher (95% CI: 0.1, 0.3 percentage points higher). The score was not associated with the mass-to-volume ratio. Conclusions: A higher Mediterranean diet score is cross-sectionally associated with a higher LV mass, which is balanced by a higher LV volume as well as a higher ejection fraction and stroke volume. Participants in this healthy, multiethnic sample whose dietary patterns most closely conformed to a Mediterranean-type pattern had a modestly better LV structure and function than did participants with less

  3. Human and Server Docking Prediction for CAPRI Round 30–35 Using LZerD with Combined Scoring Functions

    PubMed Central

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

    2016-01-01

    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, i.e. 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. PMID:27654025

  4. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

    PubMed

    Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

    2018-01-15

    Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Scoring ligand similarity in structure-based virtual screening.

    PubMed

    Zavodszky, Maria I; Rohatgi, Anjali; Van Voorst, Jeffrey R; Yan, Honggao; Kuhn, Leslie A

    2009-01-01

    Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein-ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein-ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein-ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein-ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring

  6. 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

  7. Evaluation of novel computerized tomography scoring systems in human traumatic brain injury: An observational, multicenter study

    PubMed Central

    Kivisaari, Riku; Svensson, Mikael; Skrifvars, Markus B.

    2017-01-01

    Background Traumatic brain injury (TBI) is a major contributor to morbidity and mortality. Computerized tomography (CT) scanning of the brain is essential for diagnostic screening of intracranial injuries in need of neurosurgical intervention, but may also provide information concerning patient prognosis and enable baseline risk stratification in clinical trials. Novel CT scoring systems have been developed to improve current prognostic models, including the Stockholm and Helsinki CT scores, but so far have not been extensively validated. The primary aim of this study was to evaluate the Stockholm and Helsinki CT scores for predicting functional outcome, in comparison with the Rotterdam CT score and Marshall CT classification. The secondary aims were to assess which individual components of the CT scores best predict outcome and what additional prognostic value the CT scoring systems contribute to a clinical prognostic model. Methods and findings TBI patients requiring neuro-intensive care and not included in the initial creation of the Stockholm and Helsinki CT scoring systems were retrospectively included from prospectively collected data at the Karolinska University Hospital (n = 720 from 1 January 2005 to 31 December 2014) and Helsinki University Hospital (n = 395 from 1 January 2013 to 31 December 2014), totaling 1,115 patients. The Marshall CT classification and the Rotterdam, Stockholm, and Helsinki CT scores were assessed using the admission CT scans. Known outcome predictors at admission were acquired (age, pupil responsiveness, admission Glasgow Coma Scale, glucose level, and hemoglobin level) and used in univariate, and multivariable, regression models to predict long-term functional outcome (dichotomizations of the Glasgow Outcome Scale [GOS]). In total, 478 patients (43%) had an unfavorable outcome (GOS 1–3). In the combined cohort, overall prognostic performance was more accurate for the Stockholm CT score (Nagelkerke’s pseudo-R2 range 0.24–0

  8. Estimation of a Preference-Based Summary Score for the Patient-Reported Outcomes Measurement Information System: The PROMIS®-Preference (PROPr) Scoring System.

    PubMed

    Dewitt, Barry; Feeny, David; Fischhoff, Baruch; Cella, David; Hays, Ron D; Hess, Rachel; Pilkonis, Paul A; Revicki, Dennis A; Roberts, Mark S; Tsevat, Joel; Yu, Lan; Hanmer, Janel

    2018-06-01

    Health-related quality of life (HRQL) preference-based scores are used to assess the health of populations and patients and for cost-effectiveness analyses. The National Institutes of Health Patient-Reported Outcomes Measurement Information System (PROMIS ® ) consists of patient-reported outcome measures developed using item response theory. PROMIS is in need of a direct preference-based scoring system for assigning values to health states. To produce societal preference-based scores for 7 PROMIS domains: Cognitive Function-Abilities, Depression, Fatigue, Pain Interference, Physical Function, Sleep Disturbance, and Ability to Participate in Social Roles and Activities. Online survey of a US nationally representative sample ( n = 983). Preferences for PROMIS health states were elicited with the standard gamble to obtain both single-attribute scoring functions for each of the 7 PROMIS domains and a multiplicative multiattribute utility (scoring) function. The 7 single-attribute scoring functions were fit using isotonic regression with linear interpolation. The multiplicative multiattribute summary function estimates utilities for PROMIS multiattribute health states on a scale where 0 is the utility of being dead and 1 the utility of "full health." The lowest possible score is -0.022 (for a state viewed as worse than dead), and the highest possible score is 1. The online survey systematically excludes some subgroups, such as the visually impaired and illiterate. A generic societal preference-based scoring system is now available for all studies using these 7 PROMIS health domains.

  9. How reliable are Functional Movement Screening scores? A systematic review of rater reliability.

    PubMed

    Moran, Robert W; Schneiders, Anthony G; Major, Katherine M; Sullivan, S John

    2016-05-01

    Several physical assessment protocols to identify intrinsic risk factors for injury aetiology related to movement quality have been described. The Functional Movement Screen (FMS) is a standardised, field-expedient test battery intended to assess movement quality and has been used clinically in preparticipation screening and in sports injury research. To critically appraise and summarise research investigating the reliability of scores obtained using the FMS battery. Systematic literature review. Systematic search of Google Scholar, Scopus (including ScienceDirect and PubMed), EBSCO (including Academic Search Complete, AMED, CINAHL, Health Source: Nursing/Academic Edition), MEDLINE and SPORTDiscus. Studies meeting eligibility criteria were assessed by 2 reviewers for risk of bias using the Quality Appraisal of Reliability Studies checklist. Overall quality of evidence was determined using van Tulder's levels of evidence approach. 12 studies were appraised. Overall, there was a 'moderate' level of evidence in favour of 'acceptable' (intraclass correlation coefficient ≥0.6) inter-rater and intra-rater reliability for composite scores derived from live scoring. For inter-rater reliability of composite scores derived from video recordings there was 'conflicting' evidence, and 'limited' evidence for intra-rater reliability. For inter-rater reliability based on live scoring of individual subtests there was 'moderate' evidence of 'acceptable' reliability (κ≥0.4) for 4 subtests (Deep Squat, Shoulder Mobility, Active Straight-leg Raise, Trunk Stability Push-up) and 'conflicting' evidence for the remaining 3 (Hurdle Step, In-line Lunge, Rotary Stability). This review found 'moderate' evidence that raters can achieve acceptable levels of inter-rater and intra-rater reliability of composite FMS scores when using live ratings. Overall, there were few high-quality studies, and the quality of several studies was impacted by poor study reporting particularly in relation to

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  11. An appraisal of the Functional Movement Screen™ grading criteria--Is the composite score sensitive to risky movement behavior?

    PubMed

    Frost, David M; Beach, Tyson A C; Campbell, Troy L; Callaghan, Jack P; McGill, Stuart M

    2015-11-01

    To examine the relationship between the composite Functional Movement Screen (FMS) score and performers' spine and frontal plane knee motion. Examined the spine and frontal plane knee motion exhibited by performers who received high (>14) and low (<14) composite FMS scores. Participants' body motions were quantified while they performed the FMS. Biomechanics laboratory. Twelve men who received composite FMS scores greater than 14 were assigned to a high-scoring group. Twelve age-, height- and weight-matched men with FMS scores below 14 were assigned to a low-scoring group. Composite FMS scores and peak lumbar spine flexion/extension, lateral bend and axial twist, and left and right frontal plane knee motion. Significant differences (p < 0.05) and large effect sizes (>0.8) were noted between the high- and low-scoring groups when performing the FMS tasks; high-scorers employed less spine and frontal plane knee motion. Substantial variation was also observed amongst participants. Participants with high composite FMS scores exhibited less spine and frontal plane knee motion while performing the FMS in comparison to their low-scoring counterparts. However, because substantial variation was observed amongst performers, the FMS may not provide the specificity needed for individualized injury risk assessment and exercise prescription. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    PubMed Central

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

    2011-01-01

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

  13. Applying computerized-scoring models of written biological explanations across courses and colleges: prospects and limitations.

    PubMed

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

    2011-01-01

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

  14. Co-Attention Based Neural Network for Source-Dependent Essay Scoring

    ERIC Educational Resources Information Center

    Zhang, Haoran; Litman, Diane

    2018-01-01

    This paper presents an investigation of using a co-attention based neural network for source-dependent essay scoring. We use a co-attention mechanism to help the model learn the importance of each part of the essay more accurately. Also, this paper shows that the co-attention based neural network model provides reliable score prediction of…

  15. Meta-analysis of Results of Testosterone Therapy on Sexual Function Based on International Index of Erectile Function Scores.

    PubMed

    Corona, Giovanni; Rastrelli, Giulia; Morgentaler, Abraham; Sforza, Alessandra; Mannucci, Edoardo; Maggi, Mario

    2017-12-01

    The interpretation of available clinical evidence related to the effect of testosterone (T) treatment (TTh) on sexual function has been inconsistent, in part due to the use of different and self-reported measures to assess outcomes. The International Index of Erectile Function (IIEF) is the most frequently used validated tool to assess male sexual function. To perform a meta-analysis of available data evaluating the effect of TTh on male sexual function using IIEF as the primary outcome. An extensive Medline, Embase, and Cochrane search was performed including all placebo-controlled randomized clinical trials enrolling men comparing the effect of TTh on sexual function. Out of 137 retrieved articles, 14 were included in the study enrolling 2298 participants, with a mean follow-up of 40.1 wk and mean age of 60.2±6.5 yr. Using IIEF-erectile function domain (IIEF-EFD) as the outcome, we found that TTh significantly improved erectile function compared with placebo (mean difference=2.31 [1.41;3.22] IIEF-EFD score, p<0.0001). Patients with more severe hypogonadism (total T<8 nmol/l) reported greater changes in final IIEF-EFD score when compared with those with a milder T deficiency (total T<12 nmol/l; 1.47 [0.90;2.03] and 2.95 [1.86;4.03] for total T<12 nmol/l and <8 nmol/l, respectively, Q=5.61, p=0.02). The magnitude of the effect was lower in the presence of metabolic derangements, such as diabetes and obesity. Other aspects of sexual function, as evaluated by IIEF subdomains, were also improved with TTh including libido, intercourse satisfaction, orgasm, and overall sexual satisfaction. TTh significantly improves erectile function and other sexual parameters as measured by IIEF in hypogonadal men. These results argue that sexual dysfunction should be considered a hallmark manifestation of T deficiency, since those symptoms can be significantly improved with normalization of serum T. In addition, these results suggest that TTh alone may be considered a reasonable

  16. 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.

  17. A scoring system for ascertainment of incident stroke; the Risk Index Score (RISc).

    PubMed

    Kass-Hout, T A; Moyé, L A; Smith, M A; Morgenstern, L B

    2006-01-01

    The main objective of this study was to develop and validate a computer-based statistical algorithm that could be translated into a simple scoring system in order to ascertain incident stroke cases using hospital admission medical records data. The Risk Index Score (RISc) algorithm was developed using data collected prospectively by the Brain Attack Surveillance in Corpus Christi (BASIC) project, 2000. The validity of RISc was evaluated by estimating the concordance of scoring system stroke ascertainment to stroke ascertainment by physician and/or abstractor review of hospital admission records. RISc was developed on 1718 randomly selected patients (training set) and then statistically validated on an independent sample of 858 patients (validation set). A multivariable logistic model was used to develop RISc and subsequently evaluated by goodness-of-fit and receiver operating characteristic (ROC) analyses. The higher the value of RISc, the higher the patient's risk of potential stroke. The study showed RISc was well calibrated and discriminated those who had potential stroke from those that did not on initial screening. In this study we developed and validated a rapid, easy, efficient, and accurate method to ascertain incident stroke cases from routine hospital admission records for epidemiologic investigations. Validation of this scoring system was achieved statistically; however, clinical validation in a community hospital setting is warranted.

  18. The TASS Method for Scoring Production Work

    ERIC Educational Resources Information Center

    Orsborn, Karen J.

    1977-01-01

    Describes and recommends to typing teachers the Time and Speed Scoring (TASS) method for testing typewriting production and figuring production rates. This method measures speed and quality as two separate items, because proficiency in production typewriting should reflect the student's skill in typing both accurately and quickly. (MF)

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

    PubMed Central

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

    2015-01-01

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

  20. Hindered rotor models with variable kinetic functions for accurate thermodynamic and kinetic predictions

    NASA Astrophysics Data System (ADS)

    Reinisch, Guillaume; Leyssale, Jean-Marc; Vignoles, Gérard L.

    2010-10-01

    We present an extension of some popular hindered rotor (HR) models, namely, the one-dimensional HR (1DHR) and the degenerated two-dimensional HR (d2DHR) models, allowing for a simple and accurate treatment of internal rotations. This extension, based on the use of a variable kinetic function in the Hamiltonian instead of a constant reduced moment of inertia, is extremely suitable in the case of rocking/wagging motions involved in dissociation or atom transfer reactions. The variable kinetic function is first introduced in the framework of a classical 1DHR model. Then, an effective temperature and potential dependent constant is proposed in the cases of quantum 1DHR and classical d2DHR models. These methods are finally applied to the atom transfer reaction SiCl3+BCl3→SiCl4+BCl2. We show, for this particular case, that a proper accounting of internal rotations greatly improves the accuracy of thermodynamic and kinetic predictions. Moreover, our results confirm (i) that using a suitably defined kinetic function appears to be very adapted to such problems; (ii) that the separability assumption of independent rotations seems justified; and (iii) that a quantum mechanical treatment is not a substantial improvement with respect to a classical one.

  1. A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.

    PubMed

    Barradas-Bautista, Didier; Moal, Iain H; Fernández-Recio, Juan

    2017-07-01

    Protein-protein interactions play fundamental roles in biological processes including signaling, metabolism, and trafficking. While the structure of a protein complex reveals crucial details about the interaction, it is often difficult to acquire this information experimentally. As the number of interactions discovered increases faster than they can be characterized, protein-protein docking calculations may be able to reduce this disparity by providing models of the interacting proteins. Rigid-body docking is a widely used docking approach, and is often capable of generating a pool of models within which a near-native structure can be found. These models need to be scored in order to select the acceptable ones from the set of poses. Recently, more than 100 scoring functions from the CCharPPI server were evaluated for this task using decoy structures generated with SwarmDock. Here, we extend this analysis to identify the predictive success rates of the scoring functions on decoys from three rigid-body docking programs, ZDOCK, FTDock, and SDOCK, allowing us to assess the transferability of the functions. We also apply set-theoretic measure to test whether the scoring functions are capable of identifying near-native poses within different subsets of the benchmark. This information can provide guides for the use of the most efficient scoring function for each docking method, as well as instruct future scoring functions development efforts. Proteins 2017; 85:1287-1297. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  2. Application of kernel functions for accurate similarity search in large chemical databases.

    PubMed

    Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

    2010-04-29

    Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

  3. European Society of Cardiology-Recommended Coronary Artery Disease Consortium Pretest Probability Scores More Accurately Predict Obstructive Coronary Disease and Cardiovascular Events Than the Diamond and Forrester Score: The Partners Registry.

    PubMed

    Bittencourt, Marcio Sommer; Hulten, Edward; Polonsky, Tamar S; Hoffman, Udo; Nasir, Khurram; Abbara, Suhny; Di Carli, Marcelo; Blankstein, Ron

    2016-07-19

    The most appropriate score for evaluating the pretest probability of obstructive coronary artery disease (CAD) is unknown. We sought to compare the Diamond-Forrester (DF) score with the 2 CAD consortium scores recently recommended by the European Society of Cardiology. We included 2274 consecutive patients (age, 56±13 years; 57% male) without prior CAD referred for coronary computed tomographic angiography. Computed tomographic angiography findings were used to determine the presence or absence of obstructive CAD (≥50% stenosis). We compared the DF score with the 2 CAD consortium scores with respect to their ability to predict obstructive CAD and the potential implications of these scores on the downstream use of testing for CAD, as recommended by current guidelines. The DF score did not satisfactorily fit the data and resulted in a significant overestimation of the prevalence of obstructive CAD (P<0.001); the CAD consortium basic score had no significant lack of fitness; and the CAD consortium clinical provided adequate goodness of fit (P=0.39). The DF score had a lower discrimination for obstructive CAD, with an area under the receiver-operating characteristics curve of 0.713 versus 0.752 and 0.791 for the CAD consortium models (P<0.001 for both). Consequently, the use of the DF score was associated with fewer individuals being categorized as requiring no additional testing (8.3%) compared with the CAD consortium models (24.6% and 30.0%; P<0.001). The proportion of individuals with a high pretest probability was 18% with the DF and only 1.1% with the CAD consortium scores (P<0.001) CONCLUSIONS: Among contemporary patients referred for noninvasive testing, the DF risk score overestimates the risk of obstructive CAD. On the other hand, the CAD consortium scores offered improved goodness of fit and discrimination; thus, their use could decrease the need for noninvasive or invasive testing while increasing the yield of such tests. © 2016 American Heart

  4. 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

  5. Accurate Ionization Energies for Mononuclear Copper Complexes Remain a Challenge for Density Functional Theory.

    PubMed

    Dereli, Büsra; Ortuño, Manuel A; Cramer, Christopher J

    2018-04-17

    Copper is ubiquitous and its one-electron redox chemistry is central to many catalytic processes. Modeling such chemistry requires electronic structure methods capable of the accurate prediction of ionization energies (IEs) for compounds including copper in different oxidation states and supported by various ligands. Herein, we estimate IEs for 12 mononuclear Cu species previously reported in the literature by using 21 modern density functionals and the DLPNO-CCSD(T) wave function theory model; we consider extrapolated values of the latter to provide reference values of acceptable accuracy. Our results reveal a considerable diversity in functional performance. Although there is nearly always at least one functional that performs well for any given species, there are none that do so for every member of the test set, and certain cases are particularly pathological. Over the entire test set, the SOGGA11-X functional performs best with a mean unsigned error (MUE) of 0.22 eV. PBE0, ωB97X-D, CAM-B3LYP, M11-L, B3LYP, and M11 exhibit MUEs ranging between 0.23 and 0.34 eV. When including relativistic effects with the zero-order regular approximation, ωB97X-D, CAM-B3LYP, and PBE0 are found to provide the best accuracy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Relationship between CHA2DS2-VASc score and atrial electromechanical function in patients with paroxysmal atrial fibrillation: A pilot study.

    PubMed

    Vatan, Mehmet Bülent; Yılmaz, Sabiye; Ağaç, Mustafa Tarık; Çakar, Mehmet Akif; Erkan, Hakan; Aksoy, Murat; Demirtas, Saadet; Varım, Ceyhun; Akdemir, Ramazan; Gündüz, Hüseyin

    2015-11-01

    CHA2DS2-VASc score is the most widely preferred method for prediction of stroke risk in patients with atrial fibrillation. We hypothesized that CHA2DS2-VASc score may represent atrial remodeling status, and therefore echocardiographic evaluation of left atrial electromechanical remodeling can be used to identify patients with high risk. A total of 65 patients who had documented diagnosis of paroxysmal atrial fibrillation (PAF) were divided into three risk groups according to the CHA2DS2-VASc score: patients with low risk (score=0, group 1), with moderate risk (score=1, group 2), and with high risk score (score ≥2, group 3). We compared groups according to atrial electromechanical intervals and left atrium mechanical functions. Atrial electromechanical intervals including inter-atrial and intra-atrial electromechanical delay were not different between groups. However, parameters reflecting atrial mechanical functions including LA phasic volumes (Vmax, Vmin and Vp) were significantly higher in groups 2 and 3 compared with group 1. Likewise, LA passive emptying volume (LATEV) in the groups 2 and 3 was significantly higher than low-risk group (14.12±8.13ml/m(2), 22.36±8.78ml/m(2), 22.89±7.23ml/m(2), p: 0.031). Univariate analysis demonstrated that Vmax, Vmin and Vp were significantly correlated with CHA2DS2-VASc score (r=0.428, r=0.456, r=0.451 and p<0.001). Also, LATEV (r=0.397, p=0.016) and LA active emptying volume (LAAEV) (r=0.281, p=0.023) were positively correlated with CHA2DS2-VASc score. In the ROC analysis, Vmin≥11ml/m(2) has the highest predictive value for CHA2DS2-VASc score ≥2 (88% sensitivity and 89% specificity; ROC area 0.88, p<0.001, CI [0.76-0.99]). Echocardiographic evaluation of left atrial electromechanical function might represent a useful method to identify patients with high risk. Copyright © 2015 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.

  7. Dereplication, Aggregation and Scoring Tool (DAS Tool) v1.0

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

    SIEBER, CHRISTIAN

    Communities of uncultivated microbes are critical to ecosystem function and microorganism health, and a key objective of metagenomic studies is to analyze organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of genes to genomes, yet existing binning methods often fail to predict a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotypes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tools applied to a constructedmore » community generated more accurate bins than any automated method. Further, when applied to samples of different complexity, including soil, natural oil seeps, and the human gut, DAS Tool recovered substantially more near-complete genomes than any single binning method alone. Included were three genomes from a novel lineage . The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.« less

  8. 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

  9. 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.

  10. Conversion of the Mini-Mental State Examination to the International Classification of Functioning, Disability and Health terminology and scoring system.

    PubMed

    De Vriendt, P; Gorus, E; Bautmans, I; Mets, T

    2012-01-01

    In older patients, evaluation of the cognitive status is crucial. The Mini-Mental State Examination (MMSE) is widely used for screening of cognition, providing fairly high sensitivity, specificity and reproducibility. Recently, a consensus emerged on the necessity of an international and transparent language, as provided by the WHO's International Classification of Functioning, Disability and Health (ICF). Most assessment tools however are not in accordance with the ICF. To reformulate the MMSE according to the ICF, both for the individual items and for the scoring system. MMSE data (scores varying from 3 to 30/30) of (1) 217 cognitively healthy elderly, (2) 60 persons with mild cognitive impairment, (3) 60 patients with mild Alzheimer's disease (AD), and (4) 60 patients with moderate/severe AD were obtained from studies at a university hospital setting. Subjects were aged 65 years or more and recruited either through advertisement (group 1), from the geriatric day hospital (groups 2 and 3), or the geriatric ward (group 4). The allocation to the groups was done after multidisciplinary evaluation. The conversion of the MMSE to ICF-MMSE was done by content comparison and by subsequent translation of the scoring system using automatic algorithms. All MMSE items were converted to the corresponding ICF categories. Three ICF domains were addressed: global and specific mental functions, general tasks and demands, divided over 6 ICF categories (orientation time/place, sustaining attention, memory functions, mental functions of language, undertaking a simple task). Scores on individual items were transformed according to their relative weight on the original MMSE scale, and a total ICF-MMSE score from 0 (no problem) to 100 (complete problem) was generated. Translation was satisfying, as illustrated by a good correlation between MMSE and ICF-MMSE. The diagnostic groups were distributed over the ICF-MMSE scores as expected. For each ICF domain, ICF-MMSE subscores were higher

  11. Immediate Postoperative Pain Scores Predict Neck Pain Profile up to 1 Year Following Anterior Cervical Discectomy and Fusion.

    PubMed

    Adogwa, Owoicho; Elsamadicy, Aladine A; Vuong, Victoria D; Mehta, Ankit I; Vasquez, Raul A; Cheng, Joseph; Bagley, Carlos A; Karikari, Isaac O

    2018-05-01

    Retrospective cohort review. To assess whether immediate postoperative neck pain scores accurately predict 12-month visual analog scale-neck pain (VAS-NP) outcomes following Anterior Cervical Discectomy and Fusion surgery (ACDF). This was a retrospective study of 82 patients undergoing elective ACDF surgery at a major academic medical center. Patient reported outcomes measures VAS-NP scores were recorded on the first postoperative day, then at 6-weeks, 3, 6, and 12-months after surgery. Multivariate correlation and logistic regression methods were utilized to determine whether immediate postoperative VAS-NP score accurately predicted 1-year patient reported VAS-NP Scores. Overall, 46.3% male, 25.6% were smokers, and the mean age and body mass index (BMI) were 53.7 years and 28.28 kg/m 2 , respectively. There were significant correlations between immediate postoperative pain scores and neck pain scores at 6 weeks VAS-NP ( P = .0015), 6 months VAS-NP ( P = .0333), and 12 months VAS-NP ( P = .0247) after surgery. Furthermore, immediate postoperative pain score is an independent predictor of 6 weeks, 6 months, and 1 year VAS-NP scores. Our study suggests that immediate postoperative patient reported neck pain scores accurately predicts and correlates with 12-month VAS-NP scores after an ACDF procedure. Patients with high neck pain scores after surgery are more likely to report persistent neck pain 12 months after index surgery.

  12. Score Estimating Equations from Embedded Likelihood Functions under Accelerated Failure Time Model

    PubMed Central

    NING, JING; QIN, JING; SHEN, YU

    2014-01-01

    SUMMARY The semiparametric accelerated failure time (AFT) model is one of the most popular models for analyzing time-to-event outcomes. One appealing feature of the AFT model is that the observed failure time data can be transformed to identically independent distributed random variables without covariate effects. We describe a class of estimating equations based on the score functions for the transformed data, which are derived from the full likelihood function under commonly used semiparametric models such as the proportional hazards or proportional odds model. The methods of estimating regression parameters under the AFT model can be applied to traditional right-censored survival data as well as more complex time-to-event data subject to length-biased sampling. We establish the asymptotic properties and evaluate the small sample performance of the proposed estimators. We illustrate the proposed methods through applications in two examples. PMID:25663727

  13. Comparison of Harmless Acute Pancreatitis Score with Ranson's Score in Predicting the Severity of Acute Pancreatitis.

    PubMed

    Al-Qahtani, Hamad Hadi; Alam, Mohammed Khurshid; Waheed, Muhammad

    2017-02-01

    To determine the predictability of harmless acute pancreatitis score (HAPS) in determining the severity of acute pancreatitis (AP) and compare it with Ranson's score. Prospective cohort study. King Saud Medical City, Riyadh, Kingdom of Saudi Arabia, between January 2012 and December 2015. All patients admitted with AP at King Saud Medical City, Riyadh, during 2012 - 2015 were studied prospectively. Patients were assessed by HAPS and Ranson's score. Predictability values of the two systems were analysed and compared. Out of 116 patients studied, 104 (89.6%) were HAPS positive and predicted to have mild disease. Pancreatitis was mild in 101 (87%) but severe in 3 (2.6%) patients who scored ≥ 3 Ranson's criteria. Among 12 HAPS negative patients, 10 scored ≥ 3 Ranson's criteria and developed severe pancreatitis while 2 (1.7%) with 2 positive Ranson's criteria developed mild pancreatitis. HAPS correctly predicted the disease severity in 101 (87%) patients, a sensitivity of 98% specificity of 77% and accuracy of 96%. Ranson's system predicted correctly in all but took 48 hours for assessment. Statistical analysis showed moderate agreement (Kappa = 0.776, p < 0.001), and positive relation (rs = 0.777, p < 0.001) between the two scores. HAPS is effective in rapid identification of patient who will run non-severe course of AP. Assessment can be completed within one hour from presentation. Ranson's score, although more accurate, takes 48 hours to complete.

  14. 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

  15. The Veterans Affairs Cardiac Risk Score: Recalibrating the Atherosclerotic Cardiovascular Disease Score for Applied Use.

    PubMed

    Sussman, Jeremy B; Wiitala, Wyndy L; Zawistowski, Matthew; Hofer, Timothy P; Bentley, Douglas; Hayward, Rodney A

    2017-09-01

    Accurately estimating cardiovascular risk is fundamental to good decision-making in cardiovascular disease (CVD) prevention, but risk scores developed in one population often perform poorly in dissimilar populations. We sought to examine whether a large integrated health system can use their electronic health data to better predict individual patients' risk of developing CVD. We created a cohort using all patients ages 45-80 who used Department of Veterans Affairs (VA) ambulatory care services in 2006 with no history of CVD, heart failure, or loop diuretics. Our outcome variable was new-onset CVD in 2007-2011. We then developed a series of recalibrated scores, including a fully refit "VA Risk Score-CVD (VARS-CVD)." We tested the different scores using standard measures of prediction quality. For the 1,512,092 patients in the study, the Atherosclerotic cardiovascular disease risk score had similar discrimination as the VARS-CVD (c-statistic of 0.66 in men and 0.73 in women), but the Atherosclerotic cardiovascular disease model had poor calibration, predicting 63% more events than observed. Calibration was excellent in the fully recalibrated VARS-CVD tool, but simpler techniques tested proved less reliable. We found that local electronic health record data can be used to estimate CVD better than an established risk score based on research populations. Recalibration improved estimates dramatically, and the type of recalibration was important. Such tools can also easily be integrated into health system's electronic health record and can be more readily updated.

  16. A Surgical Business Composite Score for Army Medicine.

    PubMed

    Stoddard, Douglas R; Robinson, Andrew B; Comer, Tracy A; Meno, Jenifer A; Welder, Matthew D

    2016-06-01

    Measuring surgical business performance for Army military treatment facilities is currently done through 6 business metrics developed by the Army Medical Command (MEDCOM) Surgical Services Service Line (3SL). Development of a composite score for business performance has the potential to simplify and synthesize measurement, improving focus for strategic goal setting and implementation. However, several considerations, ranging from data availability to submetric selection, must be addressed to ensure the score is accurate and representative. This article presents the methodology used in the composite score's creation and presents a metric based on return on investment and a measure of cases recaptured from private networks. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

  17. Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation

    PubMed Central

    Hardison, Ross C.

    2017-01-01

    Abstract The Roadmap Epigenomics Consortium has published whole-genome functional annotation maps in 127 human cell types by integrating data from studies of multiple epigenetic marks. These maps have been widely used for studying gene regulation in cell type-specific contexts and predicting the functional impact of DNA mutations on disease. Here, we present a new map of functional elements produced by applying a method called IDEAS on the same data. The method has several unique advantages and outperforms existing methods, including that used by the Roadmap Epigenomics Consortium. Using five categories of independent experimental datasets, we compared the IDEAS and Roadmap Epigenomics maps. While the overall concordance between the two maps is high, the maps differ substantially in the prediction details and in their consistency of annotation of a given genomic position across cell types. The annotation from IDEAS is uniformly more accurate than the Roadmap Epigenomics annotation and the improvement is substantial based on several criteria. We further introduce a pipeline that improves the reproducibility of functional annotation maps. Thus, we provide a high-quality map of candidate functional regions across 127 human cell types and compare the quality of different annotation methods in order to facilitate biomedical research in epigenomics. PMID:28973456

  18. 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,…

  19. Examining the Relationship Between the Functional Movement Screen and the Landing Error Scoring System in an Active, Male Collegiate Population.

    PubMed

    Everard, Eoin M; Harrison, Andrew J; Lyons, Mark

    2017-05-01

    Everard, EM, Harrison, AJ, and Lyons, M. Examining the relationship between the functional movement screen and the landing error scoring system in an active, male collegiate population. J Strength Cond Res 31(5): 1265-1272, 2017-In recent years, there has been an increasing focus on movement screening as the principal aspect of preparticipation 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 2 screening tools against each other. Therefore, the purpose of this study was to determine the relationship between FMS scores and LESS scores. Ninety-eight male college athletes actively competing in sport (Gaelic games, soccer, athletics, boxing/mixed martial arts, Olympic weightlifting) 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 2 screening scores. The results showed a significant moderate correlation between FMS and LESS scores (rho 100 and 21 point = -0.528; -0.487; p < 0.001). In addition, r values of 0.26 and 0.23 indicate a poor shared variance between the 2 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.

  20. The New York State risk score for predicting in-hospital/30-day mortality following percutaneous coronary intervention.

    PubMed

    Hannan, Edward L; Farrell, Louise Szypulski; Walford, Gary; Jacobs, Alice K; Berger, Peter B; Holmes, David R; Stamato, Nicholas J; Sharma, Samin; King, Spencer B

    2013-06-01

    This study sought to develop a percutaneous coronary intervention (PCI) risk score for in-hospital/30-day mortality. Risk scores are simplified linear scores that provide clinicians with quick estimates of patients' short-term mortality rates for informed consent and to determine the appropriate intervention. Earlier PCI risk scores were based on in-hospital mortality. However, for PCI, a substantial percentage of patients die within 30 days of the procedure after discharge. New York's Percutaneous Coronary Interventions Reporting System was used to develop an in-hospital/30-day logistic regression model for patients undergoing PCI in 2010, and this model was converted into a simple linear risk score that estimates mortality rates. The score was validated by applying it to 2009 New York PCI data. Subsequent analyses evaluated the ability of the score to predict complications and length of stay. A total of 54,223 patients were used to develop the risk score. There are 11 risk factors that make up the score, with risk factor scores ranging from 1 to 9, and the highest total score is 34. The score was validated based on patients undergoing PCI in the previous year, and accurately predicted mortality for all patients as well as patients who recently suffered a myocardial infarction (MI). The PCI risk score developed here enables clinicians to estimate in-hospital/30-day mortality very quickly and quite accurately. It accurately predicts mortality for patients undergoing PCI in the previous year and for MI patients, and is also moderately related to perioperative complications and length of stay. Copyright © 2013 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  1. 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…

  2. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

    PubMed Central

    Moitessier, N; Englebienne, P; Lee, D; Lawandi, J; Corbeil, C R

    2008-01-01

    Accelerating the drug discovery process requires predictive computational protocols capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking-based virtual screening methods have been developed and successfully applied to a number of pharmaceutical targets. In this review, we first present the current status of docking and scoring methods, with exhaustive lists of these. We next discuss reported comparative studies, outlining criteria for their interpretation. In the final section, we describe some of the remaining developments that would potentially lead to a universally applicable docking/scoring method. PMID:18037925

  3. 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%.

  4. A composite score combining waist circumference and body mass index more accurately predicts body fat percentage in 6- to 13-year-old children.

    PubMed

    Aeberli, I; Gut-Knabenhans, M; Kusche-Ammann, R S; Molinari, L; Zimmermann, M B

    2013-02-01

    Body mass index (BMI) and waist circumference (WC) are widely used to predict % body fat (BF) and classify degrees of pediatric adiposity. However, both measures have limitations. The aim of this study was to evaluate whether a combination of WC and BMI would more accurately predict %BF than either alone. In a nationally representative sample of 2,303 6- to 13-year-old Swiss children, weight, height, and WC were measured, and %BF was determined from multiple skinfold thicknesses. Regression and receiver operating characteristic (ROC) curves were used to evaluate the combination of WC and BMI in predicting %BF against WC or BMI alone. An optimized composite score (CS) was generated. A quadratic polynomial combination of WC and BMI led to a better prediction of %BF (r (2) = 0.68) compared with the two measures alone (r (2) = 0.58-0.62). The areas under the ROC curve for the CS [0.6 * WC-SDS + 0.4 * BMI-SDS] ranged from 0.962 ± 0.0053 (overweight girls) to 0.982 ± 0.0046 (obese boys) and were somewhat greater than the AUCs for either BMI or WC alone. At a given specificity, the sensitivity of the prediction of overweight and obesity based on the CS was higher than that based on either WC or BMI alone, although the improvement was small. Both BMI and WC are good predictors of %BF in primary school children. However, a composite score incorporating both measures increased sensitivity at a constant specificity as compared to the individual measures. It may therefore be a useful tool for clinical and epidemiological studies of pediatric adiposity.

  5. Influence of accurate and inaccurate 'split-time' feedback upon 10-mile time trial cycling performance.

    PubMed

    Wilson, Mathew G; Lane, Andy M; Beedie, Chris J; Farooq, Abdulaziz

    2012-01-01

    The objective of the study is to examine the impact of accurate and inaccurate 'split-time' feedback upon a 10-mile time trial (TT) performance and to quantify power output into a practically meaningful unit of variation. Seven well-trained cyclists completed four randomised bouts of a 10-mile TT on a SRM™ cycle ergometer. TTs were performed with (1) accurate performance feedback, (2) without performance feedback, (3) and (4) false negative and false positive 'split-time' feedback showing performance 5% slower or 5% faster than actual performance. There were no significant differences in completion time, average power output, heart rate or blood lactate between the four feedback conditions. There were significantly lower (p < 0.001) average [Formula: see text] (ml min(-1)) and [Formula: see text] (l min(-1)) scores in the false positive (3,485 ± 596; 119 ± 33) and accurate (3,471 ± 513; 117 ± 22) feedback conditions compared to the false negative (3,753 ± 410; 127 ± 27) and blind (3,772 ± 378; 124 ± 21) feedback conditions. Cyclists spent a greater amount of time in a '20 watt zone' 10 W either side of average power in the negative feedback condition (fastest) than the accurate feedback (slowest) condition (39.3 vs. 32.2%, p < 0.05). There were no significant differences in the 10-mile TT performance time between accurate and inaccurate feedback conditions, despite significantly lower average [Formula: see text] and [Formula: see text] scores in the false positive and accurate feedback conditions. Additionally, cycling with a small variation in power output (10 W either side of average power) produced the fastest TT. Further psycho-physiological research should examine the mechanism(s) why lower [Formula: see text] and [Formula: see text] scores are observed when cycling in a false positive or accurate feedback condition compared to a false negative or blind feedback condition.

  6. Prognostic Value of Risk Score and Urinary Markers in Idiopathic Membranous Nephropathy

    PubMed Central

    Hofstra, Julia M.; Wetzels, Jack F.M.

    2012-01-01

    Summary Background and objectives Accurate prediction of prognosis may improve management of patients with idiopathic membranous nephropathy. This study compared the Toronto Risk Score and urinary low-molecular weight proteins. Design, setting, participants, & measurements One hundred four patients with biopsy-proven idiopathic membranous nephropathy who presented between 1995 and 2008 with a well-preserved kidney function and nephrotic range proteinuria were included. Urinary β2-microglobulin and α1-microglobulin measurements were obtained by timed standardized measurements, and the Toronto Risk Score was calculated using data obtained from medical records. The endpoint was progression, which was defined as an increase in serum creatinine>50% or >25% with a concentration>135 μmol/L. Results Forty-nine patients showed progression. The area under the receiver-operating characteristics curve was 0.78 (95% confidence interval=0.69–0.88) for the risk score versus 0.80 (0.71–0.89) and 0.79 (0.71–0.88) for urinary β2- and α1-microglobulin, respectively. Differences were not significant. Persistent proteinuria did not add accuracy to the Toronto Risk Score. Conversely, its accuracy was not reduced when data from the first 6 months of follow-up were used. Furthermore, a score based on GFR estimated with the six-variable Modification of Diet in Renal Disease equation, calculated in the first 6 months of follow-up, gave an area under the receiver-operating characteristics curve of 0.83 (0.74–0.92), which was not statistically different from other markers. Conclusions The prognostic accuracies of the Toronto Risk Score and urinary low-molecular weight proteins were not significantly different. The risk score can be calculated within 6 months of diagnosis, and a simplified risk score using estimated GFR–Modification of Diet in Renal Disease may be sufficient. PMID:22595828

  7. Validation of the DRAGON Score in a Chinese Population to Predict Functional Outcome of Intravenous Thrombolysis-Treated Stroke Patients.

    PubMed

    Zhang, Xinmiao; Liao, Xiaoling; Wang, Chunjuan; Liu, Liping; Wang, Chunxue; Zhao, Xingquan; Pan, Yuesong; Wang, Yilong; Wang, Yongjun

    2015-08-01

    The DRAGON score predicts functional outcome of ischemic stroke patients treated with intravenous thrombolysis. Our aim was to evaluate its utility in a Chinese stroke population. Patients with acute ischemic stroke treated with intravenous thrombolysis were prospectively registered in the Thrombolysis Implementation and Monitor of acute ischemic Stroke in China. We excluded patients with basilar artery occlusion and missing data, leaving 970 eligible patients. We calculated the DRAGON score, and the clinical outcome was measured by the modified Rankin Scale at 3 months. Model discrimination was quantified by calculating the C statistic. Calibration was assessed using Pearson correlation coefficient. The C statistic was .73 (.70-.76) for good outcome and .75 (.70-.79) for miserable outcome. Proportions of patients with good outcome were 94%, 83%, 70%, and 0% for 0 to 1, 2, 3, and 8 to 10 score points, respectively. Proportions of patients with miserable outcome were 0%, 3%, 9%, and 50% for 0 to 1, 2, 3, and 8 to 10 points, respectively. There was high correlation between predicted and observed probability of 3-month favorable and miserable outcome in the external validation cohort (Pearson correlation coefficient, .98 and .98, respectively, both P < .0001). The DRAGON score showed good performance to predict functional outcome after tissue-type plasminogen activator treatment in the Chinese population. This study demonstrated the accuracy and usability of the DRAGON score in the Chinese population in daily practice. Copyright © 2015 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  8. Evaluation of modified Alvarado scoring system and RIPASA scoring system as diagnostic tools of acute appendicitis.

    PubMed

    Shuaib, Abdullah; Shuaib, Ali; Fakhra, Zainab; Marafi, Bader; Alsharaf, Khalid; Behbehani, Abdullah

    2017-01-01

    clinical parameters that can be obtained from a good patient history, clinical examination and laboratory investigations. The RIPASA scoring system is more accurate and specific than the modified Alvarado scoring system for Kuwait population.

  9. "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. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Hartree-Fock theory of the inhomogeneous electron gas at a jellium metal surface: Rigorous upper bounds to the surface energy and accurate work functions

    NASA Astrophysics Data System (ADS)

    Sahni, V.; Ma, C. Q.

    1980-12-01

    The inhomogeneous electron gas at a jellium metal surface is studied in the Hartree-Fock approximation by Kohn-Sham density functional theory. Rigorous upper bounds to the surface energy are derived by application of the Rayleigh-Ritz variational principle for the energy, the surface kinetic, electrostatic, and nonlocal exchange energy functionals being determined exactly for the accurate linear-potential model electronic wave functions. The densities obtained by the energy minimization constraint are then employed to determine work-function results via the variationally accurate "displaced-profile change-in-self-consistent-field" expression. The theoretical basis of this non-self-consistent procedure and its demonstrated accuracy for the fully correlated system (as treated within the local-density approximation for exchange and correlation) leads us to conclude these results for the surface energies and work functions to be essentially exact. Work-function values are also determined by the Koopmans'-theorem expression, both for these densities as well as for those obtained by satisfaction of the constraint set on the electrostatic potential by the Budd-Vannimenus theorem. The use of the Hartree-Fock results in the accurate estimation of correlation-effect contributions to these surface properties of the nonuniform electron gas is also indicated. In addition, the original work and approximations made by Bardeen in this attempt at a solution of the Hartree-Fock problem are briefly reviewed in order to contrast with the present work.

  11. Automated large-scale file preparation, docking, and scoring: evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource benchmark.

    PubMed

    Grinter, Sam Z; Yan, Chengfei; Huang, Sheng-You; Jiang, Lin; Zou, Xiaoqin

    2013-08-26

    In this study, we use the recently released 2012 Community Structure-Activity Resource (CSAR) data set to evaluate two knowledge-based scoring functions, ITScore and STScore, and a simple force-field-based potential (VDWScore). The CSAR data set contains 757 compounds, most with known affinities, and 57 crystal structures. With the help of the script files for docking preparation, we use the full CSAR data set to evaluate the performances of the scoring functions on binding affinity prediction and active/inactive compound discrimination. The CSAR subset that includes crystal structures is used as well, to evaluate the performances of the scoring functions on binding mode and affinity predictions. Within this structure subset, we investigate the importance of accurate ligand and protein conformational sampling and find that the binding affinity predictions are less sensitive to non-native ligand and protein conformations than the binding mode predictions. We also find the full CSAR data set to be more challenging in making binding mode predictions than the subset with structures. The script files used for preparing the CSAR data set for docking, including scripts for canonicalization of the ligand atoms, are offered freely to the academic community.

  12. A Propensity Score Analysis of the Impact of Dexamethasone Use on Delayed Cerebral Ischemia and Poor Functional Outcomes After Subarachnoid Hemorrhage.

    PubMed

    Mohney, Nathaniel; Williamson, Craig A; Rothman, Edward; Ball, Ron; Sheehan, Kyle M; Pandey, Aditya S; Fletcher, Jeffrey J; Jacobs, Teresa L; Thompson, B Gregory; Rajajee, Venkatakrishna

    2018-01-01

    An inflammatory response occurs after aneurysmal subarachnoid hemorrhage (aSAH) and predicts poor outcomes. Glucocorticoids suppress inflammation and promote fluid retention. Dexamethasone is often administered after aSAH for postoperative cerebral edema and refractory headache. Our objective was to examine the impact of dexamethasone use on functional outcomes and delayed cerebral ischemia (DCI) after aSAH. Patients with aSAH admitted between 2010 and 2015 were included; the data source was a single-center subarachnoid hemorrhage registry. The intervention of interest was a dexamethasone taper used <7 days from ictus. The primary outcome was poor discharge functional outcome, with a modified Rankin Scale score >3. Other outcomes included DCI and infection. A propensity score for use of dexamethasone was calculated using a logistic regression model that included potential predictors of dexamethasone use and outcome. The impact of dexamethasone on outcomes of interest was calculated and the propensity score was controlled for. A total of 440 patients with subarachnoid hemorrhage were admitted during the study period and 309 met eligibility criteria. Dexamethasone was administered in 101 patients (33%). A total of 127 patients (41%) had a discharge modified Rankin Scale score >3, 105 (34%) developed DCI, and 94 (30%) developed an infection. After propensity score analysis, dexamethasone use was associated with a significant reduction in poor functional outcomes (odds ratio [OR], 0.35; 95% confidence interval [CI], 0.19-0.66) but showed no significant association with DCI (OR, 0.93; 95% CI, 0.53-1.64) or infection (OR, 0.60; 95% CI, 0.34-1.06). Dexamethasone use after aSAH was associated with a reduction in poor functional outcomes at discharge but not DCI, controlling for predictors of dexamethasone use. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2011-02-01

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

  14. Development and Validation of a Disease Severity Scoring Model for Pediatric Sepsis.

    PubMed

    Hu, Li; Zhu, Yimin; Chen, Mengshi; Li, Xun; Lu, Xiulan; Liang, Ying; Tan, Hongzhuan

    2016-07-01

    Multiple severity scoring systems have been devised and evaluated in adult sepsis, but a simplified scoring model for pediatric sepsis has not yet been developed. This study aimed to develop and validate a new scoring model to stratify the severity of pediatric sepsis, thus assisting the treatment of sepsis in children. Data from 634 consecutive patients who presented with sepsis at Children's hospital of Hunan province in China in 2011-2013 were analyzed, with 476 patients placed in training group and 158 patients in validation group. Stepwise discriminant analysis was used to develop the accurate discriminate model. A simplified scoring model was generated using weightings defined by the discriminate coefficients. The discriminant ability of the model was tested by receiver operating characteristic curves (ROC). The discriminant analysis showed that prothrombin time, D-dimer, total bilirubin, serum total protein, uric acid, PaO2/FiO2 ratio, myoglobin were associated with severity of sepsis. These seven variables were assigned with values of 4, 3, 3, 4, 3, 3, 3 respectively based on the standardized discriminant coefficients. Patients with higher scores had higher risk of severe sepsis. The areas under ROC (AROC) were 0.836 for accurate discriminate model, and 0.825 for simplified scoring model in validation group. The proposed disease severity scoring model for pediatric sepsis showed adequate discriminatory capacity and sufficient accuracy, which has important clinical significance in evaluating the severity of pediatric sepsis and predicting its progress.

  15. A critique of the use of indicator-species scores for identifying thresholds in species responses

    USGS Publications Warehouse

    Cuffney, Thomas F.; Qian, Song S.

    2013-01-01

    Identification of ecological thresholds is important both for theoretical and applied ecology. Recently, Baker and King (2010, King and Baker 2010) proposed a method, threshold indicator analysis (TITAN), to calculate species and community thresholds based on indicator species scores adapted from Dufrêne and Legendre (1997). We tested the ability of TITAN to detect thresholds using models with (broken-stick, disjointed broken-stick, dose-response, step-function, Gaussian) and without (linear) definitive thresholds. TITAN accurately and consistently detected thresholds in step-function models, but not in models characterized by abrupt changes in response slopes or response direction. Threshold detection in TITAN was very sensitive to the distribution of 0 values, which caused TITAN to identify thresholds associated with relatively small differences in the distribution of 0 values while ignoring thresholds associated with large changes in abundance. Threshold identification and tests of statistical significance were based on the same data permutations resulting in inflated estimates of statistical significance. Application of bootstrapping to the split-point problem that underlies TITAN led to underestimates of the confidence intervals of thresholds. Bias in the derivation of the z-scores used to identify TITAN thresholds and skewedness in the distribution of data along the gradient produced TITAN thresholds that were much more similar than the actual thresholds. This tendency may account for the synchronicity of thresholds reported in TITAN analyses. The thresholds identified by TITAN represented disparate characteristics of species responses that, when coupled with the inability of TITAN to identify thresholds accurately and consistently, does not support the aggregation of individual species thresholds into a community threshold.

  16. Pre-season adductor squeeze test and HAGOS function sport and recreation subscale scores predict groin injury in Gaelic football players.

    PubMed

    Delahunt, Eamonn; Fitzpatrick, Helen; Blake, Catherine

    2017-01-01

    To determine if pre-season adductor squeeze test and HAGOS function, sport and recreation subscale scores can identify Gaelic football players at risk of developing groin injury. Prospective study. Senior inter-county Gaelic football team. Fifty-five male elite Gaelic football players (age = 24.0 ± 2.8 years, body mass = 84.48 ± 7.67 kg, height = 1.85 ± 0.06 m, BMI = 24.70 ± 1.77 kg/m 2 ) from a single senior inter-county Gaelic football team. Occurrence of groin injury during the season. Ten time-loss groin injuries were registered representing 13% of all injuries. The odds ratio for sustaining a groin injury if pre-season adductor squeeze test score was below 225 mmHg, was 7.78. The odds ratio for sustaining a groin injury if pre-season HAGOS function, sport and recreation subscale score was < 87.5 was 8.94. Furthermore, for each additional point on the numerical rating scale pain rating during performance of the adductor squeeze test, the odds of groin injury increased by 2.16. This study provides preliminary evidence that pre-season adductor squeeze test and HAGOS function, sport and recreation subscale scores can be used to identify Gaelic football players at risk of developing groin injury. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Effects of special exercise programs on functional movement screen scores and injury prevention in preprofessional young football players.

    PubMed

    Dinc, Engin; Kilinc, Bekir Eray; Bulat, Muge; Erten, Yunus Turgay; Bayraktar, Bülent

    2017-10-01

    To increase movement capacity and to reduce injury risk in young soccer players by implementing a special functional exercise program based on functional movement screen (FMS) and correctives. 67 young male athletes 14-19 years of age from a Super League Football Club Academy participated in the study. Functional movement patterns were evaluated with FMS assessment protocol. Deep squat, hurdle step, inline lunge, shoulder mobility, active straight leg raise, trunk stability push-up, and rotatory stability were examined in FMS. Considering the FMS scores the number of intervention and control groups were defined as 24 and 43, respectively. Intervention program was composed of 1 hr twice a week sessions in total of 12 weeks with 4 weeks of mobility, 4 weeks of stability, and 4 weeks of integration exercises. At the end of 12-week intervention and control groups were re-evaluated with FMS protocol. Contact and noncontact sports injuries recorded during one season. In intervention group there was statistically significant difference in increase in total FMS scores ( P <0.01), deep squat ( P ≤0.001), hurdle step ( P <0.05), inline lunge ( P <0.01), and trunk stability push-up ( P <0.01). In control group total FMS, deep squat, and trunk stability push-up scores increased with a statistical difference ( P <0.01, P <0.05, P ≤0.01, respectively). The incidence of noncontact injury in control group was higher than intervention group ( P <0.05). Periodic movement screening and proper corrections with functional training is valuable in order to create better movement capacity to build better physical performance and more effective injury prevention.

  18. The ANKLe Score: An Audit of Otolaryngology Emergency Clinic Record Keeping

    PubMed Central

    Dexter, Sara C; Hayashi, Daichi; Tysome, James R

    2008-01-01

    INTRODUCTION Accurate and legible medical records are essential to good quality patient care. Guidelines from The Royal College of Surgeons of England (RCSE) state the content required to form a complete medical record, but do not address legibility. An audit of otolaryngology emergency clinic record keeping was performed using a new scoring system. PATIENTS AND METHODS The Adjusted Note Keeping and Legibility (ANKLe) score was developed as an objective and quantitative method to assess both the content and legibility of case notes, incorporating the RCSE guidelines. Twenty consecutive otolaryngology emergency clinic case notes from each of 7 senior house officers were audited against standards for legibility and content using the ANKLe score. A proforma was introduced to improve documentation and handwriting advice was given. A further set of 140 notes (20 notes for each of the 7 doctors) was audited in the same way to provide feedback. RESULTS The introduction of a proforma and advice on handwriting significantly increased the quality of case note entries in terms of content, legibility and overall ANKLe score. CONCLUSIONS Accurate note keeping can be improved by the use of a proforma. The legibility of handwriting can be improved using simple advice. The ANKLe score is an objective assessment tool of the overall quality of medical note documentation which can be adapted for use in other specialties. PMID:18430339

  19. The Relationship Between Early-Stage Knee Osteoarthritis and Lower-Extremity Alignment, Joint Laxity, and Subjective Scores of Pain, Stiffness, and Function.

    PubMed

    Hicks-Little, Charlie A; Peindl, Richard D; Hubbard-Turner, Tricia J; Cordova, Mitchell L

    2016-08-01

    Knee osteoarthritis (OA) is a debilitating disease that affects an estimated 27 million Americans. Changes in lower-extremity alignment and joint laxity have been found to redistribute the medial and/or lateral loads at the joint. However, the effect that changes in anteroposterior knee-joint laxity have on lower-extremity alignment and function in individuals with knee OA remains unclear. To examine anteroposterior knee-joint laxity, lower-extremity alignment, and subjective pain, stiffness, and function scores in individuals with early-stage knee OA and matched controls and to determine if a relationship exists among these measures. Case control. Sports-medicine research laboratory. 18 participants with knee OA and 18 healthy matched controls. Participants completed the Western Ontario McMaster (WOMAC) osteoarthritis questionnaire and were tested for total anteroposterior knee-joint laxity (A-P) and knee-joint alignment (ALIGN). WOMAC scores, A-P (mm), and ALIGN (°). A significant multivariate main effect for group (Wilks' Λ = 0.30, F7,26 = 8.58, P < .0001) was found. Knee-OA participants differed in WOMAC scores (P < .0001) but did not differ from healthy controls on ALIGN (P = .49) or total A-P (P = .66). No significant relationships were identified among main outcome measures. These data demonstrate that participants with early-stage knee OA had worse pain, stiffness, and functional outcome scores than the matched controls; however, ALIGN and A-P were no different. There was no association identified among participants' subjective scores, ALIGN, or A-P measures in this study.

  20. Gleason Score Determination with Transrectal Ultrasound-Magnetic Resonance Imaging Fusion Guided Prostate Biopsies--Are We Gaining in Accuracy?

    PubMed

    Lanz, Camille; Cornud, François; Beuvon, Frédéric; Lefèvre, Arnaud; Legmann, Paul; Zerbib, Marc; Delongchamps, Nicolas Barry

    2016-01-01

    We evaluated the accuracy of prostate magnetic resonance imaging- transrectal ultrasound targeted biopsy for Gleason score determination. We selected 125 consecutive patients treated with radical prostatectomy for a clinically localized prostate cancer diagnosed on magnetic resonance imaging-transrectal ultrasound targeted biopsy and/or systematic biopsy. On multiparametric magnetic resonance imaging each suspicious area was graded according to PI-RADS™ score. A correlation analysis between multiparametric magnetic resonance imaging and pathological findings was performed. Factors associated with determining the accuracy of Gleason score on targeted biopsy were statistically assessed. Pathological analysis of radical prostatectomy specimens detected 230 tumor foci. Multiparametric magnetic resonance imaging detected 151 suspicious areas. Of these areas targeted biopsy showed 126 cancer foci in 115 patients, and detected the index lesion in all of them. The primary Gleason grade, secondary Gleason grade and Gleason score of the 126 individual tumors were determined accurately in 114 (90%), 75 (59%) and 85 (67%) cases, respectively. Maximal Gleason score was determined accurately in 80 (70%) patients. Gleason score determination accuracy on targeted biopsy was significantly higher for low Gleason and high PI-RADS score tumors. Magnetic resonance imaging-transrectal ultrasound targeted biopsy allowed for an accurate estimation of Gleason score in more than two-thirds of patients. Gleason score misclassification was mostly due to a lack of accuracy in the determination of the secondary Gleason grade. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  1. A derivation of the Cramer-Rao lower bound of euclidean parameters under equality constraints via score function

    NASA Astrophysics Data System (ADS)

    Susyanto, Nanang

    2017-12-01

    We propose a simple derivation of the Cramer-Rao Lower Bound (CRLB) of parameters under equality constraints from the CRLB without constraints in regular parametric models. When a regular parametric model and an equality constraint of the parameter are given, a parametric submodel can be defined by restricting the parameter under that constraint. The tangent space of this submodel is then computed with the help of the implicit function theorem. Finally, the score function of the restricted parameter is obtained by projecting the efficient influence function of the unrestricted parameter on the appropriate inner product spaces.

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

    PubMed

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

    2007-12-01

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

  3. A new adult appendicitis score improves diagnostic accuracy of acute appendicitis - a prospective study

    PubMed Central

    2014-01-01

    Background The aim of the study was to construct a new scoring system for more accurate diagnostics of acute appendicitis. Applying the new score into clinical practice could reduce the need of potentially harmful diagnostic imaging. Methods This prospective study enrolled 829 adults presenting with clinical suspicion of appendicitis, including 392 (47%) patients with appendicitis. The collected data included clinical findings and symptoms together with laboratory tests (white cell count, neutrophil count and C-reactive protein), and the timing of the onset of symptoms. The score was constructed by logistic regression analysis using multiple imputations for missing values. Performance of the constructed score in patients with complete data (n = 725) was compared with Alvarado score and Appendicitis inflammatory response score. Results 343 (47%) of patients with complete data had appendicitis. 199 (58%) patients with appendicitis had score value at least 16 and were classified as high probability group with 93% specificity.Patients with score below 11 were classified as low probability of appendicitis. Only 4% of patients with appendicitis had a score below 11, and none of them had complicated appendicitis. In contrast, 207 (54%) of non-appendicitis patients had score below 11. There were no cases with complicated appendicitis in the low probability group. The area under ROC curve was significantly larger with the new score 0.882 (95% CI 0.858 – 0.906) compared with AUC of Alvarado score 0.790 (0.758 – 0.823) and Appendicitis inflammatory response score 0.810 (0.779 – 0.840). Conclusions The new diagnostic score is fast and accurate in categorizing patients with suspected appendicitis, and roughly halves the need of diagnostic imaging. PMID:24970111

  4. Correlation between CHA2DS2-VASc Score and Glaucoma Treatment and Prognosis.

    PubMed

    Pikkel, Yoav Y; Krebs, Daniel; Igal, Vadim; Sharabi-Nov, Adi; Epstein, Irena; Pikkel, Joseph

    2018-01-01

    To find if CHA 2 DS 2 -VASc scale can accurately predict the treatment, prognosis, and outcome for primary open-angle glaucoma (POAG). A survey of 250,000 patient years was taken, using the records of the Ophthalmology Department at Ziv Medical Center. Data was collected regarding the retinal nerve fiber layer (RNFL), visual field (VF), line of treatment (LOT) of glaucoma, and all the data needed to accurately calculate CHA 2 DS 2 -VASc score for each patient. Sixty-seven patients were included in the statistical analysis. The mean age was 72.5 years. The mean CHA 2 DS 2 -VASc score was 3.27 + -1.7. Positive Pearson's correlation coefficients were found for LOT and CHA 2 DS 2 -VASc score, 0.35, and for RNFL grade and CHA2DS2-VASc score, 0.37. The correlation was negative for RNFL width and CHA2DS2-VASc score, -0.35. CHA 2 DS 2 -VASc score was shown to be correlated with glaucoma. This correlation was manifested positively by the LOT needed to stop glaucoma progression, with higher CHA 2 DS 2 -VASc scores correlated with more aggressive treatment. Since glaucoma is a disease with a progressing nature, it is important to treat patients aggressively on one hand, while offering the most benign treatment as possible on the other hand. Modification of the CHA 2 DS 2 -VASc score could achieve an even higher correlation.

  5. AFAST - Adult Female Acne Scoring Tool: an easy-to-use tool for scoring acne in adult females.

    PubMed

    Auffret, N; Claudel, J-P; Leccia, M-T; Poli, F; Farhi, D; Dréno, B

    2016-05-01

    Acne is a concern in adults, especially in women. The specifications in current acne grading systems are not applicable to this particular population. To develop and validate a measurement tool (AFAST: adult female acne scoring tool) for acne in women by taking into account the specific locations of adult female acne, and to evaluate the impact of the photographic modalities on rating reproducibility. Six experts in dermatology rated pictures of 54 women with a phototype from I to IV during two sessions, with an interval of 24 h. They rated the acne severity on the face using the GEA scale (Score 1) together with a new scale to assess acne on the mandibular zone (Score 2). Pictures of 30 women were taken using a standardized photographic device; pictures of the other 24 women were taken by their own dermatologists during daily practice. At session 1, the inter-rater's reproducibility was good for Score 1 with an ICC of 0.77 [0.72-0.83], and excellent for Score 2 with an ICC of 0.87 [0.82-0.91]. Between sessions 1 and 2, the mean intra-rater's reproducibility was excellent for both scores with an ICC of 0.88 [0.84-0.92] for Score 1, and an ICC of 0.87 [0.78-0.92] for Score 2. Photographic modalities had no significant effect on the inter- and intra-rater's reproducibility. For the first time, it has been demonstrated that AFAST can accurately rate acne severity in women. It is a promising, easy-to-use tool for both daily practice and clinical investigation. © 2015 European Academy of Dermatology and Venereology.

  6. Podiatry Ankle Duplex Scan: Readily Learned and Accurate in Diabetes.

    PubMed

    Normahani, Pasha; Powezka, Katarzyna; Aslam, Mohammed; Standfield, Nigel J; Jaffer, Usman

    2018-03-01

    We aimed to train podiatrists to perform a focused duplex ultrasound scan (DUS) of the tibial vessels at the ankle in diabetic patients; podiatry ankle (PodAnk) duplex scan. Thirteen podiatrists underwent an intensive 3-hour long simulation training session. Participants were then assessed performing bilateral PodAnk duplex scans of 3 diabetic patients with peripheral arterial disease. Participants were assessed using the duplex ultrasound objective structured assessment of technical skills (DUOSATS) tool and an "Imaging Score". A total of 156 vessel assessments were performed. All patients had abnormal waveforms with a loss of triphasic flow. Loss of triphasic flow was accurately detected in 145 (92.9%) vessels; the correct waveform was identified in 139 (89.1%) cases. Participants achieved excellent DUOSATS scores (median 24 [interquartile range: 23-25], max attainable score of 26) as well as "Imaging Scores" (8 [8-8], max attainable score of 8) indicating proficiency in technical skills. The mean time taken for each bilateral ankle assessment was 20.4 minutes (standard deviation ±6.7). We have demonstrated that a focused DUS for the purpose of vascular assessment of the diabetic foot is readily learned using intensive simulation training.

  7. The relation of functional visual acuity measurement methodology to tear functions and ocular surface status.

    PubMed

    Kaido, Minako; Ishida, Reiko; Dogru, Murat; Tsubota, Kazuo

    2011-09-01

    To investigate the relation of functional visual acuity (FVA) measurements with dry eye test parameters and to compare the testing methods with and without blink suppression and anesthetic instillation. A prospective comparative case series. Thirty right eyes of 30 dry eye patients and 25 right eyes of 25 normal subjects seen at Keio University School of Medicine, Department of Ophthalmology were studied. FVA testing was performed using a FVA measurement system with two different approaches, one in which measurements were made under natural blinking conditions without topical anesthesia (FVA-N) and the other in which the measurements were made under the blink suppression condition with topical anesthetic eye drops (FVA-BS). Tear function examinations, such as the Schirmer test, tear film break-up time, and fluorescein and Rose Bengal vital staining as ocular surface evaluation, were performed. The mean logMAR FVA-N scores and logMAR Landolt visual acuity scores were significantly lower in the dry eye subjects than in the healthy controls (p < 0.05), while there were no statistical differences between the logMAR FVA-BS scores of the dry eye subjects and those of the healthy controls. There was a significant correlation between the logMAR Landolt visual acuities and the logMAR FVA-N and logMAR FVA-BS scores. The FVA-N scores correlated significantly with tear quantities, tear stability and, especially, the ocular surface vital staining scores. FVA measurements performed under natural blinking significantly reflected the tear functions and ocular surface status of the eye and would appear to be a reliable method of FVA testing. FVA measurement is also an accurate predictor of dry eye status.

  8. 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. © 2016 American Academy of Forensic Sciences.

  9. Automated and visual scoring methods of cerebral white matter hyperintensities: relation with age and cognitive function.

    PubMed

    Tiehuis, A M; Vincken, K L; Mali, W P T M; Kappelle, L J; Anbeek, P; Algra, A; Biessels, G J

    2008-01-01

    A reliable scoring method for ischemic cerebral white matter hyperintensities (WMH) will help to clarify the causes and consequences of these brain lesions. We compared an automated and two visual WMH scoring methods in their relations with age and cognitive function. MRI of the brain was performed on 154 participants of the Utrecht Diabetic Encephalopathy Study. WMH volumes were obtained with an automated segmentation method. Visual rating of deep and periventricular WMH (DWMH and PWMH) was performed with the Scheltens scale and the Rotterdam Scan Study (RSS) scale, respectively. Cognition was assessed with a battery of 11 tests. Within the whole study group, the association with age was most evident for the automated measured WMH volume (beta = 0.43, 95% CI = 0.29-0.57). With regard to cognition, automated measured WMH volume and Scheltens DWMH were significantly associated with information processing speed (beta = -0.22, 95% CI = -0.40 to -0.06; beta = -0.26, 95% CI = -0.42 to -0.10), whereas RSS PWMH were associated with attention and executive function (beta = -0.19, 95% CI = -0.36 to -0.02). Measurements of WMH with an automated quantitative segmentation method are comparable with visual rating scales and highly suitable for use in future studies to assess the relationship between WMH and subtle impairments in cognitive function. (c) 2007 S. Karger AG, Basel.

  10. ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

    PubMed Central

    2012-01-01

    Background Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results. Results Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy. Conclusion ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration. PMID:22946927

  11. Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

    NASA Astrophysics Data System (ADS)

    Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

    2018-04-01

    Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

  12. 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…

  13. Accurate evaluation of exchange fields in finite element micromagnetic solvers

    NASA Astrophysics Data System (ADS)

    Chang, R.; Escobar, M. A.; Li, S.; Lubarda, M. V.; Lomakin, V.

    2012-04-01

    Quadratic basis functions (QBFs) are implemented for solving the Landau-Lifshitz-Gilbert equation via the finite element method. This involves the introduction of a set of special testing functions compatible with the QBFs for evaluating the Laplacian operator. The results by using QBFs are significantly more accurate than those via linear basis functions. QBF approach leads to significantly more accurate results than conventionally used approaches based on linear basis functions. Importantly QBFs allow reducing the error of computing the exchange field by increasing the mesh density for structured and unstructured meshes. Numerical examples demonstrate the feasibility of the method.

  14. An Accurate New Potential Function for Ground-State X{e}_2 from UV and Virial Coefficient Data

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Mackie, J. Cameron; Chandrasekhar, Pragna

    2011-06-01

    Determining accurate analytic pair potentials for rare gas dimers has been a longstanding goal in molecular physics. However, most potential energy functions reported to date fail to optimally represent the available spectroscopic data, in spite of the fact that such data provide constraints of unparalleled precision on the attractive potential energy wells of these species. A recent study of ArXe showed that it is a straightforward matter to combine multi-isotopologue spectroscopic data (in that case, microwave, and high resolution UV measurements) and virial coefficients in a direct fit to obtain a flexible analytic potential function that incorporates the theoretically predicted damped inverse-power long-range behaviour. The present work reports the application of this approach to Xe_2, with a direct fit to high resolution rotationally resolved UV emission data for v''=0 and 1, band head data for v''=0-9, and virial coefficient data for T=165-950 K being used to obtain an accurate new potential energy function for the ground state of this Van der Waals molecule. Analogous results for other rare-gas pairs will also be presented, as time permits. L. Piticco, F. Merkt, A.A. Cholewinski, F.R. McCourt and R.J. Le Roy, J. Mol. Spectrosc. 264, 83 (2010). A. Wüest and K.G. Bruin and F. Merkt, Can. J. Chem. 82, 750 (2004). D.E. Freeman, K. Yoshino, and Y. Tanaka, J. Chem. Phys. 61, 4880 (1974). J.H. Dymond, K.N. Marsh, R.C. Wilhoit and K.C. Wong, in Landold-Börnstein, New Series, Group IV, edited by M. Frenkel and K.N. Marsh, Vol. 21 (2003).

  15. Use of Internal Consistency Coefficients for Estimating Reliability of Experimental Tasks Scores

    PubMed Central

    Green, Samuel B.; Yang, Yanyun; Alt, Mary; Brinkley, Shara; Gray, Shelley; Hogan, Tiffany; Cowan, Nelson

    2017-01-01

    Reliabilities of scores for experimental tasks are likely to differ from one study to another to the extent that the task stimuli change, the number of trials varies, the type of individuals taking the task changes, the administration conditions are altered, or the focal task variable differs. Given reliabilities vary as a function of the design of these tasks and the characteristics of the individuals taking them, making inferences about the reliability of scores in an ongoing study based on reliability estimates from prior studies is precarious. Thus, it would be advantageous to estimate reliability based on data from the ongoing study. We argue that internal consistency estimates of reliability are underutilized for experimental task data and in many applications could provide this information using a single administration of a task. We discuss different methods for computing internal consistency estimates with a generalized coefficient alpha and the conditions under which these estimates are accurate. We illustrate use of these coefficients using data for three different tasks. PMID:26546100

  16. The Relationship Between Total Neuropathy Score-reduced, Neuropathy Symptoms and Function

    NASA Astrophysics Data System (ADS)

    Abulhaija, Ashraf

    Chemotherapy Induced Peripheral Neuropathy (CIPN) is a common problem among cancer patients who receive a wide range of chemotherapy. This problem causes a decline in quality of life and increased disabilities. CIPN assessment instruments are either subjective, objective, or a combination of both. So far, there is no agreement on the best way for assessment. The goal of this study was to explore the relationships among subjective and objective CIPN assessment instruments. Specifically, this study aimed to 1) evaluate the relationship between the Total Neuropathy Score-reduced (mainly objective) and patients' function, as measured by the interference scale of the Chemotherapy-Induced Peripheral Neuropathy Assessment Tool (subjective); and 2) evaluate the relationship between the Total Neuropathy Score-reduced and neuropathy symptom experience, as measured by the symptom experience scale of the Chemotherapy-Induced Peripheral Neuropathy Assessment Tool (Subjective). To achieve those aims, a secondary data analysis for 56 participants who participated in a study entitled: Group Acupuncture for Treatment of Neuropathy from Chemotherapy was done. After Pearson correlations were calculated, the study found that there is a positive, weak relationship between the TNSr and the symptom experience scale of the CIPNAT(r=0.34). A positive, week relationship was found between the TNSr and the interference with activity scale of the CIPNAT(r=0.28). These results suggest that objective and subjective assessment are not highly correlated, and likely measure different aspects of CIPN. A comprehensive assessment approach is needed for decision making in the clinical oncology setting.

  17. Principles and Practices of Test Score Equating. Research Report. ETS RR-10-29

    ERIC Educational Resources Information Center

    Dorans, Neil J.; Moses, Tim P.; Eignor, Daniel R.

    2010-01-01

    Score equating is essential for any testing program that continually produces new editions of a test and for which the expectation is that scores from these editions have the same meaning over time. Particularly in testing programs that help make high-stakes decisions, it is extremely important that test equating be done carefully and accurately.…

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

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

    Buda, I. G.; Lane, C.; Barbiellini, B.

    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 functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

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

    DOE PAGES

    Buda, I. G.; Lane, C.; Barbiellini, B.; ...

    2017-03-23

    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 functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

  20. New reference charts for testicular volume in Dutch children and adolescents allow the calculation of standard deviation scores.

    PubMed

    Joustra, Sjoerd D; van der Plas, Evelyn M; Goede, Joery; Oostdijk, Wilma; Delemarre-van de Waal, Henriette A; Hack, Wilfried W M; van Buuren, Stef; Wit, Jan M

    2015-06-01

    Accurate calculations of testicular volume standard deviation (SD) scores are not currently available. We constructed LMS-smoothed age-reference charts for testicular volume in healthy boys. The LMS method was used to calculate reference data, based on testicular volumes from ultrasonography and Prader orchidometer of 769 healthy Dutch boys aged 6 months to 19 years. We also explored the association between testicular growth and pubic hair development, and data were compared to orchidometric testicular volumes from the 1997 Dutch nationwide growth study. The LMS-smoothed reference charts showed that no revision of the definition of normal onset of male puberty - from nine to 14 years of age - was warranted. In healthy boys, the pubic hair stage SD scores corresponded with testicular volume SD scores (r = 0.394). However, testes were relatively small for pubic hair stage in Klinefelter's syndrome and relatively large in immunoglobulin superfamily member 1 deficiency syndrome. The age-corrected SD scores for testicular volume will aid in the diagnosis and follow-up of abnormalities in the timing and progression of male puberty and in research evaluations. The SD scores can be compared with pubic hair SD scores to identify discrepancies between cell functions that result in relative microorchidism or macroorchidism. ©2015 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

  1. 3D Encoding of Musical Score Information and the Playback Method Used by the Cellular Phone

    NASA Astrophysics Data System (ADS)

    Kubo, Hitoshi; Sugiura, Akihiko

    Recently, 3G cellular phone that can take a movie has spread by improving the digital camera function. And, 2Dcode has accurate readout and high operability. And it has spread as an information transmission means. However, the symbol is expanded and complicated when information of 2D codes increases. To solve these, 3D code was proposed. But it need the special equipment for readout, and specializes in the enhancing reality feeling technology. Therefore, it is difficult to apply it to the cellular phone. And so, we propose 3D code that can be recognized by the movie shooting function of the cellular phone. And, score information was encoded. We apply Gray Code to the property of music, and encode it. And the effectiveness was verified.

  2. Brazilian version of the Functional Status Score for the ICU: translation and cross-cultural adaptation

    PubMed Central

    da Silva, Vinicius Zacarias Maldaner; de Araújo Neto, Jose Aires; Cipriano Jr., Gerson; Pinedo, Mariela; Needham, Dale M.; Zanni, Jennifer M.; Guimarães, Fernando Silva

    2017-01-01

    Objective The aim of the present study was to translate and cross-culturally adapt the Functional Status Score for the intensive care unit (FSS-ICU) into Brazilian Portuguese. Methods This study consisted of the following steps: translation (performed by two independent translators), synthesis of the initial translation, back-translation (by two independent translators who were unaware of the original FSS-ICU), and testing to evaluate the target audience's understanding. An Expert Committee supervised all steps and was responsible for the modifications made throughout the process and the final translated version. Results The testing phase included two experienced physiotherapists who assessed a total of 30 critical care patients (mean FSS-ICU score = 25 ± 6). As the physiotherapists did not report any uncertainties or problems with interpretation affecting their performance, no additional adjustments were made to the Brazilian Portuguese version after the testing phase. Good interobserver reliability between the two assessors was obtained for each of the 5 FSS-ICU tasks and for the total FSS-ICU score (intraclass correlation coefficients ranged from 0.88 to 0.91). Conclusion The adapted version of the FSS-ICU in Brazilian Portuguese was easy to understand and apply in an intensive care unit environment. PMID:28444070

  3. The exponential function transforms the Abbreviated Injury Scale, which both improves accuracy and simplifies scoring.

    PubMed

    Wang, M D; Fan, W H; Qiu, W S; Zhang, Z L; Mo, Y N; Qiu, F

    2014-06-01

    We present here the exponential function which transforms the Abbreviated Injury Scale (AIS). It is called the Exponential Injury Severity Score (EISS), and significantly outperforms the venerable but dated New Injury Severity Score (NISS) and Injury Severity Score (ISS) as a predictor of mortality. The EISS is defined as a change of AIS values by raising each AIS severity score (1-6) by 3 taking a power of AIS minus 2 and then summing the three most severe injuries (i.e., highest AIS), regardless of body regions. EISS values were calculated for every patient in two large independent data sets: 3,911 and 4,129 patients treated during a 6-year period at the Class A tertiary hospitals in China. The power of the EISS to predict mortality was then compared with previously calculated NISS values for the same patients in each of the two data sets. We found that the EISS is more predictive of survival [Zhejiang: area under the receiver operating characteristic curve (AUC): NISS = 0.932, EISS = 0.949, P = 0.0115; Liaoning: AUC: NISS = 0.924, EISS = 0.942, P = 0.0139]. Moreover, the EISS provides a better fit throughout its entire range of prediction (Hosmer-Lemeshow statistic for Zhejiang: NISS = 21.86, P = 0.0027, EISS = 13.52, P = 0.0604; Liaoning: NISS = 23.27, P = 0.0015, EISS = 15.55, P = 0.0164). The EISS may be used as the standard summary measure of human trauma.

  4. Zonal NePhRO scoring system: a superior renal tumor complexity classification model.

    PubMed

    Hakky, Tariq S; Baumgarten, Adam S; Allen, Bryan; Lin, Hui-Yi; Ercole, Cesar E; Sexton, Wade J; Spiess, Philippe E

    2014-02-01

    Since the advent of the first standardized renal tumor complexity system, many subsequent scoring systems have been introduced, many of which are complicated and can make it difficult to accurately measure data end points. In light of these limitations, we introduce the new zonal NePhRO scoring system. The zonal NePhRO score is based on 4 anatomical components that are assigned a score of 1, 2, or 3, and their sum is used to classify renal tumors. The zonal NePhRO scoring system is made up of the (Ne)arness to collecting system, (Ph)ysical location of the tumor in the kidney, (R)adius of the tumor, and (O)rganization of the tumor. In this retrospective study, we evaluated patients exhibiting clinical stage T1a or T1b who underwent open partial nephrectomy performed by 2 genitourinary surgeons. Each renal unit was assigned both a zonal NePhRO score and a RENAL (radius, exophytic/endophytic properties, nearness of tumor to the collecting system or sinus in millimeters, anterior/posterior, location relative to polar lines) score, and a blinded reviewer used the same preoperative imaging study to obtain both scores. Additional data points gathered included age, clamp time, complication rate, urine leak rate, intraoperative blood loss, and pathologic tumor size. One hundred sixty-six patients underwent open partial nephrectomy. There were 37 perioperative complications quantitated using the validated Clavien-Dindo system; their occurrence was predicted by the NePhRO score on both univariate and multivariate analyses (P = .0008). Clinical stage, intraoperative blood loss, and tumor diameter were all correlated with the zonal NePhRO score on univariate analysis only. The zonal NePhRO scoring system is a simpler tool that accurately predicts the surgical complexity of a renal lesion. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Scoring Coreference Partitions of Predicted Mentions: A Reference Implementation.

    PubMed

    Pradhan, Sameer; Luo, Xiaoqiang; Recasens, Marta; Hovy, Eduard; Ng, Vincent; Strube, Michael

    2014-06-01

    The definitions of two coreference scoring metrics- B 3 and CEAF-are underspecified with respect to predicted , as opposed to key (or gold ) mentions. Several variations have been proposed that manipulate either, or both, the key and predicted mentions in order to get a one-to-one mapping. On the other hand, the metric BLANC was, until recently, limited to scoring partitions of key mentions. In this paper, we (i) argue that mention manipulation for scoring predicted mentions is unnecessary, and potentially harmful as it could produce unintuitive results; (ii) illustrate the application of all these measures to scoring predicted mentions; (iii) make available an open-source, thoroughly-tested reference implementation of the main coreference evaluation measures; and (iv) rescore the results of the CoNLL-2011/2012 shared task systems with this implementation. This will help the community accurately measure and compare new end-to-end coreference resolution algorithms.

  6. Influence of early variables in traumatic brain injury on functional independence measure scores and rehabilitation length of stay and charges.

    PubMed

    Cowen, T D; Meythaler, J M; DeVivo, M J; Ivie, C S; Lebow, J; Novack, T A

    1995-09-01

    To determine the relationship between early variables (initial Glasgow Coma Scale [GCS] scores, computed tomography [CT] findings, presence of skeletal trauma, age, length of acute hospitalization) and outcome variables (Functional Independence Measure [FIM] scores, rehabilitation length of stay [LOS], rehabilitation charges) in traumatic brain injury (TBI). Inception cohort. University tertiary care rehabilitation center. 91 patients with TBI. Inpatient rehabilitation. FIM, rehabilitation LOS, and rehabilitation charges. Patients in the severely impaired (GCS = 3 to 7) group showed significantly lower (p = .01) mean admission and discharge motor scores (21.26, 39.83) than patients in the mildly impaired (GCS = 13 to 15) group (38.86, 55.29). Cognitive scores were also significantly lower (p < .01) in the severely impaired group on admission (26.73 vs 54.14) and discharge (42.28 vs 66.48). These findings continued to be statistically significant (p < .01) after regression analysis accounted for the other early variables previously listed. Regression analysis also illustrated that longer acute hospitalization LOS was independently associated with significantly lower admission motor (p < .01) and cognitive (p = .05) scores, and significantly higher (p = .01) rehabilitation charges. Patients with CT findings of intracranial bleed with skull fracture had longer total LOS (70.88 vs 43.08 days; p < .05), rehabilitation LOS (30.01 vs 19.68 days; p < .10), and higher rehabilitation charges ($43,346 vs $25,780; p < .05). Paradoxically, those patients in a motor vehicle crash with an extremity bone fracture had significantly higher (p = .002; p = .04 after regression analysis) FIM cognitive scores on admission (48.30 vs 27.28) and discharge (64.74 vs 45.78) than those without a fracture. Finally, data available on rehabilitation admission were used to predict discharge outcomes. The percentage of explained variance for each outcome variable is as follows: discharge FIM motor

  7. Premorbid functioning of patients with first-episode nonaffective psychosis: a comparison of deterioration in academic and social performance, and clinical correlates of Premorbid Adjustment Scale scores.

    PubMed

    Monte, Ralph C; Goulding, Sandra M; Compton, Michael T

    2008-09-01

    Motivated by a previous study among male veterans [Allen, D.N., Frantom, L.V., Strauss, G.P., van Kammen, D.P., 2005. Differential patterns of premorbid academic and social deterioration in patients with schizophrenia. Schizophr. Res. 75, 389-397], the present analysis examined: (1) patterns of premorbid academic and social functioning during childhood, early adolescence, and late adolescence, and (2) associations between these premorbid functioning dimensions and a number of clinical variables. Data on premorbid functioning were collected using the Premorbid Adjustment Scale (PAS) in 95 hospitalized first-episode patients. Analyses were similar to those conducted by Allen and colleagues (2005). Deterioration was evident in both academic and social functioning from childhood to early adolescence, along with a pronounced/accelerated deterioration in academic functioning from early adolescence to late adolescence, occurring in both male and female patients. Age at onset of prodromal symptoms was predicted by childhood/early adolescent/late adolescent academic functioning scores, and age at onset of psychotic symptoms was significantly associated only with childhood academic functioning. Severity of negative symptoms was predicted by childhood and late adolescent social functioning scores, and severity of general psychopathology symptoms was predicted by late adolescent academic functioning, as well as childhood and late adolescent social functioning scores. Consistent with prior findings, deterioration in premorbid functioning appears to be more pronounced in the academic than social dimension of the PAS. Some PAS scores are predictive of ages at onset of prodrome/psychosis and severity of psychotic symptoms. Ongoing research on premorbid adjustment in schizophrenia may have implications for future prevention goals.

  8. Commercial Building Energy Asset Score

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

    This software (Asset Scoring Tool) is designed to help building owners and managers to gain insight into the as-built efficiency of their buildings. It is a web tool where users can enter their building information and obtain an asset score report. The asset score report consists of modeled building energy use (by end use and by fuel type), building systems (envelope, lighting, heating, cooling, service hot water) evaluations, and recommended energy efficiency measures. The intended users are building owners and operators who have limited knowledge of building energy efficiency. The scoring tool collects minimum building data (~20 data entries) frommore » users and build a full-scale energy model using the inference functionalities from Facility Energy Decision System (FEDS). The scoring tool runs real-time building energy simulation using EnergyPlus and performs life-cycle cost analysis using FEDS. An API is also under development to allow the third-party applications to exchange data with the web service of the scoring tool.« less

  9. 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

  10. Accurate lithography simulation model based on convolutional neural networks

    NASA Astrophysics Data System (ADS)

    Watanabe, Yuki; Kimura, Taiki; Matsunawa, Tetsuaki; Nojima, Shigeki

    2017-07-01

    Lithography simulation is an essential technique for today's semiconductor manufacturing process. In order to calculate an entire chip in realistic time, compact resist model is commonly used. The model is established for faster calculation. To have accurate compact resist model, it is necessary to fix a complicated non-linear model function. However, it is difficult to decide an appropriate function manually because there are many options. This paper proposes a new compact resist model using CNN (Convolutional Neural Networks) which is one of deep learning techniques. CNN model makes it possible to determine an appropriate model function and achieve accurate simulation. Experimental results show CNN model can reduce CD prediction errors by 70% compared with the conventional model.

  11. Age-independent anti-Müllerian hormone (AMH) standard deviation scores to estimate ovarian function.

    PubMed

    Helden, Josef van; Weiskirchen, Ralf

    2017-06-01

    To determine single year age-specific anti-Müllerian hormone (AMH) standard deviation scores (SDS) for women associated to normal ovarian function and different ovarian disorders resulting in sub- or infertility. Determination of particular year median and mean AMH values with standard deviations (SD), calculation of age-independent cut off SDS for the discrimination between normal ovarian function and ovarian disorders. Single-year-specific median, mean, and SD values have been evaluated for the Beckman Access AMH immunoassay. While the decrease of both median and mean AMH values is strongly correlated with increasing age, calculated SDS values have been shown to be age independent with the differentiation between normal ovarian function measured as occurred ovulation with sufficient luteal activity compared with hyperandrogenemic cycle disorders or anovulation associated with high AMH values and reduced ovarian activity or insufficiency associated with low AMH, respectively. These results will be helpful for the treatment of patients and the ventilation of the different reproductive options. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

    PubMed

    Ferrada, Evandro; Vergara, Ismael A; Melo, Francisco

    2007-01-01

    The correct discrimination between native and near-native protein conformations is essential for achieving accurate computer-based protein structure prediction. However, this has proven to be a difficult task, since currently available physical energy functions, empirical potentials and statistical scoring functions are still limited in achieving this goal consistently. In this work, we assess and compare the ability of different full atom knowledge-based potentials to discriminate between native protein structures and near-native protein conformations generated by comparative modeling. Using a benchmark of 152 near-native protein models and their corresponding native structures that encompass several different folds, we demonstrate that the incorporation of close non-bonded pairwise atom terms improves the discriminating power of the empirical potentials. Since the direct and unbiased derivation of close non-bonded terms from current experimental data is not possible, we obtained and used those terms from the corresponding pseudo-energy functions of a non-local knowledge-based potential. It is shown that this methodology significantly improves the discrimination between native and near-native protein conformations, suggesting that a proper description of close non-bonded terms is important to achieve a more complete and accurate description of native protein conformations. Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge.

  13. Accurate calculation and modeling of the adiabatic connection in density functional theory

    NASA Astrophysics Data System (ADS)

    Teale, A. M.; Coriani, S.; Helgaker, T.

    2010-04-01

    AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here.

  14. 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.

  15. 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

  16. Some benefit from physiotherapy intervention in the subgroup of patients with severe ankle sprain as determined by the ankle function score: a randomised trial.

    PubMed

    van Rijn, Rogier M; van Heest, Jos A C; van der Wees, Philip; Koes, Bart W; Bierma-Zeinstra, Sita M A

    2009-01-01

    Do patients with a severe ankle injury (baseline ankle function score < or = 40) do worse in the short-term than patients with a mild injury (score > 40)? Does physiotherapy intervention have more effect on patients with a severe injury compared with a mild injury in the short- or long-term? Is self-reported recovery related to ankle function score over time? Subgroup analysis of a randomised trial. 102 adults with an acute lateral ankle sprain. The experimental group received physiotherapist-supervised exercises in addition to conventional intervention. Outcomes were self-reported recovery, pain, and instability all measured on a 10-point visual analogue scale, and incidence of re-sprain. Measurements were collected at baseline, 4 and 8 weeks, 3 and 12 months. Participants with a severe injury did worse in 3 out of 7 outcomes than those with a mild injury at 4 weeks but not at 8 weeks. There was no difference in effect of physiotherapy intervention in those with a severe injury compared with a mild injury, at 8 weeks or 12 months. However, there was an effect of physiotherapy intervention in those with a severe injury in 3 out of 7 outcomes at 8 weeks. Self-reported recovery was related to ankle function score at all points in time (r = 0.48 to 0.79). The results of this study only partially support the recommendations regarding the use of the ankle function score in the 'Acute Ankle Injury' guideline of the Royal Dutch Society of Physiotherapists.

  17. Psoriasis image representation using patch-based dictionary learning for erythema severity scoring.

    PubMed

    George, Yasmeen; Aldeen, Mohammad; Garnavi, Rahil

    2018-06-01

    Psoriasis is a chronic skin disease which can be life-threatening. Accurate severity scoring helps dermatologists to decide on the treatment. In this paper, we present a semi-supervised computer-aided system for automatic erythema severity scoring in psoriasis images. Firstly, the unsupervised stage includes a novel image representation method. We construct a dictionary, which is then used in the sparse representation for local feature extraction. To acquire the final image representation vector, an aggregation method is exploited over the local features. Secondly, the supervised phase is where various multi-class machine learning (ML) classifiers are trained for erythema severity scoring. Finally, we compare the proposed system with two popular unsupervised feature extractor methods, namely: bag of visual words model (BoVWs) and AlexNet pretrained model. Root mean square error (RMSE) and F1 score are used as performance measures for the learned dictionaries and the trained ML models, respectively. A psoriasis image set consisting of 676 images, is used in this study. Experimental results demonstrate that the use of the proposed procedure can provide a setup where erythema scoring is accurate and consistent. Also, it is revealed that dictionaries with large number of atoms and small patch sizes yield the best representative erythema severity features. Further, random forest (RF) outperforms other classifiers with F1 score 0.71, followed by support vector machine (SVM) and boosting with 0.66 and 0.64 scores, respectively. Furthermore, the conducted comparative studies confirm the effectiveness of the proposed approach with improvement of 9% and 12% over BoVWs and AlexNet based features, respectively. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

  18. Item response theory scoring and the detection of curvilinear relationships.

    PubMed

    Carter, Nathan T; Dalal, Dev K; Guan, Li; LoPilato, Alexander C; Withrow, Scott A

    2017-03-01

    Psychologists are increasingly positing theories of behavior that suggest psychological constructs are curvilinearly related to outcomes. However, results from empirical tests for such curvilinear relations have been mixed. We propose that correctly identifying the response process underlying responses to measures is important for the accuracy of these tests. Indeed, past research has indicated that item responses to many self-report measures follow an ideal point response process-wherein respondents agree only to items that reflect their own standing on the measured variable-as opposed to a dominance process, wherein stronger agreement, regardless of item content, is always indicative of higher standing on the construct. We test whether item response theory (IRT) scoring appropriate for the underlying response process to self-report measures results in more accurate tests for curvilinearity. In 2 simulation studies, we show that, regardless of the underlying response process used to generate the data, using the traditional sum-score generally results in high Type 1 error rates or low power for detecting curvilinearity, depending on the distribution of item locations. With few exceptions, appropriate power and Type 1 error rates are achieved when dominance-based and ideal point-based IRT scoring are correctly used to score dominance and ideal point response data, respectively. We conclude that (a) researchers should be theory-guided when hypothesizing and testing for curvilinear relations; (b) correctly identifying whether responses follow an ideal point versus dominance process, particularly when items are not extreme is critical; and (c) IRT model-based scoring is crucial for accurate tests of curvilinearity. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  19. Functional Status Score for the Intensive Care Unit (FSS-ICU): An International Clinimetric Analysis of Validity, Responsiveness, and Minimal Important Difference

    PubMed Central

    Huang, Minxuan; Chan, Kitty S.; Zanni, Jennifer M.; Parry, Selina M.; Neto, Saint-Clair G. B.; Neto, Jose A. A.; da Silva, Vinicius Z. M.; Kho, Michelle E.; Needham, Dale M.

    2017-01-01

    Objective To evaluate the internal consistency, validity, responsiveness, and minimal important difference of the Functional Status Score for the Intensive Care Unit (FSS-ICU), a physical function measure designed for the intensive care unit (ICU). Design Clinimetric analysis. Settings Five international data sets from the United States, Australia, and Brazil. Patients 819 ICU patients. Intervention None. Measurements and Main Results Clinimetric analyses were initially conducted separately for each data source and time point to examine generalizability of findings, with pooled analyses performed thereafter to increase power of analyses. The FSS-ICU demonstrated good to excellent internal consistency. There was good convergent and discriminant validity, with significant and positive correlations (r = 0.30 to 0.95) between FSS-ICU and other physical function measures, and generally weaker correlations with non-physical measures (|r| = 0.01 to 0.70). Known group validity was demonstrated by significantly higher FSS-ICU scores among patients without ICU-acquired weakness (Medical Research Council sumscore ≥48 versus <48) and with hospital discharge to home (versus healthcare facility). FSS-ICU at ICU discharge predicted post-ICU hospital length of stay and discharge location. Responsiveness was supported via increased FSS-ICU scores with improvements in muscle strength. Distribution-based methods indicated a minimal important difference of 2.0 to 5.0. Conclusions The FSS-ICU has good internal consistency and is a valid and responsive measure of physical function for ICU patients. The estimated minimal important difference can be used in sample size calculations and in interpreting studies comparing the physical function of groups of ICU patients. PMID:27488220

  20. Usability verification of the Emergency Trauma Score (EMTRAS) and Rapid Emergency Medicine Score (REMS) in patients with trauma: A retrospective cohort study.

    PubMed

    Park, Hyun Oh; Kim, Jong Woo; Kim, Sung Hwan; Moon, Seong Ho; Byun, Joung Hun; Kim, Ki Nyun; Yang, Jun Ho; Lee, Chung Eun; Jang, In Seok; Kang, Dong Hun; Kim, Seong Chun; Kang, Changwoo; Choi, Jun Young

    2017-11-01

    Early estimation of mortality risk in patients with trauma is essential. In this study, we evaluate the validity of the Emergency Trauma Score (EMTRAS) and Rapid Emergency Medicine Score (REMS) for predicting in-hospital mortality in patients with trauma. Furthermore, we compared the REMS and the EMTRAS with 2 other scoring systems: the Revised Trauma Score (RTS) and Injury Severity score (ISS).We performed a retrospective chart review of 6905 patients with trauma reported between July 2011 and June 2016 at a large national university hospital in South Korea. We analyzed the associations between patient characteristics, treatment course, and injury severity scoring systems (ISS, RTS, EMTRAS, and REMS) with in-hospital mortality. Discriminating power was compared between scoring systems using the areas under the curve (AUC) of receiver operating characteristic (ROC) curves.The overall in-hospital mortality rate was 3.1%. Higher EMTRAS and REMS scores were associated with hospital mortality (P < .001). The ROC curve demonstrated adequate discrimination (AUC = 0.957 for EMTRAS and 0.9 for REMS). After performing AUC analysis followed by Bonferroni correction for multiple comparisons, EMTRAS was significantly superior to REMS and ISS in predicting in-hospital mortality (P < .001), but not significantly different from the RTS (P = .057). The other scoring systems were not significantly different from each other.The EMTRAS and the REMS are simple, accurate predictors of in-hospital mortality in patients with trauma.

  1. Scoring systems of severity in patients with multiple trauma.

    PubMed

    Rapsang, Amy Grace; Shyam, Devajit Chowlek

    2015-04-01

    Trauma is a major cause of morbidity and mortality; hence severity scales are important adjuncts to trauma care in order to characterize the nature and extent of injury. Trauma scoring models can assist with triage and help in evaluation and prediction of prognosis in order to organise and improve trauma systems. Given the wide variety of scoring instruments available to assess the injured patient, it is imperative that the choice of the severity score accurately match the application. Even though trauma scores are not the key elements of trauma treatment, they are however, an essential part of improvement in triage decisions and in identifying patients with unexpected outcomes. This article provides the reader with a compendium of trauma severity scales along with their predicted death rate calculation, which can be adopted in order to improve decision making, trauma care, research and in comparative analyses in quality assessment. Copyright © 2013 AEC. Publicado por Elsevier España, S.L.U. All rights reserved.

  2. The Introduction of Adult Appendicitis Score Reduced Negative Appendectomy Rate.

    PubMed

    Sammalkorpi, H E; Mentula, P; Savolainen, H; Leppäniemi, A

    2017-09-01

    Implementation of a clinical risk score into diagnostics of acute appendicitis may provide accurate diagnosis with selective use of imaging studies. The aim of this study was to prospectively validate recently described diagnostic scoring system, Adult Appendicitis Score, and evaluate its effects on negative appendectomy rate. Adult Appendicitis Score stratifies patients into three groups: high, intermediate, and low risk of appendicitis. The score was implemented in diagnostics of adult patients suspected of acute appendicitis in two university hospitals. We analyzed the effects of Adult Appendicitis Score on diagnostic accuracy, imaging studies, and treatment. The study population was compared with a reference population of 829 patients suspected of acute appendicitis originally enrolled for the study of construction of the Adult Appendicitis Score. This study enrolled 908 patients of whom 432 (48%) had appendicitis. The score stratified 49% of all appendicitis patients into high-risk group with specificity of 93.3%. In the low-risk group, prevalence of appendicitis was 7%. The histologically confirmed negative appendectomy rate decreased from 18.2% to 8.7%, p<0.001, compared to the original dataset. Adult Appendicitis Score is a reliable tool for stratification of patients into selective imaging, which results in low negative appendectomy rate.

  3. Psychometric Functions for Shortened Administrations of a Speech Recognition Approach Using Tri-Word Presentations and Phonemic Scoring

    ERIC Educational Resources Information Center

    Gelfand, Stanley A.; Gelfand, Jessica T.

    2012-01-01

    Method: Complete psychometric functions for phoneme and word recognition scores at 8 signal-to-noise ratios from -15 dB to 20 dB were generated for the first 10, 20, and 25, as well as all 50, three-word presentations of the Tri-Word or Computer Assisted Speech Recognition Assessment (CASRA) Test (Gelfand, 1998) based on the results of 12…

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

    PubMed

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

    2014-03-01

    Vertebral compression fractures can result from advanced osteoporosis, or less commonly from metastatic or traumatic insults to the vertebral column, and result in disabling pain and decreased functional capacity. Various vertebral augmentation options including kyphoplasty aim at preventing the sequelae of pain and immobility that can develop as the result of the vertebral fractures. The mechanism for pain relief following kyphoplasty is not entirely understood, and the restoration of a portion of the lost vertebral height is a subject of debate. We retrospectively reviewed radiographic imaging, pain relief, analgesic intake and functional outcomes in 67 consecutive patients who underwent single- or multilevel kyphoplasty with the primary goal of quantifying the restoration of lost vertebral height. We observed a mean of 45% of the lost vertebral height restored postprocedurally. Secondarily, kyphoplasty was associated with significant decreases in pain scores, daily morphine consumption and improvement in patient-reported functional measures. © 2013 World Institute of Pain.

  5. The ACTA PORT-score for predicting perioperative risk of blood transfusion for adult cardiac surgery.

    PubMed

    Klein, A A; Collier, T; Yeates, J; Miles, L F; Fletcher, S N; Evans, C; Richards, T

    2017-09-01

    A simple and accurate scoring system to predict risk of transfusion for patients undergoing cardiac surgery is lacking. We identified independent risk factors associated with transfusion by performing univariate analysis, followed by logistic regression. We then simplified the score to an integer-based system and tested it using the area under the receiver operator characteristic (AUC) statistic with a Hosmer-Lemeshow goodness-of-fit test. Finally, the scoring system was applied to the external validation dataset and the same statistical methods applied to test the accuracy of the ACTA-PORT score. Several factors were independently associated with risk of transfusion, including age, sex, body surface area, logistic EuroSCORE, preoperative haemoglobin and creatinine, and type of surgery. In our primary dataset, the score accurately predicted risk of perioperative transfusion in cardiac surgery patients with an AUC of 0.76. The external validation confirmed accuracy of the scoring method with an AUC of 0.84 and good agreement across all scores, with a minor tendency to under-estimate transfusion risk in very high-risk patients. The ACTA-PORT score is a reliable, validated tool for predicting risk of transfusion for patients undergoing cardiac surgery. This and other scores can be used in research studies for risk adjustment when assessing outcomes, and might also be incorporated into a Patient Blood Management programme. © The Author 2017. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  6. 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…

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

    PubMed

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

    2014-10-27

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

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

    PubMed

    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

    2016-11-21

    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.

  10. A systematic approach to adnexal masses discovered on ultrasound: the ADNEx MR scoring system.

    PubMed

    Sadowski, Elizabeth A; Robbins, Jessica B; Rockall, Andrea G; Thomassin-Naggara, Isabelle

    2018-03-01

    Adnexal lesions are a common occurrence in radiology practice and imaging plays a crucial role in triaging women appropriately. Current trends toward early detection and characterization have increased the need for accurate imaging assessment of adnexal lesions prior to treatment. Ultrasound is the first-line imaging modality for assessing adnexal lesions; however, approximately 20% of lesions are incompletely characterized after ultrasound evaluation. Secondary assessment with MR imaging using the ADNEx MR Scoring System has been demonstrated as highly accurate in the characterization of adnexal lesions and in excluding ovarian cancer. This review will address the role of MR imaging in further assessment of adnexal lesions discovered on US, and the utility of the ADNEx MR Scoring System.

  11. Development of a new Rasch-based scoring algorithm for the National Eye Institute Visual Functioning Questionnaire to improve its interpretability.

    PubMed

    Petrillo, Jennifer; Bressler, Neil M; Lamoureux, Ecosse; Ferreira, Alberto; Cano, Stefan

    2017-08-14

    The NEI VFQ-25 has undergone psychometric evaluation in patients with varying ocular conditions and the general population. However, important limitations which may affect the interpretation of clinical trial results have been previously identified, such as concerns with reliability and validity. The purpose of this study was to evaluate the National Eye Institute Visual Functioning Questionnaire (NEI VFQ-25) and make recommendations for a revised scoring structure, with a view to improving its psychometric performance and interpretability. Rasch Measurement Theory analyses were conducted in two stages using pooled baseline NEI VFQ-25 data for 2487 participants with retinal diseases enrolled in six clinical trials. In stage 1, we examined: scale-to-sample targeting; thresholds for item response options; item fit statistics; stability; local dependence; and reliability. In stage 2, a post-hoc revision of the scoring structure (VFQ-28R) was created and psychometrically re-evaluated. In stage 1, we found that the NEI VFQ-25 was mis-targeted to the sample, and had disordered response thresholds (15/25 items) and mis-fitting items (8/25 items). However, items appeared to be stable (differential item functioning for three items), have minimal item dependency (one pair of items) and good reliability (person-separation index, 0.93). In stage 2, the modified Rasch-scored NEI VFQ-28-R was assessed. It comprised two broad domains: Activity Limitation (19 items) and Socio-Emotional Functioning (nine items). The NEI VFQ-28-R demonstrated improved performance with fewer disordered response thresholds (no items), less item misfit (three items) and improved population targeting (reduced ceiling effect) compared with the NEI VFQ-25. Compared with the original version, the proposed NEI VFQ-28-R, with Rasch-based scoring and a two-domain structure, appears to offer improved psychometric performance and interpretability of the vision-related quality of life scale for the population

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

    PubMed

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

    1996-01-01

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

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

    PubMed Central

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

    2018-01-01

    It has recently been claimed that the outstanding performance of machine-learning scoring functions (SFs) is exclusively due to the presence of training complexes with highly similar proteins to those in the test set. Here, we revisit this question using 24 similarity-based training sets, a widely used test set, and four SFs. Three of these SFs employ machine learning instead of the classical linear regression approach of the fourth SF (X-Score which has the best test set performance out of 16 classical SFs). We have found that random forest (RF)-based RF-Score-v3 outperforms X-Score even when 68% of the most similar proteins are removed from the training set. In addition, unlike X-Score, RF-Score-v3 is able to keep learning with an increasing training set size, becoming substantially more predictive than X-Score when the full 1105 complexes are used for training. These results show that machine-learning SFs owe a substantial part of their performance to training on complexes with dissimilar proteins to those in the test set, against what has been previously concluded using the same data. Given that a growing amount of structural and interaction data will be available from academic and industrial sources, this performance gap between machine-learning SFs and classical SFs is expected to enlarge in the future. PMID:29538331

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

    PubMed

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

    2018-03-14

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

  15. Influence of visual impairment and hearing impairment on functional dependence status among people in Taiwan-An evaluation using the WHODAS 2.0 score.

    PubMed

    Chang, Ko-Fang; Chang, Kwang-Hwa; Chi, Wen-Chou; Huang, Shih-Wei; Yen, Chia-Feng; Liao, Hua-Fang; Liou, Tsan-Hon; Chao, Pin-Zhir; Lin, I-Chan

    2018-04-01

    Visual impairment (VI) and hearing impairment (HI) are the two most common types of sensory disability encountered clinically. However, VI and HI result in different limitations in daily life. We assessed the level of functioning in patients with VI or HI based on the International Classification of Functioning, Disability, and Health. This nationwide, cross-sectional study included 312 people with VI and 540 people with HI. Each participant's degree of functioning and disability was evaluated using the World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0). The standardized WHODAS 2.0 scores ranged from 0 (least difficulty) to 100 (most difficulty). Patients with VI and those with HI had a mean (±standard error) 32-item WHODAS 2.0 score of 42.4 ± 2.9 and 27.1 ± 1.6, respectively. The degree of restriction was positively related to the level of VI. Specifically, the patients with VI and a WHODAS 2.0 score of 33.7-35.3 or higher were likely to experience barriers to accessing mobility products, communication products, and education products. Furthermore, patients with a score of 42.9 or higher might experience barriers to accessing ingestion products and living products. WHODAS 2.0 scores are strongly correlated with the severity of VI. Mild VI should be targeted for treatment and referral as early as possible. Compared with the patients with HI, the patients with VI more frequently experience barriers to accessing environmental factors. Copyright © 2017. Published by Elsevier Taiwan LLC.

  16. Developing a cumulative anatomic scoring system for military perineal and pelvic blast injuries.

    PubMed

    Mossadegh, Somayyeh; Midwinter, M; Parker, P

    2013-03-01

    Improvised explosive device (IED) yields in Afghanistan have increased resulting in more proximal injuries. The injury severity score (ISS) is an anatomic aggregate score of the three most severely injured anatomical areas but does not accurately predict severity in IED related pelvi-perineal trauma patients. A scoring system based on abbreviated injury score (AIS) was developed to reflect the severity of these injuries in order to better understand risk factors, develop a tool for future audit and improve performance. Using standard AIS descriptors, injury scales were constructed for the pelvis (1, minor to 6, maximal). The perineum was divided into anterior and posterior zones as relevant to injury patterns and blast direction with each soft tissue structure being allocated a score from its own severity scale. A cumulative score, from 1 to 36 for soft tissue, or a maximum of 42 if a pelvic fracture was involved, was created for all structures injured in the anterior and posterior zones. Using this new scoring system, 77% of patients survived with a pelvi-perineal trauma score (PPTS) below 5. There was a significant increase in mortality, number of pelvic fractures and amputations with increase in score when comparing the first group (score 1-5) to the second group (score 6-10). For scores between 6 and 16 survival was 42% and 22% for scores between 17 and 21. In our cohort of 62 survivors, 1 patient with an IED related pelvi-perineal injury had a 'theoretically un-survivable' maximal ISS of 75 and survived, whereas there were no survivors with a PPTS greater than 22 but this group had no-one with an ISS of 75 suggesting ISS is not an accurate reflection of the true severity of pelvi-perineal blast injury. This scoring system is the initial part of a more complex logistic regression model that will contribute towards a unique trauma scoring system to aid surgical teams in predicting fluid requirements and operative timelines. In austere environments, it may also

  17. Extended score interval in the assessment of basic surgical skills.

    PubMed

    Acosta, Stefan; Sevonius, Dan; Beckman, Anders

    2015-01-01

    The Basic Surgical Skills course uses an assessment score interval of 0-3. An extended score interval, 1-6, was proposed by the Swedish steering committee of the course. The aim of this study was to analyze the trainee scores in the current 0-3 scored version compared to a proposed 1-6 scored version. Sixteen participants, seven females and nine males, were evaluated in the current and proposed assessment forms by instructors, observers, and learners themselves during the first and second day. In each assessment form, 17 tasks were assessed. The inter-rater reliability between the current and the proposed score sheets were evaluated with intraclass correlation (ICC) with 95% confidence intervals (CI). The distribution of scores for 'knot tying' at the last time point and 'bowel anastomosis side to side' given by the instructors in the current assessment form showed that the highest score was given in 31 and 62%, respectively. No ceiling effects were found in the proposed assessment form. The overall ICC between the current and proposed score sheets after assessment by the instructors increased from 0.38 (95% CI 0.77-0.78) on Day 1 to 0.83 (95% CI 0.51-0.94) on Day 2. A clear ceiling effect of scores was demonstrated in the current assessment form, questioning its validity. The proposed score sheet provides more accurate scores and seems to be a better feedback instrument for learning technical surgical skills in the Basic Surgical Skills course.

  18. 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. Copyright © 2016 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

  19. Dynamic interaction between fetal adversity and a genetic score reflecting dopamine function on developmental outcomes at 36 months.

    PubMed

    Bischoff, Adrianne R; Pokhvisneva, Irina; Léger, Étienne; Gaudreau, Hélène; Steiner, Meir; Kennedy, James L; O'Donnell, Kieran J; Diorio, Josie; Meaney, Michael J; Silveira, Patrícia P

    2017-01-01

    Fetal adversity, evidenced by poor fetal growth for instance, is associated with increased risk for several diseases later in life. Classical cut-offs to characterize small (SGA) and large for gestational age (LGA) newborns are used to define long term vulnerability. We aimed at exploring the possible dynamism of different birth weight cut-offs in defining vulnerability in developmental outcomes (through the Bayley Scales of Infant and Toddler Development), using the example of a gene vs. fetal adversity interaction considering gene choices based on functional relevance to the studied outcome. 36-month-old children from an established prospective birth cohort (Maternal Adversity, Vulnerability, and Neurodevelopment) were classified according to birth weight ratio (BWR) (SGA ≤0.85, LGA >1.15, exploring a wide range of other cut-offs) and genotyped for polymorphisms associated with dopamine signaling (TaqIA-A1 allele, DRD2-141C Ins/Ins, DRD4 7-repeat, DAT1-10- repeat, Met/Met-COMT), composing a score based on the described function, in which hypofunctional variants received lower scores. There were 251 children (123 girls and 128 boys). Using the classic cut-offs (0.85 and 1.15), there were no statistically significant interactions between the neonatal groups and the dopamine genetic score. However, when changing the cut-offs, it is possible to see ranges of BWR that could be associated with vulnerability to poorer development according to the variation in the dopamine function. The classic birth weight cut-offs to define SGA and LGA newborns should be seen with caution, as depending on the outcome in question, the protocols for long-term follow up could be either too inclusive-therefore most costly, or unable to screen true vulnerabilities-and therefore ineffective to establish early interventions and primary prevention.

  20. Dynamic interaction between fetal adversity and a genetic score reflecting dopamine function on developmental outcomes at 36 months

    PubMed Central

    Pokhvisneva, Irina; Léger, Étienne; Gaudreau, Hélène; Steiner, Meir; Kennedy, James L.; O’Donnell, Kieran J.; Diorio, Josie; Meaney, Michael J.; Silveira, Patrícia P.

    2017-01-01

    Background Fetal adversity, evidenced by poor fetal growth for instance, is associated with increased risk for several diseases later in life. Classical cut-offs to characterize small (SGA) and large for gestational age (LGA) newborns are used to define long term vulnerability. We aimed at exploring the possible dynamism of different birth weight cut-offs in defining vulnerability in developmental outcomes (through the Bayley Scales of Infant and Toddler Development), using the example of a gene vs. fetal adversity interaction considering gene choices based on functional relevance to the studied outcome. Methods 36-month-old children from an established prospective birth cohort (Maternal Adversity, Vulnerability, and Neurodevelopment) were classified according to birth weight ratio (BWR) (SGA ≤0.85, LGA >1.15, exploring a wide range of other cut-offs) and genotyped for polymorphisms associated with dopamine signaling (TaqIA-A1 allele, DRD2-141C Ins/Ins, DRD4 7-repeat, DAT1-10- repeat, Met/Met-COMT), composing a score based on the described function, in which hypofunctional variants received lower scores. Results There were 251 children (123 girls and 128 boys). Using the classic cut-offs (0.85 and 1.15), there were no statistically significant interactions between the neonatal groups and the dopamine genetic score. However, when changing the cut-offs, it is possible to see ranges of BWR that could be associated with vulnerability to poorer development according to the variation in the dopamine function. Conclusion The classic birth weight cut-offs to define SGA and LGA newborns should be seen with caution, as depending on the outcome in question, the protocols for long-term follow up could be either too inclusive—therefore most costly, or unable to screen true vulnerabilities—and therefore ineffective to establish early interventions and primary prevention. PMID:28505190

  1. Clinical application of the FACES score for face transplantation.

    PubMed

    Chopra, Karan; Susarla, Srinivas M; Goodrich, Danielle; Bernard, Steven; Zins, James E; Papay, Frank; Lee, W P Andrew; Gordon, Chad R

    2014-01-01

    This study aimed to systematically evaluate all reported outcomes of facial allotransplantation (FT) using the previously described FACES scoring instrument. This was a retrospective study of all consecutive face transplants to date (January 2012). Candidates were identified using medical and general internet database searches. Medical literature and media reports were reviewed for details regarding demographic, operative, anatomic, and psychosocial data, which were then used to formulate FACES scores. Pre-transplant and post-transplant scores for "functional status", "aesthetic deformity", "co-morbidities", "exposed tissue", and "surgical history" were calculated. Scores were statistically compared using paired-samples analyses. Twenty consecutive patients were identified, with 18 surviving recipients. The sample was composed of 3 females and 17 males, with a mean age of 35.0 ± 11.0 years (range: 19-57 years). Overall, data reporting for functional parameters was poor. Six subjects had complete pre-transplant and post-transplant data available for all 5 FACES domains. The mean pre-transplant FACES score was 33.5 ± 8.8 (range: 23-44); the mean post-transplant score was 21.5 ± 5.9 (range: 14-32) and was statistically significantly lower than the pre-transplant score (P = 0.02). Among the individual domains, FT conferred a statistically significant improvement in aesthetic defect scores and exposed tissue scores (P ≤ 0.01) while, at the same time, it displayed no significant increases in co-morbidity (P = 0.17). There is a significant deficiency in functional outcome reports thus far. Moreover, FT resulted in improved overall FACES score, with the most dramatic improvements noted in aesthetic defect and exposed tissue scores.

  2. Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.

    PubMed

    Peterson, Lenna X; Shin, Woong-Hee; Kim, Hyungrae; Kihara, Daisuke

    2018-03-01

    We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group. To predict protein-protein complex structures, we used both multi-chain template-based modeling (TBM) and our protein-protein docking program, LZerD. LZerD represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. Because 3DZD are a soft representation of the protein surface, LZerD is tolerant to small conformational changes, making it well suited to docking unbound and TBM structures. The key to our improved performance in CAPRI Round 37 was to combine multi-chain TBM and docking. As opposed to our previous strategy of performing docking for all target complexes, we used TBM when multi-chain templates were available and docking otherwise. We also describe the combination of multiple scoring functions used by our server scorer group, which achieved the top rank for the scorer phase. © 2017 Wiley Periodicals, Inc.

  3. Establishing inter-rater reliability scoring in a state trauma system.

    PubMed

    Read-Allsopp, Christine

    2004-01-01

    Trauma systems rely on accurate Injury Severity Scoring (ISS) to describe trauma patient populations. Twenty-seven (27) Trauma Nurse Coordinators and Data Managers across the state of New South Wales, Australia trauma network were instructed in the uses and techniques of the Abbreviated Injury Scale (AIS) from the Association for the Advancement of Automotive Medicine. The aim is to provide accurate, reliable and valid data for the state trauma network. Four (4) months after the course a coding exercise was conducted to assess inter-rater reliability. The results show that inter-rater reliability is with accepted international standards.

  4. [The profile of WISC-R scores in children with high-functioning autism].

    PubMed

    Zielinska, Monika; Sterczynski, Radoslaw; Baginska, Aneta

    2014-01-01

    The aim of the study was to define the intellectual profile of Polish children suffering from autism. Our study was based on the results of previous research, mostly conducted in English-speaking countries. Although these earlier studies documented the intellectual profile of an autistic child, they also identified some discrepancies. Therefore, we decided to complement the discussion on autism with our data on intellectual functioning of autistic Polish children examined with a translated version of the intelligence test. The study followed a matching design. From among 191 children with autism and 1 400 without this diagnosis, we selected 34 pairs based on gender and age, and not differing by more than 10 points in terms of intelligence quotient. The intellectual profile of the studied children was determined with the WISC-R scale. As expected, the intellectual profile of children with autism proved more variable than that of healthy controls. Children with autism scored lower on "Comprehension" scale and (at a threshold of statistical significance) on "Object assembly" scale, and achieved higher results on "Information" and "Block design" scales. The results of our study confirmed the most typical observations from previous research conducted among an English-speaking population of autistic children. Polish autistic children did not differ significantly in terms of their quotients of verbal and non-verbal intelligence. However, the intellectual profile of autistic children showed higher variance compared to normally developing controls. Children with autism were more likely to score the lowest in the "Comprehension" subtest and the highest in the "Block design" subtest.

  5. Accurate Identification of Fear Facial Expressions Predicts Prosocial Behavior

    PubMed Central

    Marsh, Abigail A.; Kozak, Megan N.; Ambady, Nalini

    2009-01-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants’ ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale. PMID:17516803

  6. Accurate identification of fear facial expressions predicts prosocial behavior.

    PubMed

    Marsh, Abigail A; Kozak, Megan N; Ambady, Nalini

    2007-05-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants' ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale.

  7. Pharmacophore-Based Similarity Scoring for DOCK

    PubMed Central

    2015-01-01

    Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein–ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK. PMID:25229837

  8. Renal function had an independent relationship with coronary artery calcification in Chinese elderly men.

    PubMed

    Fu, Shihui; Zhang, Zhao; Luo, Leiming; Ye, Ping

    2017-04-07

    Although previous studies have analyzed the relationship between renal function and coronary artery calcification (CAC) in pre-dialysis and dialysis patients, limited studies have discussed the relationship between renal function and CAC in Chinese elderly men without obvious damage of renal function. The present study was designed to explore the relationship between renal function and CAC in Chinese elderly men without obvious damage of renal function. This cross-sectional study was carried out in 105 male participants older than 60 years with glomerular filtration rate (GFR) ≥ 45 ml/min/1.73 m 2 . CAC was detected by high-definition computerized tomography (HDCT), which is a highly sensitive technique for detecting the CAC and provides the most accurate CAC scores up to date. Age was 72 ± 8.4 years on average and ranged from 60 to 89 years. Simple correlation analysis indicated that all kinds of CAC scores including the Agatston, volume and mass scores inversely correlated with GFR values (p < 0.05 for all). In multivariate linear regression analysis, GFR values were independently associated with all these CAC scores (p < 0.05 for all). Renal function had an independent relationship with CAC detected by HDCT in Chinese elderly men, demonstrating that the relationship between renal function and CAC started at the early stage of renal function decline.

  9. Translation and validation of the new version of the Knee Society Score - The 2011 KS Score - into Brazilian Portuguese.

    PubMed

    Silva, Adriana Lucia Pastore E; Croci, Alberto Tesconi; Gobbi, Riccardo Gomes; Hinckel, Betina Bremer; Pecora, José Ricardo; Demange, Marco Kawamura

    2017-01-01

    Translation, cultural adaptation, and validation of the new version of the Knee Society Score - The 2011 KS Score - into Brazilian Portuguese and verification of its measurement properties, reproducibility, and validity. In 2012, the new version of the Knee Society Score was developed and validated. This scale comprises four separate subscales: (a) objective knee score (seven items: 100 points); (b) patient satisfaction score (five items: 40 points); (c) patient expectations score (three items: 15 points); and (d) functional activity score (19 items: 100 points). A total of 90 patients aged 55-85 years were evaluated in a clinical cross-sectional study. The pre-operative translated version was applied to patients with TKA referral, and the post-operative translated version was applied to patients who underwent TKA. Each patient answered the same questionnaire twice and was evaluated by two experts in orthopedic knee surgery. Evaluations were performed pre-operatively and three, six, or 12 months post-operatively. The reliability of the questionnaire was evaluated using the intraclass correlation coefficient (ICC) between the two applications. Internal consistency was evaluated using Cronbach's alpha. The ICC found no difference between the means of the pre-operative, three-month, and six-month post-operative evaluations between sub-scale items. The Brazilian Portuguese version of The 2011 KS Score is a valid and reliable instrument for objective and subjective evaluation of the functionality of Brazilian patients who undergo TKA and revision TKA.

  10. Analytic score distributions for a spatially continuous tridirectional Monte Carol transport problem

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

    Booth, T.E.

    1996-01-01

    The interpretation of the statistical error estimates produced by Monte Carlo transport codes is still somewhat of an art. Empirically, there are variance reduction techniques whose error estimates are almost always reliable, and there are variance reduction techniques whose error estimates are often unreliable. Unreliable error estimates usually result from inadequate large-score sampling from the score distribution`s tail. Statisticians believe that more accurate confidence interval statements are possible if the general nature of the score distribution can be characterized. Here, the analytic score distribution for the exponential transform applied to a simple, spatially continuous Monte Carlo transport problem is provided.more » Anisotropic scattering and implicit capture are included in the theory. In large part, the analytic score distributions that are derived provide the basis for the ten new statistical quality checks in MCNP.« less

  11. 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.

  12. REANALYZING THE MODIFIED FERRIMAN-GALLWEY SCORE: IS THERE A SIMPLER METHOD FOR ASSESSING THE EXTENT OF HIRSUTISM?

    PubMed Central

    Cook, Heather; Brennan, Kathleen; Azziz, Ricardo

    2011-01-01

    Objective To determine whether assessing the extent of terminal hair growth in a subset of the traditional 9 areas included in the modified Ferriman-Gallwey (mFG) score can serve as a simpler predictor of total body hirsutism when compared to the full scoring system, and to determine if this new model can accurately distinguish hirsute from non-hirsute women. Design Cross-sectional analysis Setting Two tertiary care academic referral centers. Patients 1951 patients presenting for symptoms of androgen excess. Interventions History and physical examination, including mFG score. Main Outcome Measures Total body hirsutism. Results A regression model using all nine body areas indicated that the combination of upper abdomen, lower abdomen and chin was the best predictor of the total full mFG score. Using this subset of three body areas is accurate in distinguishing true hirsute from non-hirsute women when defining true hirsutism as mFG>7. Conclusion Scoring terminal hair growth only on the chin and abdomen can serve as a simple, yet reliable predictor of total body hirsutism when compared to full body scoring using the traditional mFG system. PMID:21924716

  13. A Simple Symptom Score for Acute HIV Infection in a San Diego Community Based Screening Program.

    PubMed

    Lin, Timothy C; Gianella, Sara; Tenenbaum, Tara; Little, Susan J; Hoenigl, Martin

    2017-12-25

    Treatment of acute HIV infection (AHI) decreases transmission and preserves immune function, but AHI diagnosis remains resource-intensive. Risk-based scores predictive for AHI have been described for high-risk groups, however symptom-based scores could be more generalizable across populations. Adults who tested either positive for AHI (antibody-negative, HIV nucleic acid test [NAT]-positive) or HIV NAT-negative with the community-based Early Test HIV screening program in San Diego were retrospectively randomized 2:1 into a derivation and validation set. In the former, symptoms significant for AHI in a multivariate logistic regression model were assigned a score value (the odds ratio rounded to the nearest integer). The score was assessed in the validation set using receiver operating characteristics and areas under the curve (AUC). An optimal cut-off score was found using Youden's index. Of 998 participants (including 737 men who have sex with men (MSM), 149 non-MSM men, 109 ciswomen and 3 trans women), 113 had AHI (including 109 MSM). Compared to HIV-negative cases, AHI cases reported more symptoms (median 4 vs 0, p<0.01). Fever, myalgia and weight loss were significantly associated with AHI in the multivariate model and corresponded to 11, 8 and 4 score points, respectively. The summed score yielded AUC of 0.85 (95%CI 0.77-0.93). A score of ≥11 was 72% sensitive, 96% specific with diagnostic odds ratio of 70.27 (95%CI 28.14-175.93). A 3-symptom score accurately predicted AHI in a community based screening program and may inform allocation of resources in settings that do not routinely screen for AHI. © The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  14. Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

    PubMed

    Fox, Naomi; Streinu, Ileana

    2013-01-01

    Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future

  15. Towards accurate modeling of noncovalent interactions for protein rigidity analysis

    PubMed Central

    2013-01-01

    Background Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. Results To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. Conclusion To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all

  16. Responsiveness to Change of Functional Limitation Reporting: Cross-sectional Study Using the Intermountain ROMS Scale in Outpatient Rehabilitation.

    PubMed

    Brennan, Gerard P; Hunter, Stephen J; Snow, Greg; Minick, Kate I

    2017-12-01

    The Centers for Medicare and Medicaid Services (CMS) require physical therapists document patients' functional limitations. The process is not standardized. 
A systematic approach to determine a patient's functional limitations and responsiveness to change is needed. The purpose of this study is to compare patient-reported outcomes (PROs) responsiveness to change using 7-level severity/complexity modifier scale proposed by Medicare to a derived scale implemented by Intermountain Healthcare's Rehabilitation Outcomes Management System (ROMS). This was a retrospective, observational cohort design. 165,183 PROs prior to July 1, 2013, were compared to 46,334 records from July 1, 2013, to December 31, 2015. Histograms and ribbon plots illustrate distribution and change of patients' scores. ROMS raw score ranges were calculated and compared to CMS' severity/complexity levels based on score percentage. Distribution of the population was compared based on the 2 methods. Sensitivity and specificity were compared for responsiveness to change based on minimal clinically important difference (MCID). Histograms demonstrated few patient scores placed in CMS scale levels at the extremes, whereas the majority of scores placed in 2 middle levels (CJ, CK). ROMS distributed scores more evenly across levels. Ribbon plots illustrated advantage of ROMS' using narrower score ranges. Greater chance for patients to change levels was observed with ROMS when an MCID was achieved. ROMS narrower scale levels resulted in greater sensitivity and good specificity. Geographic representation for the United States was limited. Without patients' global rating of change, a reference standard to gauge validation of improvement could not be provided. ROMS provides a standard approach to identify accurately functional limitation modifier levels and to detect improvement more accurately than a straight across transposition using the CMS scale. © 2017 American Physical Therapy Association

  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

    2017-08-01

    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. Noninvasive assessment of extracellular and intracellular dehydration in healthy humans using the resistance-reactance-score graph method.

    PubMed

    Heavens, Kristen R; Charkoudian, Nisha; O'Brien, Catherine; Kenefick, Robert W; Cheuvront, Samuel N

    2016-03-01

    Few dehydration assessment measures provide accurate information; most are based on reference change values and very few are diagnostically accurate from a single observation or measure. Bioelectrical impedance may lack the precision to detect common forms of dehydration in healthy individuals. Limitations in bioimpedance may be addressed by a unique resistance-reactance (RXc)-score graph method, which transforms vector components into z scores for use with any impedance analyzer in any population. We tested whether the RXc-score graph method provides accurate single or serial assessments of dehydration when compared with gold-standard measures of total body water by using stable isotope dilution (deuterium oxide) combined with body-weight changes. We retrospectively analyzed data from a previous study in which 9 healthy young men participated in 3 trials: euhydration (EUH), extracellular dehydration (ED; via a diuretic), and intracellular dehydration (ID; via exercise in the heat). Participants lost 4-5% of their body weight during the dehydration trials; volume loss was similar between trials (ID compared with ED group: 3.5 ± 0.8 compared with 3.0 ± 0.6 L; P > 0.05). Despite significant losses of body water, most RXc vector scores for ED and ID groups were classified as "normal" (within the 75% population tolerance ellipse). However, directional displacement of vectors was consistent with loss of volume in both ED and ID conditions compared with the EUH condition and tended to be longer in ED than in ID conditions (P = 0.054). We conclude that, whereas individual RXc-score graph values do not provide accurate detection of dehydration from single measurements, directional changes in vector values from serial measurements are consistent with fluid loss for both ED and ID conditions. The RXc-score graph method may therefore alert clinicians to changes in hydration state, which may bolster the interpretation of other recognized change measures of hydration. © 2016

  19. Multilocus lod scores in large pedigrees: combination of exact and approximate calculations.

    PubMed

    Tong, Liping; Thompson, Elizabeth

    2008-01-01

    To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some 'key' individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. (c) 2007 S. Karger AG, Basel

  20. Multilocus Lod Scores in Large Pedigrees: Combination of Exact and Approximate Calculations

    PubMed Central

    Tong, Liping; Thompson, Elizabeth

    2007-01-01

    To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some ‘key’ individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. PMID:17934317

  1. Variceal bleeding in cirrhotic patients: What is the best prognostic score?

    PubMed

    Mohammad, Asmaa N; Morsy, Khairy H; Ali, Moustafa A

    2016-09-01

    To find the most accurate, suitable, and applicable scoring system for the prediction of outcome in cirrhotic patients with bleeding varices. A prospective study was conducted comprising 120 cirrhotic patients with acute variceal bleeding who were admitted to Tropical Medicine and Gastroenterology Department in Sohag University Hospital, over a 1-year period (1/2015 to 1/2016). The clinical, laboratory, and endoscopic parameters were studied. Child-Turcotte-Pugh (CTP) classification score, Model for end-stage liver disease (MELD) score, acute physiology and chronic health evaluation II (APACHE II) score, sequential organ failure assessment (SOFA) score, and AIMS65 score were calculated for all patients. Univariate and multivariate analyses were performed for all the measured parameters and scores. Of the 120 patients (92 male) admitted during the study period, eight patients (6.67%) died in the hospital. Advanced age, the presence of encephalopathy, rebleeding, and higher serum bilirubin were independent factors associated with higher hospital mortality. The largest area under the receiver operator curve (AUROC) was obtained for the AIMS65 score and SOFA score, followed by the MELD score and APACHEII score, then CTP score, all of which achieved very good performance (AUROC>0.8). AIMS65 score showed the best sensitivity, specificity, and negative and positive predictive values. Although the AIMS65 score was not significantly different from the MELD, SOFA, and APACHEII scores, it was the optimum among them in terms of the prediction of mortality. AIMS65 score is the best simple and applicable scoring system for independently predicting mortality in cirrhotic patients with acute variceal bleeding.

  2. Extended score interval in the assessment of basic surgical skills.

    PubMed

    Acosta, Stefan; Sevonius, Dan; Beckman, Anders

    2015-01-01

    Introduction The Basic Surgical Skills course uses an assessment score interval of 0-3. An extended score interval, 1-6, was proposed by the Swedish steering committee of the course. The aim of this study was to analyze the trainee scores in the current 0-3 scored version compared to a proposed 1-6 scored version. Methods Sixteen participants, seven females and nine males, were evaluated in the current and proposed assessment forms by instructors, observers, and learners themselves during the first and second day. In each assessment form, 17 tasks were assessed. The inter-rater reliability between the current and the proposed score sheets were evaluated with intraclass correlation (ICC) with 95% confidence intervals (CI). Results The distribution of scores for 'knot tying' at the last time point and 'bowel anastomosis side to side' given by the instructors in the current assessment form showed that the highest score was given in 31 and 62%, respectively. No ceiling effects were found in the proposed assessment form. The overall ICC between the current and proposed score sheets after assessment by the instructors increased from 0.38 (95% CI 0.77-0.78) on Day 1 to 0.83 (95% CI 0.51-0.94) on Day 2. Discussion A clear ceiling effect of scores was demonstrated in the current assessment form, questioning its validity. The proposed score sheet provides more accurate scores and seems to be a better feedback instrument for learning technical surgical skills in the Basic Surgical Skills course.

  3. 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.

  4. An Evaluation of Statistical Strategies for Making Equating Function Selections. Research Report. ETS RR-08-60

    ERIC Educational Resources Information Center

    Moses, Tim

    2008-01-01

    Nine statistical strategies for selecting equating functions in an equivalent groups design were evaluated. The strategies of interest were likelihood ratio chi-square tests, regression tests, Kolmogorov-Smirnov tests, and significance tests for equated score differences. The most accurate strategies in the study were the likelihood ratio tests…

  5. Can pain and function be distinguished in the Oxford Hip Score in a meaningful way? : an exploratory and confirmatory factor analysis.

    PubMed

    Harris, K K; Price, A J; Beard, D J; Fitzpatrick, R; Jenkinson, C; Dawson, J

    2014-11-01

    The objective of this study was to explore dimensionality of the Oxford Hip Score (OHS) and examine whether self-reported pain and functioning can be distinguished in the form of subscales. This was a secondary data analysis of the UK NHS hospital episode statistics/patient-reported outcome measures dataset containing pre-operative OHS scores on 97 487 patients who were undergoing hip replacement surgery. The proposed number of factors to extract depended on the method of extraction employed. Velicer's Minimum Average Partial test and the Parallel Analysis suggested one factor, the Cattell's scree test and Kaiser-over-1 rule suggested two factors. Exploratory factor analysis demonstrated that the two-factor OHS had most of the items saliently loading either of the two factors. These factors were named 'Pain' and 'Function' and their respective subscales were created. There was some cross-loading of items: 8 (pain on standing up from a chair) and 11 (pain during work). These items were assigned to the 'Pain' subscale. The final 'Pain' subscale consisted of items 1, 8, 9, 10, 11 and 12. The 'Function' subscale consisted of items 2, 3, 4, 5, 6 and 7, with the recommended scoring of the subscales being from 0 (worst) to 100 (best). Cronbach's alpha was 0.855 for the 'Pain' subscale and 0.861 for the 'Function' subscale. A confirmatory factor analysis demonstrated that the two-factor model of the OHS had a better fit. However, none of the one-factor or two-factor models was rejected. Factor analyses demonstrated that, in addition to current usage as a single summary scale, separate information on pain and self-reported function can be extracted from the OHS in a meaningful way in the form of subscales. Cite this article: Bone Joint Res 2014;3:305-9. ©2014 The British Editorial Society of Bone & Joint Surgery.

  6. Cell-accurate optical mapping across the entire developing heart.

    PubMed

    Weber, Michael; Scherf, Nico; Meyer, Alexander M; Panáková, Daniela; Kohl, Peter; Huisken, Jan

    2017-12-29

    Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca 2+ -mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs.

  7. Cell-accurate optical mapping across the entire developing heart

    PubMed Central

    Meyer, Alexander M; Panáková, Daniela; Kohl, Peter

    2017-01-01

    Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca2+-mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs. PMID:29286002

  8. Preoperative PROMIS Scores Predict Postoperative Success in Foot and Ankle Patients.

    PubMed

    Ho, Bryant; Houck, Jeff R; Flemister, Adolph S; Ketz, John; Oh, Irvin; DiGiovanni, Benedict F; Baumhauer, Judith F

    2016-09-01

    The use of patient-reported outcomes continues to expand beyond the scope of clinical research to involve standard of care assessments across orthopedic practices. It is currently unclear how to interpret and apply this information in the daily care of patients in a foot and ankle clinic. We prospectively examined the relationship between preoperative patient-reported outcomes (PROMIS Physical Function, Pain Interference and Depression scores), determined minimal clinical important differences for these values, and assessed if these preoperative values were predictors of improvement after operative intervention. Prospective collection of all consecutive patient visits to a multisurgeon tertiary foot and ankle clinic was obtained between February 2015 and April 2016. This consisted of 16 023 unique visits across 7996 patients, with 3611 new patients. Patients undergoing elective operative intervention were identified by ICD-9 and CPT code. PROMIS physical function, pain interference, and depression scores were assessed at initial and follow-up visits. Minimum clinically important differences (MCIDs) were calculated using a distribution-based method. Receiver operating characteristic (ROC) curves were calculated to determine whether preoperative PROMIS scores were predictive of achieving MCID. Cutoff values for PROMIS scores that would predict achieving MCID and not achieving MCID with 95% specificity were determined. Prognostic pre- and posttest probabilities based off these cutoffs were calculated. Patients with a minimum of 7-month follow-up (mean 9.9) who completed all PROMIS domains were included, resulting in 61 patients. ROC curves demonstrated that preoperative physical function scores were predictive of postoperative improvement in physical function (area under the curve [AUC] 0.83). Similarly, preoperative pain interference scores were predictive of postoperative pain improvement (AUC 0.73) and preoperative depression scores were also predictive of

  9. 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…

  10. The Glasgow Prognostic Score, an inflammation based prognostic score, predicts survival in patients with hepatocellular carcinoma

    PubMed Central

    2013-01-01

    Background Elevated Glasgow Prognostic Score (GPS) has been related to poor prognosis in patients with hepatocellular carcinoma (HCC) undergoing surgical resection or receiving sorafenib. The aim of this study was to investigate the prognostic value of GPS in patients with various stages of the disease and with different liver functional status. Methods One hundred and fifty patients with newly diagnosed HCC were prospectively evaluated. Patients were divided according to their GPS scores. Univariate and multivariate analyses were performed to identify clinicopathological variables associated with overall survival; the identified variables were then compared with those of other validated staging systems. Results Elevated GPS were associated with increased asparate aminotransferase (P<0.0001), total bilirubin (P<0.0001), decreased albumin (P<0.0001), α-fetoprotein (P=0.008), larger tumor diameter (P=0.003), tumor number (P=0.041), vascular invasion (P=0.0002), extra hepatic metastasis (P=0.02), higher Child-Pugh scores (P<0.0001), and higher Cancer Liver Italian Program scores (P<0.0001). On multivariate analysis, the elevated GPS was independently associated with worse overall survival. Conclusions Our results demonstrate that the GPS can serve as an independent marker of poor prognosis in patients with HCC in various stages of disease and different liver functional status. PMID:23374755

  11. An accurate and efficient method for piezoelectric coated functional devices based on the two-dimensional Green’s function for a normal line force and line charge

    NASA Astrophysics Data System (ADS)

    Hou, Peng-Fei; Zhang, Yang

    2017-09-01

    Because most piezoelectric functional devices, including sensors, actuators and energy harvesters, are in the form of a piezoelectric coated structure, it is valuable to present an accurate and efficient method for obtaining the electro-mechanical coupling fields of this coated structure under mechanical and electrical loads. With this aim, the two-dimensional Green’s function for a normal line force and line charge on the surface of coated structure, which is a combination of an orthotropic piezoelectric coating and orthotropic elastic substrate, is presented in the form of elementary functions based on the general solution method. The corresponding electro-mechanical coupling fields of this coated structure under arbitrary mechanical and electrical loads can then be obtained by the superposition principle and Gauss integration. Numerical results show that the presented method has high computational precision, efficiency and stability. It can be used to design the best coating thickness in functional devices, improve the sensitivity of sensors, and improve the efficiency of actuators and energy harvesters. This method could be an efficient tool for engineers in engineering applications.

  12. Validation of the LOD score compared with APACHE II score in prediction of the hospital outcome in critically ill patients.

    PubMed

    Khwannimit, Bodin

    2008-01-01

    The Logistic Organ Dysfunction score (LOD) is an organ dysfunction score that can predict hospital mortality. The aim of this study was to validate the performance of the LOD score compared with the Acute Physiology and Chronic Health Evaluation II (APACHE II) score in a mixed intensive care unit (ICU) at a tertiary referral university hospital in Thailand. The data were collected prospectively on consecutive ICU admissions over a 24 month period from July1, 2004 until June 30, 2006. Discrimination was evaluated by the area under the receiver operating characteristic curve (AUROC). The calibration was assessed by the Hosmer-Lemeshow goodness-of-fit H statistic. The overall fit of the model was evaluated by the Brier's score. Overall, 1,429 patients were enrolled during the study period. The mortality in the ICU was 20.9% and in the hospital was 27.9%. The median ICU and hospital lengths of stay were 3 and 18 days, respectively, for all patients. Both models showed excellent discrimination. The AUROC for the LOD and APACHE II were 0.860 [95% confidence interval (CI) = 0.838-0.882] and 0.898 (95% Cl = 0.879-0.917), respectively. The LOD score had perfect calibration with the Hosmer-Lemeshow goodness-of-fit H chi-2 = 10 (p = 0.44). However, the APACHE II had poor calibration with the Hosmer-Lemeshow goodness-of-fit H chi-2 = 75.69 (p < 0.001). Brier's score showed the overall fit for both models were 0.123 (95%Cl = 0.107-0.141) and 0.114 (0.098-0.132) for the LOD and APACHE II, respectively. Thus, the LOD score was found to be accurate for predicting hospital mortality for general critically ill patients in Thailand.

  13. RAPID3 scores and hand outcome measurements in RA patients: a preliminary study.

    PubMed

    Qorolli, Merita; Hundozi-Hysenaj, Hajrije; Rexhepi, Sylejman; Rehxepi, Blerta; Grazio, Simeon

    2017-06-01

    The Routine Assessment of Patient Index Data 3 (RAPID3) is a patient-reported disease activity measure used to assess physical function, pain, and global health in patients with rheumatoid arthritis (RA) without formal joint counts. Since hand involvement and its decreased function are hallmarks of RA, the aim of our study was to investigate the performance of RAPID3 scores with regard to hand function and to confirm previous findings that the RAPID3 score as a disease activity measure is strongly correlated with the DAS28 score. Sixty-eight consecutive patients with RA (85% female), aged 18-75 years, were included in the study and were recruited during their outpatient visit. Apart from demographic and clinical data, the obtained parameters of interest included RAPID3 scores and assessments of the function of the hand, namely, the signal of functional impairment (SOFI)-hand, grip strength, and pulp-to-palm distance, as well the Health Assessment Questionnaire- Disability Index (HAQ-DI) and DAS28 scores. Pearson's correlation coefficient, Student's t test and linear regression were used in the statistical analysis of the results. The significance was set to p < 0.05. A positive correlation was found between RAPID3 scores and HAQ-DI scores, SOFI-hand scores, and pulp-to-palm distance, and negative correlation was observed between RAPID3 scores and grip strength. The order regarding the strength of correlations between RAPID3 scores and other variables (from the strongest to the weakest) was as follows: HAQ-DI, grip strength, SOFI-hand and pulp-to-palm distance. The hand assessment variables had stronger correlations with RAPID3 scores than with DAS28 scores. Our preliminary study showed that RAPID3 scores were strongly correlated with measurements of the functional ability of the hand, demonstrating that RAPID3 can be used as a measure of disease activity in clinical practice and to characterize hand function. Further studies are needed to confirm this result.

  14. Pediatric ocular trauma score as a prognostic tool in the management of pediatric traumatic cataracts.

    PubMed

    Shah, Mehul A; Agrawal, Rupesh; Teoh, Ryan; Shah, Shreya M; Patel, Kashyap; Gupta, Satyam; Gosai, Siddharth

    2017-05-01

    To introduce and validate the pediatric ocular trauma score (POTS) - a mathematical model to predict visual outcome trauma in children with traumatic cataract METHODS: In this retrospective cohort study, medical records of consecutive children with traumatic cataracts aged 18 and below were retrieved and analysed. Data collected included age, gender, visual acuity, anterior segment and posterior segment findings, nature of surgery, treatment for amblyopia, follow-up, and final outcome was recorded on a precoded data information sheet. POTS was derived based on the ocular trauma score (OTS), adjusting for age of patient and location of the injury. Visual outcome was predicted using the OTS and the POTS and using receiver operating characteristic (ROC) curves. POTS predicted outcomes were more accurate compared to that of OTS (p = 0.014). POTS is a more sensitive and specific score with more accurate predicted outcomes compared to OTS, and is a viable tool to predict visual outcomes of pediatric ocular trauma with traumatic cataract.

  15. The Effect of Stakes on Accountability Test Scores and Pass Rates

    ERIC Educational Resources Information Center

    Steedle, Jeffrey T.; Grochowalski, Joseph

    2017-01-01

    Students may not fully demonstrate their knowledge and skills on accountability tests if there are no stakes attached to individual performance. In that case, assessment results may not accurately reflect student achievement, so the validity of score interpretations and uses suffers. For this study, matched samples of students taking state…

  16. Using an educational electronic documentation system to help nursing students accurately identify patient data.

    PubMed

    Pobocik, Tamara

    2015-01-01

    This quantitative research study used a pretest/posttest design and reviewed how an educational electronic documentation system helped nursing students to identify the accurate "related to" statement of the nursing diagnosis for the patient in the case study. Students in the sample population were senior nursing students in a bachelor of science nursing program in the northeastern United States. Two distinct groups were used for a control and intervention group. The intervention group used the educational electronic documentation system for three class assignments. Both groups were given a pretest and posttest case study. The Accuracy Tool was used to score the students' responses to the related to statement of a nursing diagnosis given at the end of the case study. The scores of the Accuracy Tool were analyzed, and then the numeric scores were placed in SPSS, and the paired t test scores were analyzed for statistical significance. The intervention group's scores were statistically different from the pretest scores to posttest scores, while the control group's scores remained the same from pretest to posttest. The recommendation to nursing education is to use the educational electronic documentation system as a teaching pedagogy to help nursing students prepare for nursing practice. © 2014 NANDA International, Inc.

  17. 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.

  18. 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.

  19. Risk-adjusted scoring systems in colorectal surgery.

    PubMed

    Leung, Edmund; McArdle, Kirsten; Wong, Ling S

    2011-01-01

    Consequent to recent advances in surgical techniques and management, survival rate has increased substantially over the last 25 years, particularly in colorectal cancer patients. However, post-operative morbidity and mortality from colorectal cancer vary widely across the country. Therefore, standardised outcome measures are emphasised not only for professional accountability, but also for comparison between treatment units and regions. In a heterogeneous population, the use of crude mortality as an outcome measure for patients undergoing surgery is simply misleading. Meaningful comparisons, however, require accurate risk stratification of patients being analysed before conclusions can be reached regarding the outcomes recorded. Sub-specialised colorectal surgical units usually dedicated to more complex and high-risk operations. The need for accurate risk prediction is necessary in these units as both mortality and morbidity often are tools to justify the practice of high-risk surgery. The Acute Physiology And Chronic Health Evaluation (APACHE) is a system for classifying patients in the intensive care unit. However, APACHE score was considered too complex for general surgical use. The American Society of Anaesthesiologists (ASA) grade has been considered useful as an adjunct to informed consent and for monitoring surgical performance through time. ASA grade is simple but too subjective. The Physiological & Operative Severity Score for the enUmeration of Mortality and morbidity (POSSUM) and its variant Portsmouth POSSUM (P-POSSUM) were devised to predict outcomes in surgical patients in general, taking into account of the variables in the case-mix. POSSUM has two parts, which include assessment of physiological parameters and operative scores. There are 12 physiological parameters and 6 operative measures. The physiological parameters are taken at the time of surgery. Each physiological parameter or operative variable is sub-divided into three or four levels with

  20. Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition

    PubMed Central

    2012-01-01

    Background Existing methods for predicting protein solubility on overexpression in Escherichia coli advance performance by using ensemble classifiers such as two-stage support vector machine (SVM) based classifiers and a number of feature types such as physicochemical properties, amino acid and dipeptide composition, accompanied with feature selection. It is desirable to develop a simple and easily interpretable method for predicting protein solubility, compared to existing complex SVM-based methods. Results This study proposes a novel scoring card method (SCM) by using dipeptide composition only to estimate solubility scores of sequences for predicting protein solubility. SCM calculates the propensities of 400 individual dipeptides to be soluble using statistic discrimination between soluble and insoluble proteins of a training data set. Consequently, the propensity scores of all dipeptides are further optimized using an intelligent genetic algorithm. The solubility score of a sequence is determined by the weighted sum of all propensity scores and dipeptide composition. To evaluate SCM by performance comparisons, four data sets with different sizes and variation degrees of experimental conditions were used. The results show that the simple method SCM with interpretable propensities of dipeptides has promising performance, compared with existing SVM-based ensemble methods with a number of feature types. Furthermore, the propensities of dipeptides and solubility scores of sequences can provide insights to protein solubility. For example, the analysis of dipeptide scores shows high propensity of α-helix structure and thermophilic proteins to be soluble. Conclusions The propensities of individual dipeptides to be soluble are varied for proteins under altered experimental conditions. For accurately predicting protein solubility using SCM, it is better to customize the score card of dipeptide propensities by using a training data set under the same specified

  1. Pediatric trauma BIG score: predicting mortality in children after military and civilian trauma.

    PubMed

    Borgman, Matthew A; Maegele, Marc; Wade, Charles E; Blackbourne, Lorne H; Spinella, Philip C

    2011-04-01

    To develop a validated mortality prediction score for children with traumatic injuries. We identified all children (<18 years of age) in the US military established Joint Theater Trauma Registry from 2002 to 2009 who were admitted to combat-support hospitals with traumatic injuries in Iraq and Afghanistan. We identified factors associated with mortality using univariate and then multivariate regression modeling. The developed mortality prediction score was then validated on a data set of pediatric patients (≤ 18 years of age) from the German Trauma Registry, 2002-2007. Admission base deficit, international normalized ratio, and Glasgow Coma Scale were independently associated with mortality in 707 patients from the derivation set and 1101 patients in the validation set. These variables were combined into the pediatric "BIG" score (base deficit + [2.5 × international normalized ratio] + [15 - Glasgow Coma Scale), which were each calculated to have an area under the curve of 0.89 (95% confidence interval: 0.83-0.95) and 0.89 (95% confidence interval: 0.87-0.92) on the derivation and validation sets, respectively. The pediatric trauma BIG score is a simple method that can be performed rapidly on admission to evaluate severity of illness and predict mortality in children with traumatic injuries. The score has been shown to be accurate in both penetrating-injury and blunt-injury populations and may have significant utility in comparing severity of injury in future pediatric trauma research and quality-assurance studies. In addition, this score may be used to determine inclusion criteria on admission for prospective studies when accurately estimating the mortality for sample size calculation is required.

  2. Differences in MMPI-2 FBS and RBS scores in brain injury, probable malingering, and conversion disorder groups: a preliminary study.

    PubMed

    Peck, C P; Schroeder, R W; Heinrichs, R J; Vondran, E J; Brockman, C J; Webster, B K; Baade, L E

    2013-01-01

    This study examined differences in raw scores on the Symptom Validity Scale and Response Bias Scale (RBS) from the Minnesota Multiphasic Personality Inventory-2 in three criterion groups: (i) valid traumatic brain injured, (ii) invalid traumatic brain injured, and (iii) psychogenic non-epileptic seizure disorders. Results indicate that a >30 raw score cutoff for the Symptom Validity Scale accurately identified 50% of the invalid traumatic brain injured group, while misclassifying none of the valid traumatic brain injured group and 6% of the psychogenic non-epileptic seizure disorder group. Using a >15 RBS raw cutoff score accurately classified 50% of the invalid traumatic brain injured group and misclassified fewer than 10% of the valid traumatic brain injured and psychogenic non-epileptic seizure disorder groups. These cutoff scores used conjunctively did not misclassify any members of the psychogenic non-epileptic seizure disorder or valid traumatic brain injured groups, while accurately classifying 44% of the invalid traumatic brain injured individuals. Findings from this preliminary study suggest that the conjunctive use of the Symptom Validity Scale and the RBS from the Minnesota Multiphasic Personality Inventory-2 may be useful in differentiating probable malingering from individuals with brain injuries and conversion disorders.

  3. Correlation of Patient-Reported Outcomes Measurement Information System (PROMIS) scores with legacy patient-reported outcome scores in patients undergoing rotator cuff repair.

    PubMed

    Patterson, Brendan M; Orvets, Nathan D; Aleem, Alexander W; Keener, Jay D; Calfee, Ryan P; Nixon, Devon C; Chamberlain, Aaron M

    2018-06-01

    The Patient-Reported Outcomes Measurement Information System (PROMIS) is being used to assess outcomes in many patient populations despite limited validation. The purpose of this study was to investigate the relationship between American Shoulder and Elbow Surgeons (ASES) and Simple Shoulder Test (SST) scores and PROMIS Physical Function (PF) and Upper Extremity (UE) function scores collected preoperatively in patients undergoing rotator cuff repair. This cross-sectional study analyzed 164 consecutive patients undergoing arthroscopic rotator cuff repair. Study inclusion required preoperative completion of the ASES and SST evaluations, as well as the PROMIS PF, UE, and Pain Interference computerized adaptive tests. Descriptive statistics were produced, and Pearson correlation coefficients were calculated between each of the outcome measures. Average PROMIS UE scores indicated greater impairment than PROMIS PF scores (34 vs 44). Three percent of patients reached the PROMIS UE ceiling score of 56. PROMIS PF scores demonstrated a weak correlation with ASES scores (r = 0.43, P < .001) and a moderate correlation with SST scores (r = 0.51, P < .001). PROMIS UE scores demonstrated a moderate correlation with both ASES scores (r = 0.59, P < .001) and SST scores (r = 0.62, P < .001). PROMIS Pain Interference scores demonstrated weak negative correlations with both ASES scores (r = -0.43, P < .001) and SST scores (r = -0.41, P < .001). Patients answered fewer questions on average using the PROMIS PF and UE instruments as compared with the ASES and SST instruments. PROMIS UE scores indicate greater impairment and demonstrate a stronger correlation with the legacy shoulder scores than PROMIS PF scores in patients with symptomatic rotator cuff tears. PROMIS computerized adaptive tests allow for more efficient patient-reported outcome data collection compared with traditional outcome scores. Copyright © 2018 Journal of Shoulder and

  4. Simple new risk score model for adult cardiac extracorporeal membrane oxygenation: simple cardiac ECMO score.

    PubMed

    Peigh, Graham; Cavarocchi, Nicholas; Keith, Scott W; Hirose, Hitoshi

    2015-10-01

    Although the use of cardiac extracorporeal membrane oxygenation (ECMO) is increasing in adult patients, the field lacks understanding of associated risk factors. While standard intensive care unit risk scores such as SAPS II (simplified acute physiology score II), SOFA (sequential organ failure assessment), and APACHE II (acute physiology and chronic health evaluation II), or disease-specific scores such as MELD (model for end-stage liver disease) and RIFLE (kidney risk, injury, failure, loss of function, ESRD) exist, they may not apply to adult cardiac ECMO patients as their risk factors differ from variables used in these scores. Between 2010 and 2014, 73 ECMOs were performed for cardiac support at our institution. Patient demographics and survival were retrospectively analyzed. A new easily calculated score for predicting ECMO mortality was created using identified risk factors from univariate and multivariate analyses, and model discrimination was compared with other scoring systems. Cardiac ECMO was performed on 73 patients (47 males and 26 females) with a mean age of 48 ± 14 y. Sixty-four percent of patients (47/73) survived ECMO support. Pre-ECMO SAPS II, SOFA, APACHE II, MELD, RIFLE, PRESERVE, and ECMOnet scores, were not correlated with survival. Univariate analysis of pre-ECMO risk factors demonstrated that increased lactate, renal dysfunction, and postcardiotomy cardiogenic shock were risk factors for death. Applying these data into a new simplified cardiac ECMO score (minimal risk = 0, maximal = 5) predicted patient survival. Survivors had a lower risk score (1.8 ± 1.2) versus the nonsurvivors (3.0 ± 0.99), P < 0.0001. Common intensive care unit or disease-specific risk scores calculated for cardiac ECMO patients did not correlate with ECMO survival, whereas a new simplified cardiac ECMO score provides survival predictability. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. A New Wrist Clinical Evaluation Score.

    PubMed

    Herzberg, Guillaume; Burnier, Marion; Nakamura, Toshiyasu

    2018-04-01

    Background  The number of available wrist scoring systems is limited; some of them do not include forearm rotation criteria. Purpose  To describe a new electronic wrist clinical score and to present a new patient's generated wrist evaluation criterion, the subjective wrist value (SWV). Materials and Methods  A new electronic wrist clinical score, the Lyon wrist score (LWS) including wrist VAS pain and function, active range of motion and strength was built into an excel file. VAS flexion-extension pain and function were evaluated independently from pronation-supination pain and function. A new patient's generated wrist evaluation criterion, SWV was described. Results  The LWS is available in two versions, standard and full (the latter including forearm rotation strength). Both standard and full LWS are displayed into an automatically generated diamond-shaped graph providing a comprehensive visual display of the clinical status of most osteoarticular wrist disorders. The graph also includes SWV. The LWS, combined with SWV into a graph that may be directly exported to a PowerPoint presentation, provide a new practical and comprehensive tool for following/comparing wrist osteoarticular clinical status/outcomes. Both standard and full LWS charts are available in colored versions on a related website for free download. Conclusion  A comprehensive updated electronic display of osteoarticular wrist clinical status including forearm rotation criteria is provided and displayed into a graph which may be exported as such into a PowerPoint presentation for clinical analysis/comparisons. Level of Evidence  Level II.

  6. Comparison of Glasgow-Blatchford score and full Rockall score systems to predict clinical outcomes in patients with upper gastrointestinal bleeding.

    PubMed

    Mokhtare, Marjan; Bozorgi, Vida; Agah, Shahram; Nikkhah, Mehdi; Faghihi, Amirhossein; Boghratian, Amirhossein; Shalbaf, Neda; Khanlari, Abbas; Seifmanesh, Hamidreza

    2016-01-01

    Various risk scoring systems have been recently developed to predict clinical outcomes in patients with upper gastrointestinal bleeding (UGIB). The two commonly used scoring systems include full Rockall score (RS) and the Glasgow-Blatchford score (GBS). Bleeding scores were assessed in terms of prediction of clinical outcomes in patients with UGIB. Two hundred patients (age >18 years) with obvious symptoms of UGIB in the emergency department of Rasoul Akram Hospital were enrolled. Full RS and GBS were calculated. We followed the patients for records of rebleeding and 1-month mortality. A receiver operating characteristic curve by using areas under the curve (AUCs) was used to statistically identify the best cutoff point. Eighteen patients were excluded from the study due to failure to follow-up. Rebleeding and mortality rate were 9.34% (n=17) and 11.53% (n=21), respectively. Regarding 1-month mortality, full RS was better than GBS (AUC, 0.648 versus 0.582; P =0.021). GBS was more accurate in terms of detecting transfusion need (AUC, 0.757 versus 0.528; P =0.001), rebleeding rate (AUC, 0.722 versus 0.520; P =0.002), intensive care unit admission rate (AUC, 0.648 versus 0.582; P =0.021), and endoscopic intervention rate (AUC, 0.771 versus 0.650; P <0.001). We found the full RS system is better for 1-month mortality prediction while GBS system is better for prediction of other outcomes.

  7. 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,…

  8. 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)

  9. Predicting stroke through genetic risk functions: the CHARGE Risk Score Project.

    PubMed

    Ibrahim-Verbaas, Carla A; Fornage, Myriam; Bis, Joshua C; Choi, Seung Hoan; Psaty, Bruce M; Meigs, James B; Rao, Madhu; Nalls, Mike; Fontes, Joao D; O'Donnell, Christopher J; Kathiresan, Sekar; Ehret, Georg B; Fox, Caroline S; Malik, Rainer; Dichgans, Martin; Schmidt, Helena; Lahti, Jari; Heckbert, Susan R; Lumley, Thomas; Rice, Kenneth; Rotter, Jerome I; Taylor, Kent D; Folsom, Aaron R; Boerwinkle, Eric; Rosamond, Wayne D; Shahar, Eyal; Gottesman, Rebecca F; Koudstaal, Peter J; Amin, Najaf; Wieberdink, Renske G; Dehghan, Abbas; Hofman, Albert; Uitterlinden, André G; Destefano, Anita L; Debette, Stephanie; Xue, Luting; Beiser, Alexa; Wolf, Philip A; Decarli, Charles; Ikram, M Arfan; Seshadri, Sudha; Mosley, Thomas H; Longstreth, W T; van Duijn, Cornelia M; Launer, Lenore J

    2014-02-01

    Beyond the Framingham Stroke Risk Score, prediction of future stroke may improve with a genetic risk score (GRS) based on single-nucleotide polymorphisms associated with stroke and its risk factors. The study includes 4 population-based cohorts with 2047 first incident strokes from 22,720 initially stroke-free European origin participants aged ≥55 years, who were followed for up to 20 years. GRSs were constructed with 324 single-nucleotide polymorphisms implicated in stroke and 9 risk factors. The association of the GRS to first incident stroke was tested using Cox regression; the GRS predictive properties were assessed with area under the curve statistics comparing the GRS with age and sex, Framingham Stroke Risk Score models, and reclassification statistics. These analyses were performed per cohort and in a meta-analysis of pooled data. Replication was sought in a case-control study of ischemic stroke. In the meta-analysis, adding the GRS to the Framingham Stroke Risk Score, age and sex model resulted in a significant improvement in discrimination (all stroke: Δjoint area under the curve=0.016, P=2.3×10(-6); ischemic stroke: Δjoint area under the curve=0.021, P=3.7×10(-7)), although the overall area under the curve remained low. In all the studies, there was a highly significantly improved net reclassification index (P<10(-4)). The single-nucleotide polymorphisms associated with stroke and its risk factors result only in a small improvement in prediction of future stroke compared with the classical epidemiological risk factors for stroke.

  10. 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…

  11. Dynamic and accurate assessment of acetaminophen-induced hepatotoxicity by integrated photoacoustic imaging and mechanistic biomarkers in vivo.

    PubMed

    Brillant, Nathalie; Elmasry, Mohamed; Burton, Neal C; Rodriguez, Josep Monne; Sharkey, Jack W; Fenwick, Stephen; Poptani, Harish; Kitteringham, Neil R; Goldring, Christopher E; Kipar, Anja; Park, B Kevin; Antoine, Daniel J

    2017-10-01

    The prediction and understanding of acetaminophen (APAP)-induced liver injury (APAP-ILI) and the response to therapeutic interventions is complex. This is due in part to sensitivity and specificity limitations of currently used assessment techniques. Here we sought to determine the utility of integrating translational non-invasive photoacoustic imaging of liver function with mechanistic circulating biomarkers of hepatotoxicity with histological assessment to facilitate the more accurate and precise characterization of APAP-ILI and the efficacy of therapeutic intervention. Perturbation of liver function and cellular viability was assessed in C57BL/6J male mice by Indocyanine green (ICG) clearance (Multispectral Optoacoustic Tomography (MSOT)) and by measurement of mechanistic (miR-122, HMGB1) and established (ALT, bilirubin) circulating biomarkers in response to the acetaminophen and its treatment with acetylcysteine (NAC) in vivo. We utilised a 60% partial hepatectomy model as a situation of defined hepatic functional mass loss to compared acetaminophen-induced changes to. Integration of these mechanistic markers correlated with histological features of APAP hepatotoxicity in a time-dependent manner. They accurately reflected the onset and recovery from hepatotoxicity compared to traditional biomarkers and also reported the efficacy of NAC with high sensitivity. ICG clearance kinetics correlated with histological scores for acute liver damage for APAP (i.e. 3h timepoint; r=0.90, P<0.0001) and elevations in both of the mechanistic biomarkers, miR-122 (e.g. 6h timepoint; r=0.70, P=0.005) and HMGB1 (e.g. 6h timepoint; r=0.56, P=0.04). For the first time we report the utility of this non-invasive longitudinal imaging approach to provide direct visualisation of the liver function coupled with mechanistic biomarkers, in the same animal, allowing the investigation of the toxicological and pharmacological aspects of APAP-ILI and hepatic regeneration. Copyright © 2017

  12. An audit of the current U.S. Department of Agriculture frame size scoring system.

    PubMed

    Reinhardt, C D; Busby, W D

    2014-06-01

    Feedlot and carcass data from steers (n = 16,700) and heifers (n = 6,357) originating from 16 different states and fed in 17 feedlots located in southwest Iowa were used to evaluate the accuracy of the USDA frame score for predicting final BW of fed cattle. Frame score was recorded by USDA or state personnel for cattle either before leaving the state of origin or on arrival at the terminal feedlot. Mixed model procedures were used to investigate relationships between USDA frame score and measures of live performance and carcass traits. Other fixed effects included in the model included USDA muscle score, sex, age classification on feedlot entry (calf: ≤270 d of age, yearling: 271-365 d of age, and long yearling: >365 d of age), BCS on feedlot arrival, number of treatments for respiratory disease, hide color, and site of frame or muscle scoring; the interactions of sex × frame score and hide color × frame score were also included; fat thickness was included as a fixed effect (covariate) in the analysis of ADG, final BW, days on feed, LM area, marbling score, and quality grade. Random effects included in the model were year of feedlot arrival and feedlot in which cattle were fed. The system accurately projects the minimum target final BW for large frame steers and heifers; however, the final BW of the smallest medium frame steers and heifers exceeds the target minimum final BW by 35 and 40 kg, respectively. When frame score was assigned post facto based on actual final BW (adjusted to 1.27 cm fat thickness), it was determined that large frame was over-assigned by graders (62 vs. 35% for steers and 54 vs. 32% for heifers, actual score vs. postharvest score, respectively), medium frame was underassigned (37 vs. 51% and 46 vs. 58% for steers and heifers), and small frame was underassigned (0.7 vs. 15% and 0.6 vs. 10% for steers and heifers; K = 0.01, P < 0.01). Across sexes, of the cattle assigned to small, medium, or large frame score, 40, 59, and 43% actually had

  13. Accurate atomistic first-principles calculations of electronic stopping

    DOE PAGES

    Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

    2015-01-20

    In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

  14. The New York risk score for in-hospital and 30-day mortality for coronary artery bypass graft surgery.

    PubMed

    Hannan, Edward L; Farrell, Louise Szypulski; Wechsler, Andrew; Jordan, Desmond; Lahey, Stephen J; Culliford, Alfred T; Gold, Jeffrey P; Higgins, Robert S D; Smith, Craig R

    2013-01-01

    Simplified risk scores for coronary artery bypass graft surgery are frequently in lieu of more complicated statistical models and are valuable for informed consent and choice of intervention. Previous risk scores have been based on in-hospital mortality, but a substantial number of patients die within 30 days of the procedure. These deaths should also be accounted for, so we have developed a risk score based on in-hospital and 30-day mortality. New York's Cardiac Surgery Reporting System was used to develop an in-hospital and 30-day logistic regression model for patients undergoing coronary artery bypass graft surgery in 2009, and this model was converted into a simple linear risk score that provides estimated in-hospital and 30-day mortality rates for different values of the score. The accuracy of the risk score in predicting mortality was tested. This score was also validated by applying it to 2008 New York coronary artery bypass graft data. Subsequent analyses evaluated the ability of the risk score to predict complications and length of stay. The overall in-hospital and 30-day mortality rate for the 10,148 patients in the study was 1.79%. There are seven risk factors comprising the score, with risk factor scores ranging from 1 to 5, and the highest possible total score is 23. The score accurately predicted mortality in 2009 as well as in 2008, and was strongly correlated with complications and length of stay. The risk score is a simple way of estimating short-term mortality that accurately predicts mortality in the year the model was developed as well as in the previous year. Perioperative complications and length of stay are also well predicted by the risk score. Copyright © 2013 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  15. Rayleigh Scattering in Planetary Atmospheres: Corrected Tables Through Accurate Computation of X and Y Functions

    NASA Astrophysics Data System (ADS)

    Natraj, Vijay; Li, King-Fai; Yung, Yuk L.

    2009-02-01

    Tables that have been used as a reference for nearly 50 years for the intensity and polarization of reflected and transmitted light in Rayleigh scattering atmospheres have been found to be inaccurate, even to four decimal places. We convert the integral equations describing the X and Y functions into a pair of coupled integro-differential equations that can be efficiently solved numerically. Special care has been taken in evaluating Cauchy principal value integrals and their derivatives that appear in the solution of the Rayleigh scattering problem. The new approach gives results accurate to eight decimal places for the entire range of tabulation (optical thicknesses 0.02-1.0, surface reflectances 0-0.8, solar and viewing zenith angles 0°-88.85°, and relative azimuth angles 0°-180°), including the most difficult case of direct transmission in the direction of the sun. Revised tables have been created and stored electronically for easy reference by the planetary science and astrophysics community.

  16. Quantum-Mechanics Methodologies in Drug Discovery: Applications of Docking and Scoring in Lead Optimization.

    PubMed

    Crespo, Alejandro; Rodriguez-Granillo, Agustina; Lim, Victoria T

    2017-01-01

    The development and application of quantum mechanics (QM) methodologies in computer- aided drug design have flourished in the last 10 years. Despite the natural advantage of QM methods to predict binding affinities with a higher level of theory than those methods based on molecular mechanics (MM), there are only a few examples where diverse sets of protein-ligand targets have been evaluated simultaneously. In this work, we review recent advances in QM docking and scoring for those cases in which a systematic analysis has been performed. In addition, we introduce and validate a simplified QM/MM expression to compute protein-ligand binding energies. Overall, QMbased scoring functions are generally better to predict ligand affinities than those based on classical mechanics. However, the agreement between experimental activities and calculated binding energies is highly dependent on the specific chemical series considered. The advantage of more accurate QM methods is evident in cases where charge transfer and polarization effects are important, for example when metals are involved in the binding process or when dispersion forces play a significant role as in the case of hydrophobic or stacking interactions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Re-adjusting the cut-off score of the Korean version of the Childhood Autism Rating Scale for high-functioning individuals with autism spectrum disorder.

    PubMed

    Kwon, Hyuk-Jin; Yoo, Hee-Jeong; Kim, Joo-Hyun; Noh, Dong-Hyun; Sunwoo, Hyun-Jung; Jeon, Ye Seul; Lee, Sang-Youn; Jo, Ye-Ul; Bong, Gui-Young

    2017-10-01

    The current cut-off score of the Korean version of the Childhood Autism Rating Scale (K-CARS) does not seem to be sensitive enough to precisely diagnose high-functioning autism. The aim of this study was to identify the optimal cut-off score of K-CARS for diagnosing high-functioning individuals with autism spectrum disorders (ASD). A total of 329 participants were assessed by the Korean versions of the Autism Diagnostic Interview - Revised (K-ADI-R), Autism Diagnostic Observation Schedule (K-ADOS), and K-CARS. IQ and Social Maturity Scale scores were also obtained. The true positive and false negative rates of K-CARS were 77.2% and 22.8%, respectively. Verbal IQ (VIQ) and Social Quotient (SQ) were significant predictors of misclassification. The false negative rate increased to 36.0% from 19.8% when VIQ was >69.5, and the rate increased to 44.1% for participants with VIQ > 69.5 and SQ > 75.5. In addition, if SQ was >83.5, the false negative rate increased to 46.7%, even if the participant's VIQ was ≤69.5. Optimal cut-off scores were 28.5 (for VIQ ≤ 69.5 and SQ ≤ 75.5), 24.25 (for VIQ > 69.5 and SQ > 75.5), and 24.5 (for SQ > 83.5), respectively. The likelihood of a false negative error increases when K-CARS is used to diagnose high-functioning autism and Asperger's syndrome. For subjects with ASD and substantial verbal ability, the cut-off score for K-CARS should be re-adjusted and/or supplementary diagnostic tools might be needed to enhance diagnostic accuracy for ASD. © 2017 The Authors. Psychiatry and Clinical Neurosciences © 2017 Japanese Society of Psychiatry and Neurology.

  18. 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

  19. Relationship between Age and the Ability to Break Scored Tablets

    PubMed Central

    Notenboom, Kim; Vromans, Herman; Schipper, Maarten; Leufkens, Hubert G. M.; Bouvy, Marcel L.

    2016-01-01

    Background: Practical problems with the use of medicines, such as difficulties with breaking tablets, are an often overlooked cause for non-adherence. Tablets frequently break in uneven parts and loss of product can occur due to crumbling and powdering. Health characteristics, such as the presence of peripheral neuropathy, decreased grip strength and manual dexterity, can affect a patient's ability to break tablets. As these impairments are associated with aging and age-related diseases, such as Parkinson's disease and arthritis, difficulties with breaking tablets could be more prevalent among older adults. The objective of this study was to investigate the relationship between age and the ability to break scored tablets. Methods: A comparative study design was chosen. Thirty-six older adults and 36 young adults were systematically observed with breaking scored tablets. Twelve different tablets were included. All participants were asked to break each tablet by three techniques: in between the fingers with the use of nails, in between the fingers without the use of nails and pushing the tablet downward with one finger on a solid surface. It was established whether a tablet was broken or not, and if broken, whether the tablet was broken accurately or not. Results: The older adults experienced more difficulties to break tablets compared to the young adults. On average, the older persons broke 38.1% of the tablets, of which 71.0% was broken accurately. The young adults broke 78.2% of the tablets, of which 77.4% was broken accurately. Further analysis by mixed effects logistic regression revealed that age was associated with the ability to break tablets, but not with the accuracy of breaking. Conclusions: Breaking scored tablets by hand is less successful in an elderly population compared to a group of young adults. Health care providers should be aware that tablet breaking is not appropriate for all patients and for all drugs. In case tablet breaking is unavoidable, a

  20. The S.A.C.S. (Satisfaction-Anatomy-Continence-Safety) score for evaluating pelvic organ prolapse surgery: a proposal for an outcome-based scoring system.

    PubMed

    Mearini, Luigi; Zucchi, Alessandro; Nunzi, Elisabetta; Di Biase, Manuel; Bini, Vittorio; Costantini, Elisabetta

    2015-07-01

    To date, there is no overall consensus on the definition of cure after surgery for pelvic organ prolapse (POP). The aim of the study was to design and test the scoring system S.A.C.S. (Satisfaction-Anatomy-Continence-Safety) to assess and compare the outcomes of POP repair. A total of 233 women underwent open sacrocolpopexy. The S.A.C.S. outcome scoring system was scheduled at 24 months of follow-up, and each component was detected according to: Satisfaction by mean of Patient Global Improvement Inventory scale, Anatomy by mean of POP Quantification system and bulge symptom, Continence by mean of pad use, and Safety by mean of the Clavien-Dindo classification of surgical complications. Each component produced a binary nominal categorical variable (1 or 0), with a total score of 4 representing cure. As a comparative tool, patients answered a simple yes/no question: "If you had to undergo surgery all over again, would you still do it?". The degree of concordance was estimated using Cohen's Kappa test. According to the S.A.C.S. scoring system, only 160 patients (68.6 %) reached the maximum score of cure. Sensitivity of the S.A.C.S. score was 74.1 %, specificity was 90 %, total diagnostic capacity was 75.5 %. The S.A.C.S. score internal consistency was good; the k-coefficient was higher for the satisfaction component of the score (k = 0.560). This study proposes an original, simple post-operative scoring system integrating satisfaction, anatomy, continence, and safety reports for patients undergoing surgery for POP, providing a complete, although perfectible, method to accurately report outcomes in all clinical scenarios.

  1. Improving causal inference with a doubly robust estimator that combines propensity score stratification and weighting.

    PubMed

    Linden, Ariel

    2017-08-01

    When a randomized controlled trial is not feasible, health researchers typically use observational data and rely on statistical methods to adjust for confounding when estimating treatment effects. These methods generally fall into 3 categories: (1) estimators based on a model for the outcome using conventional regression adjustment; (2) weighted estimators based on the propensity score (ie, a model for the treatment assignment); and (3) "doubly robust" (DR) estimators that model both the outcome and propensity score within the same framework. In this paper, we introduce a new DR estimator that utilizes marginal mean weighting through stratification (MMWS) as the basis for weighted adjustment. This estimator may prove more accurate than treatment effect estimators because MMWS has been shown to be more accurate than other models when the propensity score is misspecified. We therefore compare the performance of this new estimator to other commonly used treatment effects estimators. Monte Carlo simulation is used to compare the DR-MMWS estimator to regression adjustment, 2 weighted estimators based on the propensity score and 2 other DR methods. To assess performance under varied conditions, we vary the level of misspecification of the propensity score model as well as misspecify the outcome model. Overall, DR estimators generally outperform methods that model one or the other components (eg, propensity score or outcome). The DR-MMWS estimator outperforms all other estimators when both the propensity score and outcome models are misspecified and performs equally as well as other DR estimators when only the propensity score is misspecified. Health researchers should consider using DR-MMWS as the principal evaluation strategy in observational studies, as this estimator appears to outperform other estimators in its class. © 2017 John Wiley & Sons, Ltd.

  2. Moje first metatarsophalangeal replacement--a case series with functional outcomes using the AOFAS-HMI score.

    PubMed

    Brewster, Mark; McArthur, John; Mauffrey, Cyril; Lewis, Andrew Charles; Hull, Peter; Ramos, James

    2010-01-01

    We report the functional results of a case series of Moje first metatarsophalangeal total joint replacements carried out between February 2001 and November 2006. All patients who underwent Moje arthroplasty under the care of a single surgeon were included; outcome scores and complications were recorded annually. A total of 32 joints in 29 consecutive patients were followed for a mean duration of 34 (range 6 to 74) months, and the mean patient age at the time of operation was 56 (range 38 to 79) years. Hallux rigidus was the primary diagnosis in 28 (87.5%) of the cases. The mean American Orthopaedic Foot & Ankle Society Hallux-Metatarsophalangeal-Interphalangeal score at final follow-up was 74/100 (range 9 to 100), with 13 (40.63%) joints rated good to excellent. Two (6.25%) joints were revised to arthrodesis at a mean of 52 (range 41 to 63) months following the arthroplasty procedure, and the overall prevalence of postoperative complications was 6 (18.75%). Based on these results, we concluded that first MTPJ total joint replacement with the Moje device remains promising, but still has room for improvement before the results match those obtained with larger joint (knee, hip) arthroplasty. Copyright 2010 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  3. Effective Score Reporting of Non-Norm-Referenced Assessment.

    ERIC Educational Resources Information Center

    Haenn, Joseph F.; And Others

    The Maryland State Department of Education issued a request for proposals to develop a score reporting system for the Maryland Functional Testing Program. RMC Research Corporation conducted a literature review of extant literature and developed a national survey of non-norm-referenced test score reporting practices. This comprehensive analysis of…

  4. A validation of the Nottingham Clavicle Score: a clavicle, acromioclavicular joint and sternoclavicular joint-specific patient-reported outcome measure.

    PubMed

    Charles, Edmund R; Kumar, Vinod; Blacknall, James; Edwards, Kimberley; Geoghegan, John M; Manning, Paul A; Wallace, W Angus

    2017-10-01

    Patients with acromioclavicular joint (ACJ) and sternoclavicular joint (SCJ) injuries and with clavicle fractures are typically younger and more active than those with other shoulder pathologies. We developed the Nottingham Clavicle Score (NCS) specifically for this group of patients to improve sensitivity for assessing the outcomes of treatment of these conditions compared with the more commonly used Constant Score (CS) and Oxford Shoulder Score (OSS). This was a cohort study in which the preoperative and 6-month postoperative NCS evaluations of outcome in 90 patients were compared with the CS, OSS, Imatani Score (IS), and the EQ-5D scores. Reliability was assessed using the Cronbach α. Reproducibility of the NCS was assessed using the test/retest method. Effect sizes were calculated for each score to assess sensitivity to change. Validity was examined by correlations between the NCS and the CS, OSS, IS, and EQ-5D scores obtained preoperatively and postoperatively. Significant correlations were demonstrated preoperatively with the OSS (P = .025) and all subcategories of the EQ-5D (P < .05) and postoperatively with the OSS (P < .001), CS (P = .008), IS (P < .001), and all subcategories of EQ-5D (P < .02). The NCS had the largest effect size (1.92) of the compared scores. Internal consistency was excellent (Cronbach α = 0.87). The NCS has been proven to be a valid, reliable and sensitive outcome measure that accurately measures the level of function and disability in the ACJ, SCJ and clavicle after traumatic injury and in degenerative disease. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  5. The comparability of English, French and Dutch scores on the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F): an assessment of differential item functioning in patients with systemic sclerosis.

    PubMed

    Kwakkenbos, Linda; Willems, Linda M; Baron, Murray; Hudson, Marie; Cella, David; van den Ende, Cornelia H M; Thombs, Brett D

    2014-01-01

    The Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F) is commonly used to assess fatigue in rheumatic diseases, and has shown to discriminate better across levels of the fatigue spectrum than other commonly used measures. The aim of this study was to assess the cross-language measurement equivalence of the English, French, and Dutch versions of the FACIT-F in systemic sclerosis (SSc) patients. The FACIT-F was completed by 871 English-speaking Canadian, 238 French-speaking Canadian and 230 Dutch SSc patients. Confirmatory factor analysis was used to assess the factor structure in the three samples. The Multiple-Indicator Multiple-Cause (MIMIC) model was utilized to assess differential item functioning (DIF), comparing English versus French and versus Dutch patient responses separately. A unidimensional factor model showed good fit in all samples. Comparing French versus English patients, statistically significant, but small-magnitude DIF was found for 3 of 13 items. French patients had 0.04 of a standard deviation (SD) lower latent fatigue scores than English patients and there was an increase of only 0.03 SD after accounting for DIF. For the Dutch versus English comparison, 4 items showed small, but statistically significant, DIF. Dutch patients had 0.20 SD lower latent fatigue scores than English patients. After correcting for DIF, there was a reduction of 0.16 SD in this difference. There was statistically significant DIF in several items, but the overall effect on fatigue scores was minimal. English, French and Dutch versions of the FACIT-F can be reasonably treated as having equivalent scoring metrics.

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

    PubMed

    Dai, Huanping; Micheyl, Christophe

    2015-05-01

    Proportion correct (Pc) is a fundamental measure of task performance in psychophysics. The maximum Pc score that can be achieved by an optimal (maximum-likelihood) observer in a given task is of both theoretical and practical importance, because it sets an upper limit on human performance. Within the framework of signal detection theory, analytical solutions for computing the maximum Pc score have been established for several common experimental paradigms under the assumption of Gaussian additive internal noise. However, as the scope of applications of psychophysical signal detection theory expands, the need is growing for psychophysicists to compute maximum Pc scores for situations involving non-Gaussian (internal or stimulus-induced) noise. In this article, we provide a general formula for computing the maximum Pc in various psychophysical experimental paradigms for arbitrary probability distributions of sensory activity. Moreover, easy-to-use MATLAB code implementing the formula is provided. Practical applications of the formula are illustrated, and its accuracy is evaluated, for two paradigms and two types of probability distributions (uniform and Gaussian). The results demonstrate that Pc scores computed using the formula remain accurate even for continuous probability distributions, as long as the conversion from continuous probability density functions to discrete probability mass functions is supported by a sufficiently high sampling resolution. We hope that the exposition in this article, and the freely available MATLAB code, facilitates calculations of maximum performance for a wider range of experimental situations, as well as explorations of the impact of different assumptions concerning internal-noise distributions on maximum performance in psychophysical experiments.

  7. Comparison of Nutech Functional Score with European Stroke Scale for Patients with Cerebrovascular Accident Treated with Human Embryonic Stem Cells: NFS for CVA Patients Treated with hESCs.

    PubMed

    Shroff, Geeta

    2017-06-01

    Stem cell therapy is a promising modality for treatment of patients with chronic cerebrovascular accident (CVA) in whom treatment other than physiotherapy or occupational therapy does not address the repair or recovery of the lost function. In this study, the author aimed at evaluating CVA patients treated with human embryonic stem cell (hESC) therapy and comparing their study outcomes with globally accepted European Stroke Scale (ESS) to that with novel scoring system, Nutech functional score (NFS), a 21-point positional and directional scoring system for assessing patients with CVA. Patients diagnosed with CVA were assessed with NFS and ESS before and after hESC therapy. NFS assessed the patients in the direction of 1-5 (bad to good), where 5 was considered as the highest possible grade (HPG). The findings were obtained for the patients who scored HPG, and had shown improvement by at least one grade. Overall, 66.7% of patients scored HPG level on the NFS scale and about 62.5% of the patients scored HPG according to the ESS scale. Approximately, 52.2% patients showed an improvement of 100% (by at least one grade) on NFS scale. None of the patients showed 100% improvement in the alteration of the score by at least one grade when scored with ESS. NFS and ESS scores show that a large population of CVA patients was benefitted with hESC therapy. NFS was found to give more convincing results than ESS, and overcomes the shortcomings of ESS.

  8. The intra- and inter-assessor reliability of measurement of functional outcome by lameness scoring in horses.

    PubMed

    Fuller, Catherine J; Bladon, Bruce M; Driver, Adam J; Barr, Alistair R S

    2006-03-01

    The objective of this study was to assess the reliability of lameness scoring in horses. One veterinary surgeon examined nineteen lame horses on four occasions. Gait was recorded by camcorder, and scored from 0 to 10 ranging from sound to non-weight bearing lameness. A global score of overall change in lameness during the study was also determined for each horse. To measure intra-assessor reliability of the scoring systems, one veterinary surgeon scored videotapes of the horses' gaits on two occasions. To measure inter-assessor reliability, three veterinary surgeons viewed the videotapes, assigning individual lameness scores plus global scores to each horse. Reliability of individual lameness scoring was good intra-assessor, but only just within our acceptable limit inter-assessor. However, global scoring of change in lameness throughout the study was found to be reliable overall. Since clinician scoring is commonly used to assess lameness in horses, this is an important finding, fundamental to future clinical studies.

  9. Hydrophobic potential of mean force as a solvation function for protein structure prediction.

    PubMed

    Lin, Matthew S; Fawzi, Nicolas Lux; Head-Gordon, Teresa

    2007-06-01

    We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.

  10. QUASAR--scoring and ranking of sequence-structure alignments.

    PubMed

    Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

    2005-12-15

    Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

  11. Pediatric blunt cerebrovascular injury: the McGovern screening score.

    PubMed

    Herbert, Joseph P; Venkataraman, Sidish S; Turkmani, Ali H; Zhu, Liang; Kerr, Marcia L; Patel, Rajan P; Ugalde, Irma T; Fletcher, Stephen A; Sandberg, David I; Cox, Charles S; Kitagawa, Ryan S; Day, Arthur L; Shah, Manish N

    2018-03-16

    OBJECTIVE The objective of this study was to assess the incidence, diagnosis, and treatment of pediatric blunt cerebrovascular injury (BCVI) at a busy Level 1 trauma center and to develop a tool for accurately predicting pediatric BCVI and the need for diagnostic testing. METHODS This is a retrospective cohort study of a prospectively collected database of pediatric patients who had sustained blunt trauma (patient age range 0-15 years) and were treated at a Level 1 trauma center between 2005 and 2015. Digital subtraction angiography, MR angiography, or CT angiography was used to confirm BCVI. Recently, the Utah score has emerged as a screening tool specifically targeted toward evaluating BCVI risk in the pediatric population. Using logistical regression and adding mechanism of injury as a logit, the McGovern score was able to use the Utah score as a starting point to create a more sensitive screening tool to identify which pediatric trauma patients should receive angiographic imaging due to a high risk for BCVI. RESULTS A total of 12,614 patients (mean age 6.6 years) were admitted with blunt trauma and prospectively registered in the trauma database. Of these, 460 (3.6%) patients underwent angiography after blunt trauma: 295 (64.1%), 107 (23.3%), 6 (1.3%), and 52 (11.3%) patients underwent CT angiography, MR angiography, digital subtraction angiography, and a combination of imaging modalities, respectively. The BCVI incidence (n = 21; 0.17%) was lower than that in a comparable adult group (p < 0.05). The mean patient was age 10.4 years with a mean follow-up of 7.5 months. Eleven patients (52.4%) were involved in a motor vehicle collision, with a mean Glasgow Coma Scale score of 8.6. There were 8 patients (38.1%) with carotid canal fracture, 6 patients (28.6%) with petrous bone fracture, and 2 patients (9.5%) with infarction on initial presentation. Eight patients (38.1%) were managed with observation alone. The Denver, modified Memphis, Eastern Association for the

  12. Differences of wells scores accuracy, caprini scores and padua scores in deep vein thrombosis diagnosis

    NASA Astrophysics Data System (ADS)

    Gatot, D.; Mardia, A. I.

    2018-03-01

    Deep Vein Thrombosis (DVT) is the venous thrombus in lower limbs. Diagnosis is by using venography or ultrasound compression. However, these examinations are not available yet in some health facilities. Therefore many scoring systems are developed for the diagnosis of DVT. The scoring method is practical and safe to use in addition to efficacy, and effectiveness in terms of treatment and costs. The existing scoring systems are wells, caprini and padua score. There have been many studies comparing the accuracy of this score but not in Medan. Therefore, we are interested in comparative research of wells, capriniand padua score in Medan.An observational, analytical, case-control study was conducted to perform diagnostic tests on the wells, caprini and padua score to predict the risk of DVT. The study was at H. Adam Malik Hospital in Medan.From a total of 72 subjects, 39 people (54.2%) are men and the mean age are 53.14 years. Wells score, caprini score and padua score has a sensitivity of 80.6%; 61.1%, 50% respectively; specificity of 80.65; 66.7%; 75% respectively, and accuracy of 87.5%; 64.3%; 65.7% respectively.Wells score has better sensitivity, specificity and accuracy than caprini and padua score in diagnosing DVT.

  13. A multi-objective optimization approach accurately resolves protein domain architectures

    PubMed Central

    Bernardes, J.S.; Vieira, F.R.J.; Zaverucha, G.; Carbone, A.

    2016-01-01

    Motivation: Given a protein sequence and a number of potential domains matching it, what are the domain content and the most likely domain architecture for the sequence? This problem is of fundamental importance in protein annotation, constituting one of the main steps of all predictive annotation strategies. On the other hand, when potential domains are several and in conflict because of overlapping domain boundaries, finding a solution for the problem might become difficult. An accurate prediction of the domain architecture of a multi-domain protein provides important information for function prediction, comparative genomics and molecular evolution. Results: We developed DAMA (Domain Annotation by a Multi-objective Approach), a novel approach that identifies architectures through a multi-objective optimization algorithm combining scores of domain matches, previously observed multi-domain co-occurrence and domain overlapping. DAMA has been validated on a known benchmark dataset based on CATH structural domain assignments and on the set of Plasmodium falciparum proteins. When compared with existing tools on both datasets, it outperforms all of them. Availability and implementation: DAMA software is implemented in C++ and the source code can be found at http://www.lcqb.upmc.fr/DAMA. Contact: juliana.silva_bernardes@upmc.fr or alessandra.carbone@lip6.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26458889

  14. Computational active site analysis of molecular pathways to improve functional classification of enzymes.

    PubMed

    Ozyurt, A Sinem; Selby, Thomas L

    2008-07-01

    This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis. 2008 Wiley-Liss, Inc.

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

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

    Pino, Francisco; Roé, Nuria; Aguiar, Pablo, E-mail: pablo.aguiar.fernandez@sergas.es

    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: Threemore » 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

  16. 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.

  17. Assessing the Effectiveness of the Functional Movement Screen in Predicting Noncontact Injury Rates in Soccer Players.

    PubMed

    Smith, Paul D; Hanlon, Michael P

    2017-12-01

    Smith, PD, and Hanlon, D. Assessing the effectiveness of the functional movement screen in predicting noncontact injury rates in soccer players. J Strength Cond Res 31(12): 3327-3332, 2017-This study assessed if the Functional Movement Screen (FMS) can accurately predict noncontact injury in adult soccer players when normalizing noncontact injury occurrence against match exposure levels. Senior male players (n = 89) from 5 League of Ireland semiprofessional clubs participated in the study (mean age = 23.2 ± 4.4 years; mean height = 179.5 ± 6.6 cm; mean body mass = 77.5 ± 7.8 kg). Participants performed the FMS during preseason, and their injury occurrence rates and match minutes were tracked throughout 1 season. In total, 66 noncontact injuries were recorded. No significant difference was found in FMS composite scores between players receiving noncontact injuries and players not suffering a noncontact injury (p = 0.96). There was no significant difference in exposure-normalized noncontact injury incidence between those scoring 14 or below and those scoring above 14 on the FMS (0.36 vs. 0.29 non-contact injuries per player per 1,000 match minutes). Players scoring 14 or below on the FMS had an odds ratio of 0.63 (p = 0.45; 95% CI = 0.19-2.07) of receiving a noncontact injury. Despite previous research showing links between low FMS composite scores and subsequent injury, these results suggest that the FMS cannot accurately predict a male soccer player's likelihood of receiving a noncontact injury and that a lower FMS composite score does not significantly increase their noncontact injury incidence rate per 1,000 match minutes. Caution should therefore be used when using the FMS as a predictor of noncontact injury, and pain prevalence during the FMS, previous injuries, and training/match exposure levels should also be taken into account.

  18. 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

    2017-01-01

    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.

  19. Examining the association of injury with the Functional Movement Screen and Landing Error Scoring System in military recruits undergoing 16 weeks of introductory fitness training.

    PubMed

    Everard, Eoin; Lyons, Mark; Harrison, Andrew J

    2018-06-01

    To examine the association of injury with the Functional Movement Screen (FMS) and Landing Error Scoring System (LESS) in military recruits undergoing an intensive 16-week training block. Prospective cohort study. One hundred and thirty-two entry-level male soldiers (18-25years) were tested using the FMS and LESS. The participants underwent an intensive 16-week training program with injury data recorded daily. Chi-squared statistics were used to examine associations between injury risk and (1) poor LESS scores, (2) any score of 1 on the FMS and (3) composite FMS score of ≤14. A composite FMS score of ≤14 was not a significant predictor of injury. LESS scores of >5 and having a score of 1 on any FMS test were significantly associated with injury. LESS scores had greater relative risk, sensitivity and specificity (2.2 (95% CI=1.48-3.34); 71% and 87% respectively) than scores of 1 on the FMS (relative risk=1.32 (95% CI=1.0-1.7); sensitivity=50% and specificity=76%). There was no association between composite FMS score and injury but LESS scores and scores of 1 in the FMS test were significantly associated with injury in varying degrees. LESS scores had a much better association with injury than both any scores of 1 on the FMS and a combination of LESS scores and scores of 1 on the FMS. Furthermore, the LESS provides comparable information related to injury risk as other well-established markers associated with injury such as age, muscular strength and previous injury. Copyright © 2017. Published by Elsevier Ltd.

  20. Co-calibrating quality-of-life scores from three pulmonary disorders: implications for comparative-effectiveness research.

    PubMed

    Rouse, M; Twiss, J; McKenna, S P

    2016-06-01

    Background Efficient use of health resources requires accurate outcome assessment. Disease-specific patient-reported outcome (PRO) measures are designed to be highly relevant to patients with a specific disease. They have advantages over generic PROs that lack relevance to patient groups and miss crucial impacts of illness. It is thought that disease-specific measurement cannot be used in comparative effectiveness research (CER). The present study provides further evidence of the value of disease-specific measures in making valid comparisons across diseases. Methods The Asthma Life Impact Scale (ALIS, 22 items), Living with Chronic Obstructive Pulmonary Disease (LCOPD, 22 items) scale, and Cambridge Pulmonary Hypertension Outcome Review (CAMPHOR, 25 items) were completed by 140, 162, and 91 patients, respectively. The three samples were analyzed for fit to the Rasch model, then combined into a scale consisting of 58 unique items and re-analyzed. Raw scores on the three measures were co-calibrated and a transformation table produced. Results The scales fit the Rasch model individually (ALIS Chi(2) probability value (p-Chi(2)) = 0.05; LCOPD p-Chi(2 )=( )0.38; CAMPHOR p-Chi(2 )=( )0.92). The combined data also fit the Rasch model (p-Chi(2 )=( )0.22). There was no differential item functioning related to age, gender, or disease. The co-calibrated scales successfully distinguished between perceived severity groups (p < 0.001). Limitations The samples were drawn from different sources. For scales to be co-calibrated using a common item design, they must be based on the same theoretical construct, be unidimensional, and have overlapping items. Conclusions The results showed that it is possible to co-calibrate scores from disease-specific PRO measures. This will permit more accurate and sensitive outcome measurement to be incorporated into CER. The co-calibration of needs-based disease-specific measures allows the calculation of γ scores that can be

  1. Apparently abnormal Wechsler Memory Scale index score patterns in the normal population.

    PubMed

    Carrasco, Roman Marcus; Grups, Josefine; Evans, Brittney; Simco, Edward; Mittenberg, Wiley

    2015-01-01

    Interpretation of the Wechsler Memory Scale-Fourth Edition may involve examination of multiple memory index score contrasts and similar comparisons with Wechsler Adult Intelligence Scale-Fourth Edition ability indexes. Standardization sample data suggest that 15-point differences between any specific pair of index scores are relatively uncommon in normal individuals, but these base rates refer to a comparison between a single pair of indexes rather than multiple simultaneous comparisons among indexes. This study provides normative data for the occurrence of multiple index score differences calculated by using Monte Carlo simulations and validated against standardization data. Differences of 15 points between any two memory indexes or between memory and ability indexes occurred in 60% and 48% of the normative sample, respectively. Wechsler index score discrepancies are normally common and therefore not clinically meaningful when numerous such comparisons are made. Explicit prior interpretive hypotheses are necessary to reduce the number of index comparisons and associated false-positive conclusions. Monte Carlo simulation accurately predicts these false-positive rates.

  2. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

    PubMed

    Hu, Jialu; Kehr, Birte; Reinert, Knut

    2014-02-15

    Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

  3. The Comparability of English, French and Dutch Scores on the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F): An Assessment of Differential Item Functioning in Patients with Systemic Sclerosis

    PubMed Central

    Kwakkenbos, Linda; Willems, Linda M.; Baron, Murray; Hudson, Marie; Cella, David; van den Ende, Cornelia H. M.; Thombs, Brett D.

    2014-01-01

    Objective The Functional Assessment of Chronic Illness Therapy- Fatigue (FACIT-F) is commonly used to assess fatigue in rheumatic diseases, and has shown to discriminate better across levels of the fatigue spectrum than other commonly used measures. The aim of this study was to assess the cross-language measurement equivalence of the English, French, and Dutch versions of the FACIT-F in systemic sclerosis (SSc) patients. Methods The FACIT-F was completed by 871 English-speaking Canadian, 238 French-speaking Canadian and 230 Dutch SSc patients. Confirmatory factor analysis was used to assess the factor structure in the three samples. The Multiple-Indicator Multiple-Cause (MIMIC) model was utilized to assess differential item functioning (DIF), comparing English versus French and versus Dutch patient responses separately. Results A unidimensional factor model showed good fit in all samples. Comparing French versus English patients, statistically significant, but small-magnitude DIF was found for 3 of 13 items. French patients had 0.04 of a standard deviation (SD) lower latent fatigue scores than English patients and there was an increase of only 0.03 SD after accounting for DIF. For the Dutch versus English comparison, 4 items showed small, but statistically significant, DIF. Dutch patients had 0.20 SD lower latent fatigue scores than English patients. After correcting for DIF, there was a reduction of 0.16 SD in this difference. Conclusions There was statistically significant DIF in several items, but the overall effect on fatigue scores was minimal. English, French and Dutch versions of the FACIT-F can be reasonably treated as having equivalent scoring metrics. PMID:24638101

  4. [Inter-rater concordance of the "Nursing Activities Score" in intensive care].

    PubMed

    Valls-Matarín, Josefa; Salamero-Amorós, Maria; Roldán-Gil, Carmen; Quintana-Riera, Salvador

    2015-01-01

    To evaluate inter-rater concordance in the valuation of the "Nursing Activities Score". Cross-sectional descriptive study conducted from December 2012 until June 2013 in a general intensive care unit with twelve beds. Three evaluator nurses, simultaneously and independently, through the patient daily charts, scored the nursing workload using Nursing Activities Score scale in all patients admitted over 18 years old. Three hundreds and thirty-nine records were collected. The intra-class correlation coefficient (ICC) between evaluators was 0.92 (0.89-0.94). A perfect concordance was obtained in 39.1% of the items, with 52.2% having a high, and 8.7% having lower concordance, corresponding to two of the items with multiple scoring options. Significant differences between two of the evaluators (P=.049) were found. Although the inter-rater concordance was high, more accurate records are needed to reduce the variability of the items with multiple options and to allow more accuracy in the interpretation and measurement of the data regarding nursing workload. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  5. The e-CRABEL score: an updated method for auditing medical records.

    PubMed

    Myuran, Tharsika; Turner, Oliver; Ben Doostdar, Bijan; Lovett, Bryony

    2017-01-01

    In 2001 the CRABEL score was devised in order to obtain a numerical score of the standard of medical note keeping. With the advent of electronic discharge letters, many components of the CRABEL score are now redundant as computers automatically include some documentation. The CRABEL score was modified to form the e-CRABEL score. "Patient details on discharge letter" and "Admission and discharge dates on discharge letter" were replaced with "Summary of investigations on discharge letter" and "Documentation of VTE prophylaxis on the drug chart". The new e-CRABEL score has been used as a monthly audit tool in a busy surgical unit to monitor long-term standards of medical note keeping, with interventions of presenting in the departmental audit meeting, and giving a teaching session to a group of junior doctors at two points. Following discussion with stakeholders: junior doctors, consultants, and the audit department; it was decided that the e-CRABEL tool was sufficiently compact to be completed on a monthly basis. Critique and interventions included using photographic examples, case note selection and clarification of the e-CRABEL criteria in a teaching session. Tools used for audit need to be updated in order to accurately represent what they measure, hence the modification of the CRABEL score to make the new e-CRABEL score. Preliminary acquisition and presentation of data using the e-CRABEL score has shown promise in improving the quality of medical record keeping. The tool is sufficiently compact as to conduct on a monthly basis, maintaining standards to a high level and also provides data on VTE documentation.

  6. The Peptic Ulcer Perforation (PULP) score: a predictor of mortality following peptic ulcer perforation. A cohort study.

    PubMed

    Møller, M H; Engebjerg, M C; Adamsen, S; Bendix, J; Thomsen, R W

    2012-05-01

    Accurate and early identification of high-risk surgical patients with perforated peptic ulcer (PPU) is important for triage and risk stratification. The objective of the present study was to develop a new and improved clinical rule to predict mortality in patients following surgical treatment for PPU. nationwide cohort study based on prospectively collected data. thirty-five hospitals in Denmark. a total of 2668 patients surgically treated for gastric or duodenal PPU between 1 February 2003 and 31 August 2009. 30-day mortality. We derived a new clinical prediction rule for 30-day mortality and evaluated and compared its prognostic performance with the American Society of Anaesthesiologists (ASA) and Boey scores. A total of 708 patients (27%) died within 30 days of surgery. The Peptic Ulcer Perforation (PULP) score - comprised eight variables with an adjusted odds ratio of more than 1.28: 1) age > 65 years, 2) active malignant disease or AIDS, 3) liver cirrhosis, 4) steroid use, 5) time from perforation to admission > 24 h, 6) pre-operative shock, 7) serum creatinine > 130 μM, and 8) the four levels of the ASA score (from 2 to 5). The score predicted mortality well (area under receiver operating characteristics curve (AUC) 0.83). It performed considerably better than the Boey score (AUC 0.70) and better than the ASA score alone (AUC 0.78). The PULP score accurately predicts 30-day mortality in patients operated for PPU and can assist in risk stratification and triage. © 2011 The Authors Acta Anaesthesiologica Scandinavica © 2011 The Acta Anaesthesiologica Scandinavica Foundation.

  7. Technical feasibility and validation of a coronary artery calcium scoring system using CT coronary angiography images.

    PubMed

    Pavitt, Christopher W; Harron, Katie; Lindsay, Alistair C; Zielke, Sayeh; Ray, Robin; Gordon, Daniel; Rubens, Michael B; Padley, Simon P; Nicol, Edward D

    2016-05-01

    We validate a novel CT coronary angiography (CCTA) coronary calcium scoring system. Calcium was quantified on CCTA images using a new patient-specific attenuation threshold: mean + 2SD of intra-coronary contrast density (HU). Using 335 patient data sets a conversion factor (CF) for predicting CACS from CCTA scores (CCTAS) was derived and validated in a separate cohort (n = 168). Bland-Altman analysis and weighted kappa for MESA centiles and Agatston risk groupings were calculated. Multivariable linear regression yielded a CF: CACS = (1.185 × CCTAS) + (0.002 × CCTAS × attenuation threshold). When applied to CCTA data sets there was excellent correlation (r = 0.95; p < 0.0001) and agreement (mean difference -10.4 [95% limits of agreement -258.9 to 238.1]) with traditional calcium scores. Agreement was better for calcium scores below 500; however, MESA percentile agreement was better for high risk patients. Risk stratification was excellent (Agatston groups k = 0.88 and MESA centiles k = 0.91). Eliminating the dedicated CACS scan decreased patient radiation exposure by approximately one-third. CCTA calcium scores can accurately predict CACS using a simple, individualized, semiautomated approach reducing acquisition time and radiation exposure when evaluating patients for CAD. This method is not affected by the ROI location, imaging protocol, or tube voltage strengthening its clinical applicability. • Coronary calcium scores can be reliably determined on contrast-enhanced cardiac CT • This score can accurately risk stratify patients • Elimination of a dedicated calcium scan reduces patient radiation by a third.

  8. Validation of the GILLS score for tongue-lip adhesion in Robin sequence patients.

    PubMed

    Abramowicz, Shelly; Bacic, Janine D; Mulliken, John B; Rogers, Gary F

    2012-03-01

    The GILLS score consists of gastroesophageal reflux disease, preoperative intubation, late surgical intervention, low birth weight, and syndromic diagnosis. The purpose of this study was to test the validity of the GILLS score in predicting success of tongue-lip adhesion (TLA) in managing Robin sequence. Infants with Robin sequence were included in the study if they had a TLA for airway compromise subsequent to formulation of the GILLS scoring system, that is, they were not included in the original GILLS analysis. The patients were prospectively considered based on the presence of the 5 factors that constitute the GILLS score. A score of ≤ 2 predicts success of TLA. Twenty patients met the inclusion criteria. Tongue-lip adhesion managed the compromised airway in 18 (90%) of 20 patients. Overall, the GILLS score had a sensitivity of 83%, specificity of 50%, positive predictive value of 94%, and negative predictive value of 25%. The GILLS score accurately predicts a successful outcome for TLA in infants with Robin sequence. For infants with a score of 2 or less, TLA is the procedure of choice. Infants with a GILLS score of 3 or greater were 5 times more likely to fail TLA than those with a score of 2 or less. In these patients, other methods of managing the airway should be considered.

  9. Portsmouth physiological and operative severity score for the Enumeration of Mortality and morbidity scoring system in general surgical practice and identifying risk factors for poor outcome

    PubMed Central

    Tyagi, Ashish; Nagpal, Nitin; Sidhu, D. S.; Singh, Amandeep; Tyagi, Anjali

    2017-01-01

    Background: Estimation of the outcome is paramount in disease stratification and subsequent management in severely ill surgical patients. Risk scoring helps us quantify the prospects of adverse outcome in a patient. Portsmouth-Physiological and Operative Severity Score for the Enumeration of Mortality and Morbidity (P-POSSUM) the world over has proved itself as a worthy scoring system and the present study was done to evaluate the feasibility of P-POSSUM as a risk scoring system as a tool in efficacious prediction of mortality and morbidity in our demographic profile. Materials and Methods: Validity of P-POSSUM was assessed prospectively in fifty major general surgeries performed at our hospital from May 2011 to October 2012. Data were collected to obtain P-POSSUM score, and statistical analysis was performed. Results: Majority (72%) of patients was male and mean age was 40.24 ± 18.6 years. Seventy-eight percentage procedures were emergency laparotomies commonly performed for perforation peritonitis. Mean physiological score was 17.56 ± 7.6, and operative score was 17.76 ± 4.5 (total score = 35.3 ± 10.4). The ratio of observed to expected mortality rate was 0.86 and morbidity rate was 0.78. Discussion: P-POSSUM accurately predicted both mortality and morbidity in patients who underwent major surgical procedures in our setup. Thus, it helped us in identifying patients who required preferential attention and aggressive management. Widespread application of this tool can result in better distribution of care among high-risk surgical patients. PMID:28250670

  10. Predicting preference-based SF-6D index scores from the SF-8 health survey.

    PubMed

    Wang, P; Fu, A Z; Wee, H L; Lee, J; Tai, E S; Thumboo, J; Luo, N

    2013-09-01

    To develop and test functions for predicting the preference-based SF-6D index scores from the SF-8 health survey. This study was a secondary analysis of data collected in a population health survey in which respondents (n = 7,529) completed both the SF-36 and the SF-8 questionnaires. We examined seven ordinary least-square estimators for their performance in predicting SF-6D scores from the SF-8 at both the individual and the group levels. In general, all functions performed similarly well in predicting SF-6D scores, and the predictions at the group level were better than predictions at the individual level. At the individual level, 42.5-51.5% of prediction errors were smaller than the minimally important difference (MID) of the SF-6D scores, depending on the function specifications, while almost all prediction errors of the tested functions were smaller than the MID of SF-6D at the group level. At both individual and group levels, the tested functions predicted lower than actual scores at the higher end of the SF-6D scale. Our study developed functions to generate preference-based SF-6D index scores from the SF-8 health survey, the first of its kind. Further research is needed to evaluate the performance and validity of the prediction functions.

  11. Indexed variation graphs for efficient and accurate resistome profiling.

    PubMed

    Rowe, Will P M; Winn, Martyn D

    2018-05-14

    Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

  12. Diffusion Tensor Fractional Anisotropy in the Superior Longitudinal Fasciculus Correlates with Functional Independence Measure Cognition Scores in Patients with Cerebral Infarction.

    PubMed

    Koyama, Tetsuo; Domen, Kazuhisa

    2017-08-01

    This study aimed to determine the relationship between fiber tract degeneration measured by diffusion-tensor imaging (DTI) and outcome of patients after cerebral infarction. Fractional anisotropy (FA) maps were generated by DTI in patients 14-21 days after the first infarction and were analyzed by tract-based spatial statistics (TBSS). Mean FA values within the corticospinal tract (CST) and the superior longitudinal fasciculus (SLF) were extracted from individual TBSS data. Relationships between FA ratios (rFAs, lesioned to non-lesioned hemisphere) and outcomes assessed by Brunnstrom stage (BRS) and Functional Independence Measure (FIM) motor and cognition scores were examined using Spearman's rank correlation test. Forty patients (21 left and 19 right hemisphere lesions) were entered into an analytical database. BRS ranged from 1 to 6 (median, 5) for shoulder, elbow, or forearm; from 2 to 6 (median, 4.5) for hand or finger; and from 3 to 6 (median, 5) for lower extremity. FIM motor ranged from 51 to 91 (median, 79.5), and FIM cognition ranged from 16 to 35 (median, 29). rFA values in the CST ranged from .692 to 1.053 (median, .933), and those in the SLF ranged from .778 to 1.076 (median, .965). Mann-Whitney U test (P <.05) revealed no significant differences between the left and the right hemisphere lesion groups. Individual rFA values in the CST correlated with BRS scores (r = .585-0.654), whereas those in the SLF correlated with FIM cognition scores (r = .409, P <.05). DTI-FA values in the SLF and CST may be useful for outcome prediction of cognitive function and extremity function, respectively. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  13. Continued Validation of the O-SCORE (Ottawa Surgical Competency Operating Room Evaluation): Use in the Simulated Environment.

    PubMed

    MacEwan, Matthew J; Dudek, Nancy L; Wood, Timothy J; Gofton, Wade T

    2016-01-01

    CONSTRUCT: The Ottawa Surgical Competency Operating Room Evaluation (O-SCORE) is a 9-item surgical evaluation tool designed to assess technical competence in surgical trainees using behavioral anchors. The initial development of the O-SCORE produced evidence for valid results. Further work is required to determine if the use of a single surgeon or an unblinded rater introduces bias. In addition, the relationship of the O-SCORE to other currently used technical assessment tools should be explored to provide validity evidence related to the relationship to other measures. We have designed this project to provide continued validity evidence for the O-SCORE related to these two issues. Nineteen residents and 2 staff Orthopedic Surgeons from the University of Ottawa volunteered to participate in a 2-part OSCE style station. Participants completed a written questionnaire followed by a videotaped 10-minute simulated open reduction and internal fixation of a midshaft radius fracture. Videos were rated individually by 2 blinded staff orthopedic surgeons using an Objective Structured Assessment of Technical Skills (OSATS) global rating scale, an OSATS checklist, and the O-SCORE in random order. O-SCORE results appeared sensitive to surgical training level even when raters were blinded. In addition, strong agreement between two independent observers using the O-SCORE suggests that the measure captures a performance easily recognized by surgical observers. Ratings on the O-SCORE also were strongly associated with global ratings on the currently most validated technical evaluation tool (OSATS). Collectively, these results suggest that the O-SCORE generates accurate, reproducible, and meaningful results when used in a randomized and blinded fashion, providing continued validity evidence for using this tool to evaluate surgical trainee competence. The O-SCORE was able to differentiate surgical trainee level using blinded raters providing further evidence of validity for the O-SCORE

  14. Validation of the Chinese Version of the Functional Oral Intake Scale (FOIS) Score in the Assessment of Acute Stroke Patients with Dysphagia.

    PubMed

    Zhou, Hongzhen; Zhu, Yafang; Zhang, Xiaomei

    2017-01-01

    This study aimed to validate the Chinese version of the Functional Oral Intake Scale (FOIS) score in acute stroke patients with dysphagia. A sample of 128 consecutive patients with acute stroke, admitted to Department of Neurology from April to October in 2016, completed the FOIS. The interrater reliability, criterion validity, discriminant validity, cross validation, and the sensitivity of FOIS scale were evaluated. Results showed that rater agreements were excellent for FOIS (Kw = 0.881, p < 0.001). A highly negative correlation between FOIS and WST (water swallow test) was detected (r = -0.937, p < 0.001). There was significant difference for FOIS level of patients with different evaluation outcomes (χ2 = 126.551, p < 0.001). The FOIS evaluation results were significantly correlated with two physiological measures of swallowing. The Chinese version of the FOIS score is a reliable scale for evaluating the level of oral feeding function in patients with acute stroke.

  15. Concurrent chart review provides more accurate documentation and increased calculated case mix index, severity of illness, and risk of mortality.

    PubMed

    Frazee, Richard C; Matejicka, Anthony V; Abernathy, Stephen W; Davis, Matthew; Isbell, Travis S; Regner, Justin L; Smith, Randall W; Jupiter, Daniel C; Papaconstantinou, Harry T

    2015-04-01

    Case mix index (CMI) is calculated to determine the relative value assigned to a Diagnosis-Related Group. Accurate documentation of patient complications and comorbidities and major complications and comorbidities changes CMI and can affect hospital reimbursement and future pay for performance metrics. Starting in 2010, a physician panel concurrently reviewed the documentation of the trauma/acute care surgeons. Clarifications of the Centers for Medicare and Medicaid Services term-specific documentation were made by the panel, and the surgeon could incorporate or decline the clinical queries. A retrospective review of trauma/acute care inpatients was performed. The mean severity of illness, risk of mortality, and CMI from 2009 were compared with the 3 subsequent years. Mean length of stay and mean Injury Severity Score by year were listed as measures of patient acuity. Statistical analysis was performed using ANOVA and t-test, with p < 0.05 for significance. Each year demonstrated an increase in severity of illness, risk of mortality, and CMI compared with baseline values (p < 0.05). Length of stay was not significantly different, reflecting similar patient populations throughout the study. Injury Severity Score decreased in 2011 and 2012 compared with 2009, reflecting a lower level of injury in the trauma population. A concurrent documentation review significantly increases severity of illness, risk of mortality, and CMI scores in a trauma/acute care service compared with pre-program levels. These changes reflect more accurate key word documentation rather than a change in patient acuity. The increased scores might impact hospital reimbursement and more accurately stratify outcomes measures for care providers. Copyright © 2015 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  16. Oncological and functional outcomes of elderly men treated with HIFU vs. minimally invasive radical prostatectomy: A propensity score analysis.

    PubMed

    Capogrosso, Paolo; Barret, Eric; Sanchez-Salas, Rafael; Nunes-Silva, Igor; Rozet, François; Galiano, Marc; Ventimiglia, Eugenio; Briganti, Alberto; Salonia, Andrea; Montorsi, Francesco; Cathelineau, Xavier

    2018-01-01

    To assess outcomes of whole gland high-intensity focused ultrasound (HIFU) as compared with minimally-invasive radical prostatectomy (MIRP) in elderly patients. Patients aged ≥70 years with, cT1-cT2 disease, biopsy Gleason score (GS) 3 + 3 or 3 + 4 and preoperative PSA ≤10 ng/mL were submitted to either whole-gland HIFU or MIRP. Propensity-score matching analysis was performed to ensure the baseline equivalence of groups. Follow-up visits were routinely performed assessing PSA and urinary function according to the International Continence Score (ICS) and the International Prostatic Symptoms Score (IPSS) questionnaires. Estimated rates of salvage-treatment free survival (SFS) overall-survival (OS), cancer-specific survival (CSS) and metastasis-free survival (MTS) were assessed and compared. Overall, 84 (33.3%) and 168 (66.7%) patients were treated with HIFU and MIRP, respectively. MIRP was associated with a 5-yrs SFS of 93.4% compared to 74.8% for HIFU (p < 0.01). The two groups did not differ in terms of OS and MTS. No cancer-related deaths were registered. Patients treated with HIFU showed better short-term (6-mos) continence outcomes [mean-ICS: 1.7 vs. 4.8; p = 0.005] but higher IPSS mean scores at 12-mos assessment. A comparable rate of patients experiencing post-treatment Clavien-Dindo grade ≥III complications was observed within the two groups. Whole-gland HIFU is a feasible treatment in elderly men with low-to intermediate-risk PCa and could be considered for patients either unfit for surgery, or willing a non-invasive treatment with a low morbidity burden, although a non-negligible risk of requiring subsequent treatment for recurrence should be expected. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

  17. More accurate depiction of adsorption energy on transition metals using work function as one additional descriptor.

    PubMed

    Shen, Xiaochen; Pan, Yanbo; Liu, Bin; Yang, Jinlong; Zeng, Jie; Peng, Zhenmeng

    2017-05-24

    The reaction mechanism and properties of a catalytic process are primarily determined by the interactions between reacting species and catalysts. However, the interactions are often challenging to be experimentally measured, especially for unstable intermediates. Therefore, it is of significant importance to establish an exact relationship between chemical-catalyst interactions and catalyst parameters, which will allow calculation of these interactions and thus advance their mechanistic understanding. Herein we report the description of adsorption energy on transition metals by considering both ionic bonding and covalent bonding contributions and introduce the work function as one additional responsible parameter. We find that the adsorption energy can be more accurately described using a two-dimensional (2D) polynomial model, which shows a significant improvement compared with the current adsorption energy-d-band center linear correlation. We also demonstrate the utilization of this new 2D polynomial model to calculate oxygen binding energy of different transition metals to help understand their catalytic properties in oxygen reduction reactions.

  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. How accurate is our clinical prediction of "minimal prostate cancer"?

    PubMed

    Leibovici, Dan; Shikanov, Sergey; Gofrit, Ofer N; Zagaja, Gregory P; Shilo, Yaniv; Shalhav, Arieh L

    2013-07-01

    Recommendations for active surveillance versus immediate treatment for low risk prostate cancer are based on biopsy and clinical data, assuming that a low volume of well-differentiated carcinoma will be associated with a low progression risk. However, the accuracy of clinical prediction of minimal prostate cancer (MPC) is unclear. To define preoperative predictors for MPC in prostatectomy specimens and to examine the accuracy of such prediction. Data collected on 1526 consecutive radical prostatectomy patients operated in a single center between 2003 and 2008 included: age, body mass index, preoperative prostate-specific antigen level, biopsy Gleason score, clinical stage, percentage of positive biopsy cores, and maximal core length (MCL) involvement. MPC was defined as < 5% of prostate volume involvement with organ-confined Gleason score < or = 6. Univariate and multivariate logistic regression analyses were used to define independent predictors of minimal disease. Classification and Regression Tree (CART) analysis was used to define cutoff values for the predictors and measure the accuracy of prediction. MPC was found in 241 patients (15.8%). Clinical stage, biopsy Gleason's score, percent of positive biopsy cores, and maximal involved core length were associated with minimal disease (OR 0.42, 0.1, 0.92, and 0.9, respectively). Independent predictors of MPC included: biopsy Gleason score, percent of positive cores and MCL (OR 0.21, 095 and 0.95, respectively). CART showed that when the MCL exceeded 11.5%, the likelihood of MPC was 3.8%. Conversely, when applying the most favorable preoperative conditions (Gleason < or = 6, < 20% positive cores, MCL < or = 11.5%) the chance of minimal disease was 41%. Biopsy Gleason score, the percent of positive cores and MCL are independently associated with MPC. While preoperative prediction of significant prostate cancer was accurate, clinical prediction of MPC was incorrect 59% of the time. Caution is necessary when

  20. S100b and BNP predict functional neurological outcome after intracerebral hemorrhage

    PubMed Central

    James, Michael L.; Blessing, Robert; Phillips-Bute, Barbara G.; Bennett, Ellen; Laskowitz, Daniel T.

    2009-01-01

    Objective To determine the predictive value of S100b and brain natriuretic peptide (BNP) to accurately and quickly determine discharge prognosis after primary supratentorial intracerebral hemorrhage (ICH). Methods After IRB approval and informed consent, blood samples were obtained and analyzed from 28 adult patients consecutively admitted to the neuroscience intensive care unit with computed tomography-proven supratentorial ICH from June 2003 and December 2004 within the first 24 h after symptom onset for S100b and BNP. Functional outcomes on discharge were dichotomized to favorable (mRS<3) or unfavorable. Results BNP (a neurohormone) and S100b (a marker of glial activation) were found to be independently highly predictive of functional neurological outcome at the time of discharge as measured by modified Rankin Score (BNP:p<0.01, r=0.46; S100b: p<0.01, r=0.42) and Barthel Index (BNP:p<0.01, r=0.54; s100b:p<0.01, r=0.50). Although inclusion of either biomarker produced additive value when included with traditional clinical prognostic variables, such as the ICH Score (Barthel index: p<0.01, r=0.66; mRS:p<0.01, r=0.96), little predictive power is added with inclusion of both biomarkers in a regression model for neurological outcome. Conclusions Serum S100b and BNP levels in the first 24 h after injury accurately predict neurological function at discharge after supratentorial ICH. PMID:19505208

  1. 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.

  2. Aiding alternatives assessment with an uncertainty-tolerant hazard scoring method.

    PubMed

    Faludi, Jeremy; Hoang, Tina; Gorman, Patrick; Mulvihill, Martin

    2016-11-01

    This research developed a single-score system to simplify and clarify decision-making in chemical alternatives assessment, accounting for uncertainty. Today, assessing alternatives to hazardous constituent chemicals is a difficult task-rather than comparing alternatives by a single definitive score, many independent toxicological variables must be considered at once, and data gaps are rampant. Thus, most hazard assessments are only comprehensible to toxicologists, but business leaders and politicians need simple scores to make decisions. In addition, they must balance hazard against other considerations, such as product functionality, and they must be aware of the high degrees of uncertainty in chemical hazard data. This research proposes a transparent, reproducible method to translate eighteen hazard endpoints into a simple numeric score with quantified uncertainty, alongside a similar product functionality score, to aid decisions between alternative products. The scoring method uses Clean Production Action's GreenScreen as a guide, but with a different method of score aggregation. It provides finer differentiation between scores than GreenScreen's four-point scale, and it displays uncertainty quantitatively in the final score. Displaying uncertainty also illustrates which alternatives are early in product development versus well-defined commercial products. This paper tested the proposed assessment method through a case study in the building industry, assessing alternatives to spray polyurethane foam insulation containing methylene diphenyl diisocyanate (MDI). The new hazard scoring method successfully identified trade-offs between different alternatives, showing finer resolution than GreenScreen Benchmarking. Sensitivity analysis showed that different weighting schemes in hazard scores had almost no effect on alternatives ranking, compared to uncertainty from data gaps. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Accurate estimation of short read mapping quality for next-generation genome sequencing

    PubMed Central

    Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

    2012-01-01

    Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

  4. Lossy compression of quality scores in genomic data.

    PubMed

    Cánovas, Rodrigo; Moffat, Alistair; Turpin, Andrew

    2014-08-01

    Next-generation sequencing technologies are revolutionizing medicine. Data from sequencing technologies are typically represented as a string of bases, an associated sequence of per-base quality scores and other metadata, and in aggregate can require a large amount of space. The quality scores show how accurate the bases are with respect to the sequencing process, that is, how confident the sequencer is of having called them correctly, and are the largest component in datasets in which they are retained. Previous research has examined how to store sequences of bases effectively; here we add to that knowledge by examining methods for compressing quality scores. The quality values originate in a continuous domain, and so if a fidelity criterion is introduced, it is possible to introduce flexibility in the way these values are represented, allowing lossy compression over the quality score data. We present existing compression options for quality score data, and then introduce two new lossy techniques. Experiments measuring the trade-off between compression ratio and information loss are reported, including quantifying the effect of lossy representations on a downstream application that carries out single nucleotide polymorphism and insert/deletion detection. The new methods are demonstrably superior to other techniques when assessed against the spectrum of possible trade-offs between storage required and fidelity of representation. An implementation of the methods described here is available at https://github.com/rcanovas/libCSAM. rcanovas@student.unimelb.edu.au Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. What's in a Grade? A Professor's Guide to Adjusting Scores on Student Assessments

    ERIC Educational Resources Information Center

    Kuhlthau, Kaitlin; Ruscio, John; Luce, Christine; Furey, Matthew

    2017-01-01

    Grades serve many important purposes, and educators agree it is important to assign them accurately and fairly. Interviews with 100 professors across a broad range of academic disciplines at a mid-sized state college revealed little consensus on whether, when, or how to adjust scores when assigning grades. Their responses informed a review of…

  6. Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries.

    PubMed

    Li, Liwei; Wang, Bo; Meroueh, Samy O

    2011-09-26

    The community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the two CSAR data sets. The features used to train SVR-KB are knowledge-based pairwise potentials, while SVR-EP is based on physicochemical properties. SVR-KB and SVR-EP were compared to seven other widely used scoring functions, including Glide, X-score, GoldScore, ChemScore, Vina, Dock, and PMF. Results showed that SVR-KB trained with features obtained from three-dimensional complexes of the PDBbind data set outperformed all other scoring functions, including best performing X-score, by nearly 0.1 using three correlation coefficients, namely Pearson, Spearman, and Kendall. It was interesting that higher performance in rank ordering did not translate into greater enrichment in virtual screening assessed using the 40 targets of the Directory of Useful Decoys (DUD). To remedy this situation, a variant of SVR-KB (SVR-KBD) was developed by following a target-specific tailoring strategy that we had previously employed to derive SVM-SP. SVR-KBD showed a much higher enrichment, outperforming all other scoring functions tested, and was comparable in performance to our previously derived scoring function SVM-SP.

  7. Prospective evaluation of the Sunshine Appendicitis Grading System score.

    PubMed

    Reid, Fiona; Choi, Julian; Williams, Marli; Chan, Steven

    2017-05-01

    Although there is a wealth of information predicting risk of post-operative intra-abdominal collection and guiding antibiotic therapy following appendicectomy, confusion remains because of lack of consensus on the clinical severity and definition of 'complicated' appendicitis. This study aimed to develop a standardized intra-operative grading system: Sunshine Appendicitis Grading System (SAGS) for acute appendicitis that correlates independently with the risk of intra-abdominal collections. Two-hundred and forty-six patients undergoing emergency laparoscopy for suspected appendicitis were prospectively scored according to the severity of appendicitis and followed up for complications including intra-abdominal collection. After termination of the study, the SAGS score was repeated by an independent surgeon based on operation notes and intra-operative photography to determine inter-rater agreement. The primary outcome measure was incidence of intra-abdominal collection, secondary outcome measures were all complications and length of stay. SAGS score demonstrated good inter-rater agreement (kappa K w 0.869; 95% CI 0.796-0.941; P < 0.001). A risk ratio of 2.594 (95% CI 0.655-4.065; P < 0.001) for intra-abdominal collection was found using SAGS score as a predictor. The discriminative ability of SAGS score was supported by an area under the curve value of 0.850 (95% CI 0.799-0.892; P < 0.001). SAGS score can be used to simply and accurately classify the severity of appendicitis and to independently predict the risk of intra-abdominal collection. It can therefore be used to stratify risk, guide antibiotic therapy, follow-up and standardize the definitions of appendicitis severity for future research. © 2015 Royal Australasian College of Surgeons.

  8. Validity of the lower extremity functional movement screen in patients with chronic ankle instability.

    PubMed

    Choi, Ho-Suk; Shin, Won-Seob

    2015-06-01

    [Purpose] The purpose of this study was to provide evidence of construct validity for the lower extremity functional movement screen (LE-FMS) based on hypothesis testing in patients with chronic ankle instability (CAI). [Subjects] The subjects were 20 healthy subjects and 20 patients with CAI who had a history of ankle sprain with pain for more than 1 day. [Methods] All participants were measured using the Foot and Ankle Disability Index (FADI) and evaluated with the LE-FMS. The screen included the deep squat, the hurdle step (HS) and the in-line lunge (ILL). The symmetry ratios (RS) were accurately measured during the deep squat trial. [Results] Between the two groups, there were significant differences in scores on the LE-FMS, HS, ILL, RS, FADI, and FADI-sport. The FADI was strongly correlated with both LE-FMS score (r=0.807) and ILL score (r=0.896). There was a strong relationship (r=0.818) between LE-FMS score and FADI-sport. [Conclusion] These results suggest that the LE-FMS may be used to detect deficits related to CAI. Additionally, this instrument is reliable in detecting functional limitations in patients with CAI.

  9. Gross Motor Function Measure Evolution Ratio: Use as a Control for Natural Progression in Cerebral Palsy.

    PubMed

    Marois, Pierre; Marois, Mikael; Pouliot-Laforte, Annie; Vanasse, Michel; Lambert, Jean; Ballaz, Laurent

    2016-05-01

    To develop a new way to interpret Gross Motor Function Measure (GMFM-66) score improvement in studies conducted without control groups in children with cerebral palsy (CP). The curves, which describe the pattern of motor development according to the children's Gross Motor Function Classification System level, were used as historical control to define the GMFM-66 expected natural evolution in children with CP. These curves have been modeled and generalized to fit the curve to particular children characteristics. Research center. Not applicable. Not applicable. Not applicable. Assuming that the GMFM-66 score evolution followed the shape of the Rosenbaum curves, by taking into account the age and GMFM-66 score of children, the expected natural evolution of the GMFM-66 score was predicted for any group of children with CP who were <8 years old. Because the expected natural evolution could be predicted for a specific group of children with CP, the efficacy of a treatment could be determined by comparing the GMFM-66 score evolution measured before and after treatment with the expected natural evolution for the same period. A new index, the Gross Motor Function Measure Evolution Ratio, was defined as follows: Gross Motor Function Measure Evolution Ratio=measured GMFM-66 score change/expected natural evolution. For practical or ethical reasons, it is almost impossible to use control groups in studies evaluating effectiveness of many therapeutic modalities. The Gross Motor Function Measure Evolution Ratio gives the opportunity to take into account the expected natural evolution of the gross motor function of children with CP, which is essential to accurately interpret the therapy effect on the GMFM-66. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  10. 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…

  11. Combining multiple positive training sets to generate confidence scores for protein-protein interactions.

    PubMed

    Yu, Jingkai; Finley, Russell L

    2009-01-01

    High-throughput experimental and computational methods are generating a wealth of protein-protein interaction data for a variety of organisms. However, data produced by current state-of-the-art methods include many false positives, which can hinder the analyses needed to derive biological insights. One way to address this problem is to assign confidence scores that reflect the reliability and biological significance of each interaction. Most previously described scoring methods use a set of likely true positives to train a model to score all interactions in a dataset. A single positive training set, however, may be biased and not representative of true interaction space. We demonstrate a method to score protein interactions by utilizing multiple independent sets of training positives to reduce the potential bias inherent in using a single training set. We used a set of benchmark yeast protein interactions to show that our approach outperforms other scoring methods. Our approach can also score interactions across data types, which makes it more widely applicable than many previously proposed methods. We applied the method to protein interaction data from both Drosophila melanogaster and Homo sapiens. Independent evaluations show that the resulting confidence scores accurately reflect the biological significance of the interactions.

  12. Patient-Reported Functional Status in Outpatients With Advanced Cancer: Correlation With Physician-Reported Scores and Survival.

    PubMed

    Popovic, Gordana; Harhara, Thana; Pope, Ashley; Al-Awamer, Ahmed; Banerjee, Subrata; Bryson, John; Mak, Ernie; Lau, Jenny; Hannon, Breffni; Swami, Nadia; Le, Lisa W; Zimmermann, Camilla

    2018-06-01

    Performance status measures are increasingly completed by patients in outpatient cancer settings, but are not well validated for this use. We assessed performance of a patient-reported functional status measure (PRFS, based on the Eastern Cooperative Oncology Group [ECOG]), compared with the physician-completed ECOG, in terms of agreement in ratings and prediction of survival. Patients and physicians independently completed five-point PRFS (lay version of ECOG) and ECOG measures on first consultation at an oncology palliative care clinic. We assessed agreement between PRFS and ECOG using weighted Kappa statistics, and used linear regression to determine factors associated with the difference between PRFS and ECOG ratings. We used the Kaplan-Meier method to estimate the patients' median survival, categorized by PRFS and ECOG, and assessed predictive accuracy of these measures using the C-statistic. For the 949 patients, there was moderate agreement between PRFS and ECOG (weighted Kappa 0.32; 95% CI: 0.28-0.36). On average, patients' ratings of performance status were worse by 0.31 points (95% CI: 0.25-0.37, P < 0.0001); this tendency was greater for younger patients (P = 0.002) and those with worse symptoms (P < 0.0001). Both PRFS and ECOG scores correlated well with overall survival; the C-statistic was higher for the average of PRFS and ECOG scores (0.619) than when reported individually (0.596 and 0.604, respectively). Patients tend to rate their performance status worse than physicians, particularly if they are younger or have greater symptom burden. Prognostic ability of performance status could be improved by using the average of patients and physician scores. Copyright © 2018 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

  13. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    PubMed

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

  14. Gender may have an influence on the relationship between Functional Movement Screen scores and gait parameters in elite junior athletes - A pilot study.

    PubMed

    Magyari, N; Szakács, V; Bartha, C; Szilágyi, B; Galamb, K; Magyar, M O; Hortobágyi, T; Kiss, R M; Tihanyi, J; Négyesi, J

    2017-09-01

    Aims The aim of this study was to examine the effects of gender on the relationship between Functional Movement Screen (FMS) and treadmill-based gait parameters. Methods Twenty elite junior athletes (10 women and 10 men) performed the FMS tests and gait analysis at a fixed speed. Between-gender differences were calculated for the relationship between FMS test scores and gait parameters, such as foot rotation, step length, and length of gait line. Results Gender did not affect the relationship between FMS and treadmill-based gait parameters. The nature of correlations between FMS test scores and gait parameters was different in women and men. Furthermore, different FMS test scores predicted different gait parameters in female and male athletes. FMS asymmetry and movement asymmetries measured by treadmill-based gait parameters did not correlate in either gender. Conclusion There were no interactions between FMS, gait parameters, and gender; however, correlation analyses support the idea that strength and conditioning coaches need to pay attention not only to how to score but also how to correctly use FMS.

  15. Question for a questionnaire: the International Index of Erectile Function.

    PubMed

    Oztürk, M İ; Koca, O; Keleş, M O; Güneş, M; Kaya, C; Karaman, M I

    2011-01-01

    The aim of this study was to analyze the impact of patient age and education level on the comprehension of the Turkish version of Index of Erectile Function (IIEF), and to determine the patient characteristics that make this questionnaire less reliable. In this study, 238 male patients presenting to our clinic were enrolled. The patients were asked to complete the Turkish version of the IIEF questionnaire upon arrival by themselves and then once again during their second visit with the assistance of a physician. 'Accurate' comprehension of the IIEF was considered to be the consistency between the 'self-administered' and 'physician-assisted' IIEF scores. The impact of patient age and education level on the 'accurate' comprehension of the IIEF was analyzed. There was a significant difference between the 'self-administered' and 'physician-assisted' IIEF scores in patients ≥ 60 years of age (P=0.045) and primary school graduates (P=0.015). Age ≥ 60 years and being primary school graduate are factors lowering the comprehension of the Turkish version of the IIEF by the patients. Older patients and patients with lower education could benefit from the assistance of a physician while completing this questionnaire.

  16. User-initialized active contour segmentation and golden-angle real-time cardiovascular magnetic resonance enable accurate assessment of LV function in patients with sinus rhythm and arrhythmias.

    PubMed

    Contijoch, Francisco; Witschey, Walter R T; Rogers, Kelly; Rears, Hannah; Hansen, Michael; Yushkevich, Paul; Gorman, Joseph; Gorman, Robert C; Han, Yuchi

    2015-05-21

    Data obtained during arrhythmia is retained in real-time cardiovascular magnetic resonance (rt-CMR), but there is limited and inconsistent evidence to show that rt-CMR can accurately assess beat-to-beat variation in left ventricular (LV) function or during an arrhythmia. Multi-slice, short axis cine and real-time golden-angle radial CMR data was collected in 22 clinical patients (18 in sinus rhythm and 4 patients with arrhythmia). A user-initialized active contour segmentation (ACS) software was validated via comparison to manual segmentation on clinically accepted software. For each image in the 2D acquisitions, slice volume was calculated and global LV volumes were estimated via summation across the LV using multiple slices. Real-time imaging data was reconstructed using different image exposure times and frame rates to evaluate the effect of temporal resolution on measured function in each slice via ACS. Finally, global volumetric function of ectopic and non-ectopic beats was measured using ACS in patients with arrhythmias. ACS provides global LV volume measurements that are not significantly different from manual quantification of retrospectively gated cine images in sinus rhythm patients. With an exposure time of 95.2 ms and a frame rate of > 89 frames per second, golden-angle real-time imaging accurately captures hemodynamic function over a range of patient heart rates. In four patients with frequent ectopic contractions, initial quantification of the impact of ectopic beats on hemodynamic function was demonstrated. User-initialized active contours and golden-angle real-time radial CMR can be used to determine time-varying LV function in patients. These methods will be very useful for the assessment of LV function in patients with frequent arrhythmias.

  17. 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.

  18. Preoperative prediction of inpatient recovery of function after total hip arthroplasty using performance-based tests: a prospective cohort study.

    PubMed

    Oosting, Ellen; Hoogeboom, Thomas J; Appelman-de Vries, Suzan A; Swets, Adam; Dronkers, Jaap J; van Meeteren, Nico L U

    2016-01-01

    The aim of this study was to evaluate the value of conventional factors, the Risk Assessment and Predictor Tool (RAPT) and performance-based functional tests as predictors of delayed recovery after total hip arthroplasty (THA). A prospective cohort study in a regional hospital in the Netherlands with 315 patients was attending for THA in 2012. The dependent variable recovery of function was assessed with the Modified Iowa Levels of Assistance scale. Delayed recovery was defined as taking more than 3 days to walk independently. Independent variables were age, sex, BMI, Charnley score, RAPT score and scores for four performance-based tests [2-minute walk test, timed up and go test (TUG), 10-meter walking test (10 mW) and hand grip strength]. Regression analysis with all variables identified older age (>70 years), Charnley score C, slow walking speed (10 mW >10.0 s) and poor functional mobility (TUG >10.5 s) as the best predictors of delayed recovery of function. This model (AUC 0.85, 95% CI 0.79-0.91) performed better than a model with conventional factors and RAPT scores, and significantly better (p = 0.04) than a model with only conventional factors (AUC 0.81, 95% CI 0.74-0.87). The combination of performance-based tests and conventional factors predicted inpatient functional recovery after THA. Two simple functional performance-based tests have a significant added value to a more conventional screening with age and comorbidities to predict recovery of functioning immediately after total hip surgery. Patients over 70 years old, with comorbidities, with a TUG score >10.5 s and a walking speed >1.0 m/s are at risk for delayed recovery of functioning. Those high risk patients need an accurate discharge plan and could benefit from targeted pre- and postoperative therapeutic exercise programs.

  19. The Weiss Functional Impairment Rating Scale-Parent Form for assessing ADHD: evaluating diagnostic accuracy and determining optimal thresholds using ROC analysis.

    PubMed

    Thompson, Trevor; Lloyd, Andrew; Joseph, Alain; Weiss, Margaret

    2017-07-01

    The Weiss Functional Impairment Rating Scale-Parent Form (WFIRS-P) is a 50-item scale that assesses functional impairment on six clinically relevant domains typically affected in attention-deficit/hyperactivity disorder (ADHD). As functional impairment is central to ADHD, the WFIRS-P offers potential as a tool for assessing functional impairment in ADHD. These analyses were designed to examine the overall performance of WFIRS-P in differentiating ADHD and non-ADHD cases using receiver operating characteristics (ROC) analysis. This is the first attempt to empirically determine the level of functional impairment that differentiates ADHD children from normal controls. This observational study comprised 5-19-year-olds with physician-diagnosed ADHD (n = 476) and non-ADHD controls (n = 202). ROC analysis evaluated the ability of WFIRS-P to discriminate between ADHD and non-ADHD, and identified a WFIRS-P cut-off score that optimises correct classification. Data were analysed for the complete sample, for males versus females and for participants in two age groups (5-12 versus 13-19 years). Area under the curve (AUC) was 0.91 (95% confidence interval 0.88-0.93) for the overall WFIRS-P score, suggesting highly accurate classification of ADHD distinct from non-ADHD. Sensitivity (0.83) and specificity (0.85) were maximal for a mean overall WFIRS-P score of 0.65, suggesting that this is an appropriate threshold for differentiation. DeLong's test found no significant differences in AUCs for males versus females or 5-12 versus 13-19 years, suggesting that WFIRS-P is an accurate classifier of ADHD across gender and age. When assessing function, WFIRS-P appears to provide a simple and effective basis for differentiating between individuals with/without ADHD in terms of functional impairment. Disease-specific applications of QOL research.

  20. Validation of prognostic scores for clinical outcomes in cirrhotic patients with acute variceal bleeding.

    PubMed

    Motola-Kuba, Miguel; Escobedo-Arzate, Angélica; Tellez-Avila, Félix; Altamirano, José; Aguilar-Olivos, Nancy; González-Angulo, Alberto; Zamarripa-Dorsey, Felipe; Uribe, Misael; Chávez-Tapia, Norberto C

    Background. The Rockall, Glasgow-Blatchford, and AIMS65 are useful and validated scoring systems for predicting the outcomes of patients with nonvariceal gastrointestinal bleeding. However, there are no validated evidence for using them to predict outcomes on variceal bleeding. The aim of this study was to evaluate and compare the prognostic accuracy of different nonvariceal bleeding scores with other liver-specific scoring systems in cirrhotic patients. A retrospective multicenter study that included 160 cirrhotic patients with acute variceal bleeding. The AUROC's to predict in-hospital mortality, and rebleeding, were analyzed for each scoring system. Overall in-hospital mortality occurred in 13% and in-hospital rebleeding in 12% of patients. The systems with the best AUROC value for predicting mortality were MELD (0.828; 95% CI 0.748-0.909), and AIMS65 (0.817; 95% CI 0.724-0.909). The best score systems for predicting rebleeding were Glasgow-Blatchford (0.756; 95% CI 0.640- 0.827), and Rockall (0.691; 95% CI 0.580-0.802). In addition to liver-specific scores, the AIMS65 score is accurate for predicting in-hospital mortality in cirrhotic patients with acute variceal bleeding. Other scoring systems might be useful for predicting significant clinical outcomes in these patients.

  1. The PER (Preoperative Esophagectomy Risk) Score: A Simple Risk Score to Predict Short-Term and Long-Term Outcome in Patients with Surgically Treated Esophageal Cancer.

    PubMed

    Reeh, Matthias; Metze, Johannes; Uzunoglu, Faik G; Nentwich, Michael; Ghadban, Tarik; Wellner, Ullrich; Bockhorn, Maximilian; Kluge, Stefan; Izbicki, Jakob R; Vashist, Yogesh K

    2016-02-01

    Esophageal resection in patients with esophageal cancer (EC) is still associated with high mortality and morbidity rates. We aimed to develop a simple preoperative risk score for the prediction of short-term and long-term outcomes for patients with EC treated by esophageal resection. In total, 498 patients suffering from esophageal carcinoma, who underwent esophageal resection, were included in this retrospective cohort study. Three preoperative esophagectomy risk (PER) groups were defined based on preoperative functional evaluation of different organ systems by validated tools (revised cardiac risk index, model for end-stage liver disease score, and pulmonary function test). Clinicopathological parameters, morbidity, and mortality as well as disease-free survival (DFS) and overall survival (OS) were correlated to the PER score. The PER score significantly predicted the short-term outcome of patients with EC who underwent esophageal resection. PER 2 and PER 3 patients had at least double the risk of morbidity and mortality compared to PER 1 patients. Furthermore, a higher PER score was associated with shorter DFS (P < 0.001) and OS (P < 0.001). The PER score was identified as an independent predictor of tumor recurrence (hazard ratio [HR] 2.1; P < 0.001) and OS (HR 2.2; P < 0.001). The PER score allows preoperative objective allocation of patients with EC into different risk categories for morbidity, mortality, and long-term outcomes. Thus, multicenter studies are needed for independent validation of the PER score.

  2. The Utility of Maze Accurate Response Rate in Assessing Reading Comprehension in Upper Elementary and Middle School Students

    ERIC Educational Resources Information Center

    McCane-Bowling, Sara J.; Strait, Andrea D.; Guess, Pamela E.; Wiedo, Jennifer R.; Muncie, Eric

    2014-01-01

    This study examined the predictive utility of five formative reading measures: words correct per minute, number of comprehension questions correct, reading comprehension rate, number of maze correct responses, and maze accurate response rate (MARR). Broad Reading cluster scores obtained via the Woodcock-Johnson III (WJ III) Tests of Achievement…

  3. Renal dysfunction in liver cirrhosis and its correlation with Child-Pugh score and MELD score

    NASA Astrophysics Data System (ADS)

    Siregar, G. A.; Gurning, M.

    2018-03-01

    Renal dysfunction (RD) is a serious and common complication in a patient with liver cirrhosis. It provides a poor prognosis. The aim of our study was to evaluate the renal function in liver cirrhosis, also to determine the correlation with the graduation of liver disease assessed by Child-Pugh Score (CPS) and MELD score. This was a cross-sectional study included patients with liver cirrhosis admitted to Adam Malik Hospital Medan in June - August 2016. We divided them into two groups as not having renal dysfunction (serum creatinine < 1.5 mg/dL) and having renal dysfunction (serum creatinine ≤ 1.5 mg/dL). For the processing of data, SPSS 22.0 was used. Statistical methods used: Chi-square, Fisher exact, one way ANOVA, Kruskal Wallis test and Pearson coefficient of correlation. The level of significance was p<0.05. 55 patients with presented with renal dysfunction were 16 (29.1 %). There was statistically significant inverse correlation between GFR and CPS (r = -0.308), GFR and MELD score (r = -0.278). There was a statistically significant correlation between creatinine and MELD score (r = 0.359), creatinine and CPS (r = 0.382). The increase of the degree of liver damage is related to the increase of renal dysfunction.

  4. Mortality Probability Model III and Simplified Acute Physiology Score II

    PubMed Central

    Vasilevskis, Eduard E.; Kuzniewicz, Michael W.; Cason, Brian A.; Lane, Rondall K.; Dean, Mitzi L.; Clay, Ted; Rennie, Deborah J.; Vittinghoff, Eric; Dudley, R. Adams

    2009-01-01

    Background: To develop and compare ICU length-of-stay (LOS) risk-adjustment models using three commonly used mortality or LOS prediction models. Methods: Between 2001 and 2004, we performed a retrospective, observational study of 11,295 ICU patients from 35 hospitals in the California Intensive Care Outcomes Project. We compared the accuracy of the following three LOS models: a recalibrated acute physiology and chronic health evaluation (APACHE) IV-LOS model; and models developed using risk factors in the mortality probability model III at zero hours (MPM0) and the simplified acute physiology score (SAPS) II mortality prediction model. We evaluated models by calculating the following: (1) grouped coefficients of determination; (2) differences between observed and predicted LOS across subgroups; and (3) intraclass correlations of observed/expected LOS ratios between models. Results: The grouped coefficients of determination were APACHE IV with coefficients recalibrated to the LOS values of the study cohort (APACHE IVrecal) [R2 = 0.422], mortality probability model III at zero hours (MPM0 III) [R2 = 0.279], and simplified acute physiology score (SAPS II) [R2 = 0.008]. For each decile of predicted ICU LOS, the mean predicted LOS vs the observed LOS was significantly different (p ≤ 0.05) for three, two, and six deciles using APACHE IVrecal, MPM0 III, and SAPS II, respectively. Plots of the predicted vs the observed LOS ratios of the hospitals revealed a threefold variation in LOS among hospitals with high model correlations. Conclusions: APACHE IV and MPM0 III were more accurate than SAPS II for the prediction of ICU LOS. APACHE IV is the most accurate and best calibrated model. Although it is less accurate, MPM0 III may be a reasonable option if the data collection burden or the treatment effect bias is a consideration. PMID:19363210

  5. LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies

    PubMed Central

    Bulik-Sullivan, Brendan K.; Loh, Po-Ru; Finucane, Hilary; Ripke, Stephan; Yang, Jian; Patterson, Nick; Daly, Mark J.; Price, Alkes L.; Neale, Benjamin M.

    2015-01-01

    Both polygenicity (i.e., many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of test statistic inflation in many GWAS of large sample size. PMID:25642630

  6. Emricasan Improves Liver Function in Patients With Cirrhosis and High Model for End-stage Liver Disease Scores Compared With Placebo.

    PubMed

    Frenette, Catherine T; Morelli, Giuseppe; Shiffman, Mitchell L; Frederick, R Todd; Rubin, Raymond A; Fallon, Michael B; Cheng, Jason T; Cave, Matt; Khaderi, Saira A; Massoud, Omar; Pyrsopoulos, Nikolaos; Park, James S; Robinson, James M; Yamashita, Mason; Spada, Alfred P; Chan, Jean L; Hagerty, David T

    2018-06-15

    cirrhosis, we found 3 months treatment with emricasan to improve liver function, compared with placebo, reducing MELD and Child-Pugh scores, INR, and total bilirubin in patients with MELD scores ≥15. ClinicalTrials.gov no: NCT002209456. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

  7. 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

  8. A pairwise maximum entropy model accurately describes resting-state human brain networks

    PubMed Central

    Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

    2013-01-01

    The resting-state human brain networks underlie fundamental cognitive functions and consist of complex interactions among brain regions. However, the level of complexity of the resting-state networks has not been quantified, which has prevented comprehensive descriptions of the brain activity as an integrative system. Here, we address this issue by demonstrating that a pairwise maximum entropy model, which takes into account region-specific activity rates and pairwise interactions, can be robustly and accurately fitted to resting-state human brain activities obtained by functional magnetic resonance imaging. Furthermore, to validate the approximation of the resting-state networks by the pairwise maximum entropy model, we show that the functional interactions estimated by the pairwise maximum entropy model reflect anatomical connexions more accurately than the conventional functional connectivity method. These findings indicate that a relatively simple statistical model not only captures the structure of the resting-state networks but also provides a possible method to derive physiological information about various large-scale brain networks. PMID:23340410

  9. INTERPRETING PHYSICAL AND BEHAVIORAL HEALTH SCORES FROM NEW WORK DISABILITY INSTRUMENTS

    PubMed Central

    Marfeo, Elizabeth E.; Ni, Pengsheng; Chan, Leighton; Rasch, Elizabeth K.; McDonough, Christine M.; Brandt, Diane E.; Bogusz, Kara; Jette, Alan M.

    2015-01-01

    Objective To develop a system to guide interpretation of scores generated from 2 new instruments measuring work-related physical and behavioral health functioning (Work Disability – Physical Function (WD-PF) and WD – Behavioral Function (WD-BH)). Design Cross-sectional, secondary data from 3 independent samples to develop and validate the functional levels for physical and behavioral health functioning. Subjects Physical group: 999 general adult subjects, 1,017 disability applicants and 497 work-disabled subjects. Behavioral health group: 1,000 general adult subjects, 1,015 disability applicants and 476 work-disabled subjects. Methods Three-phase analytic approach including item mapping, a modified-Delphi technique, and known-groups validation analysis were used to develop and validate cut-points for functional levels within each of the WD-PF and WD-BH instrument’s scales. Results Four and 5 functional levels were developed for each of the scales in the WD-PF and WD-BH instruments. Distribution of the comparative samples was in the expected direction: the general adult samples consistently demonstrated scores at higher functional levels compared with the claimant and work-disabled samples. Conclusion Using an item-response theory-based methodology paired with a qualitative process appears to be a feasible and valid approach for translating the WD-BH and WD-PF scores into meaningful levels useful for interpreting a person’s work-related physical and behavioral health functioning. PMID:25729901

  10. 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. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Accuracy of Automatic Polysomnography Scoring Using Frontal Electrodes

    PubMed Central

    Younes, Magdy; Younes, Mark; Giannouli, Eleni

    2016-01-01

    Study Objectives: The economic cost of performing sleep monitoring at home is a major deterrent to adding sleep data during home studies for investigation of sleep apnea and to investigating non-respiratory sleep complaints. Michele Sleep Scoring System (MSS) is a validated automatic system that utilizes central electroencephalography (EEG) derivations and requires minimal editing. We wished to determine if MSS' accuracy is maintained if frontal derivations are used instead. If confirmed, home sleep monitoring would not require home setup or lengthy manual scoring by technologists. Methods: One hundred two polysomnograms (PSGs) previously recorded from patients with assorted sleep disorders were scored using MSS once with central and once with frontal derivations. Total sleep time, sleep/stage R sleep onset latencies, awake time, time in different sleep stages, arousal/awakening index and apnea-hypopnea index were compared. In addition, odds ratio product (ORP), a continuous index of sleep depth/quality (Sleep 2015;38:641–54), was generated for every 30-sec epoch in each PSG and epoch-by-epoch comparison of ORP was performed. Results: Intraclass correlation coefficients (ICCs) ranged from 0.89 to 1.0 for the various sleep variables (0.96 ± 0.03). For epoch-by-epoch comparisons of ORP, ICC was > 0.85 in 96 PSGs. Lower values in the other six PSGs were related to signal artifacts in either derivation. ICC for whole-record average ORP was 0.98. Conclusions: MSS is as accurate with frontal as with central EEG derivations. The use of frontal electrodes along with MSS should make it possible to obtain high-quality sleep data without requiring home setup or lengthy scoring time by expert technologists. Citation: Younes M, Younes M, Giannouli E. Accuracy of automatic polysomnography scoring using frontal electrodes. J Clin Sleep Med 2016;12(5):735–746. PMID:26951417

  12. Accurate Structural Correlations from Maximum Likelihood Superpositions

    PubMed Central

    Theobald, Douglas L; Wuttke, Deborah S

    2008-01-01

    The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

  13. 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.

  14. Dutch validation of the low anterior resection syndrome score.

    PubMed

    Hupkens, B J P; Breukink, S O; Olde Reuver Of Briel, C; Tanis, P J; de Noo, M E; van Duijvendijk, P; van Westreenen, H L; Dekker, J W T; Chen, T Y T; Juul, T

    2018-04-21

    The aim of this study was to validate the Dutch translation of the low anterior resection syndrome (LARS) score in a population of Dutch rectal cancer patients. Patients who underwent surgery for rectal cancer received the LARS score questionnaire, a single quality of life (QoL) category question and the European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30 questionnaire. A subgroup of patients received the LARS score twice to assess the test-retest reliability. A total of 165 patients were included in the analysis, identified in six Dutch centres. The response rate was 62.0%. The percentage of patients who reported 'major LARS' was 59.4%. There was a high proportion of patients with a perfect or moderate fit between the QoL category question and the LARS score, showing a good convergent validity. The LARS score was able to discriminate between patients with or without neoadjuvant radiotherapy (P = 0.003), between total and partial mesorectal excision (P = 0.008) and between age groups (P = 0.039). There was a statistically significant association between a higher LARS score and an impaired function on the global QoL subscale and the physical, role, emotional and social functioning subscales of the EORTC QLQ-C30 questionnaire. The test-retest reliability of the LARS score was good, with an interclass correlation coefficient of 0.79. The good psychometric properties of the Dutch version of the LARS score are comparable overall to the earlier validations in other countries. Therefore, the Dutch translation can be considered to be a valid tool for assessing LARS in Dutch rectal cancer patients. Colorectal Disease © 2018 The Association of Coloproctology of Great Britain and Ireland.

  15. Evaluation of probabilistic forecasts with the scoringRules package

    NASA Astrophysics Data System (ADS)

    Jordan, Alexander; Krüger, Fabian; Lerch, Sebastian

    2017-04-01

    Over the last decades probabilistic forecasts in the form of predictive distributions have become popular in many scientific disciplines. 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 in order to better understand sources of prediction errors and to improve the models. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. In coherence with decision-theoretical principles 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 contribution presents the software package scoringRules for the statistical programming language R, which provides 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. For univariate variables, 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, ensemble weather forecasts take this form. 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. Recent developments include the addition of scoring rules to evaluate multivariate forecast distributions. The use of the scoringRules package is illustrated in an example on post-processing ensemble forecasts of temperature.

  16. Does Field Reliability for Static-99 Scores Decrease as Scores Increase?

    PubMed Central

    Rice, Amanda K.; Boccaccini, Marcus T.; Harris, Paige B.; Hawes, Samuel W.

    2015-01-01

    This study examined the field reliability of Static-99 (Hanson & Thornton, 2000) scores among 21,983 sex offenders and focused on whether rater agreement decreased as scores increased. As expected, agreement was lowest for high-scoring offenders. Initial and most recent Static-99 scores were identical for only about 40% of offenders who had been assigned a score of 6 during their initial evaluations, but for more than 60% of offenders who had been assigned a score of 2 or lower. In addition, the size of the difference between scores increased as scores increased, with pairs of scores differing by 2 or more points for about 30% of offenders scoring in the high-risk range. Because evaluators and systems use high Static-99 scores to identify sexual offenders who may require intensive supervision or even postrelease civil commitment, it is important to recognize that there may be more measurement error for high scores than low scores and to consider adopting procedures for minimizing or accounting for measurement error. PMID:24932647

  17. [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.

  18. Linear score tests for variance components in linear mixed models and applications to genetic association studies.

    PubMed

    Qu, Long; Guennel, Tobias; Marshall, Scott L

    2013-12-01

    Following the rapid development of genome-scale genotyping technologies, genetic association mapping has become a popular tool to detect genomic regions responsible for certain (disease) phenotypes, especially in early-phase pharmacogenomic studies with limited sample size. In response to such applications, a good association test needs to be (1) applicable to a wide range of possible genetic models, including, but not limited to, the presence of gene-by-environment or gene-by-gene interactions and non-linearity of a group of marker effects, (2) accurate in small samples, fast to compute on the genomic scale, and amenable to large scale multiple testing corrections, and (3) reasonably powerful to locate causal genomic regions. The kernel machine method represented in linear mixed models provides a viable solution by transforming the problem into testing the nullity of variance components. In this study, we consider score-based tests by choosing a statistic linear in the score function. When the model under the null hypothesis has only one error variance parameter, our test is exact in finite samples. When the null model has more than one variance parameter, we develop a new moment-based approximation that performs well in simulations. Through simulations and analysis of real data, we demonstrate that the new test possesses most of the aforementioned characteristics, especially when compared to existing quadratic score tests or restricted likelihood ratio tests. © 2013, The International Biometric Society.

  19. Comparing traditional and novel injury scoring systems in a US level-I trauma center: an opportunity for improved injury surveillance in low- and middle-income countries.

    PubMed

    Laytin, Adam D; Dicker, Rochelle A; Gerdin, Martin; Roy, Nobhojit; Sarang, Bhakti; Kumar, Vineet; Juillard, Catherine

    2017-07-01

    In most low- and middle-income countries (LMICs), the resources to accurately quantify injury severity using traditional injury scoring systems are limited. Novel injury scoring systems appear to have adequate discrimination for mortality in LMIC contexts, but they have not been rigorously compared where traditional injury scores can be accurately calculated. To determine whether novel injury scoring systems perform as well as traditional ones in a HIC with complete and comprehensive data collection. Data from an American level-I trauma registry collected 2008-2013 were used to compare three traditional injury scoring systems: Injury Severity Score (ISS); Revised Trauma Score (RTS); and Trauma Injury Severity Score (TRISS); and three novel injury scoring systems: Kampala Trauma Score (KTS); Mechanism, GCS, Age and Pressure (MGAP) score; and GCS, Age and Pressure (GAP) score. Logistic regression was used to assess the association between each scoring system and mortality. Standardized regression coefficients (β 2 ), Akaike information criteria, area under the receiver operating characteristics curve, and the calibration line intercept and slope were used to evaluate the discrimination and calibration of each model. Among 18,746 patients, all six scores were associated with hospital mortality. GAP had the highest effect size, and KTS had the lowest median Akaike information criteria. Although TRISS discriminated best, the discrimination of KTS approached that of TRISS and outperformed GAP, MGAP, RTS, and ISS. MGAP was best calibrated, and KTS was better calibrated than RTS, GAP, ISS, or TRISS. The novel injury scoring systems (KTS, MGAP, and GAP), which are more feasible to calculate in low-resource settings, discriminated hospital mortality as well as traditional injury scoring systems (ISS and RTS) and approached the discrimination of a sophisticated, data-intensive injury scoring system (TRISS) in a high-resource setting. Two novel injury scoring systems (KTS and

  20. 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…

  1. Chronic obstructive pulmonary disease (COPD) assessment test scores corresponding to modified Medical Research Council grades among COPD patients.

    PubMed

    Lee, Chang-Hoon; Lee, Jinwoo; Park, Young Sik; Lee, Sang-Min; Yim, Jae-Joon; Kim, Young Whan; Han, Sung Koo; Yoo, Chul-Gyu

    2015-09-01

    In assigning patients with chronic obstructive pulmonary disease (COPD) to subgroups according to the updated guidelines of the Global Initiative for Chronic Obstructive Lung Disease, discrepancies have been noted between the COPD assessment test (CAT) criteria and modified Medical Research Council (mMRC) criteria. We investigated the determinants of symptom and risk groups and sought to identify a better CAT criterion. This retrospective study included COPD patients seen between June 20, 2012, and December 5, 2012. The CAT score that can accurately predict an mMRC grade ≥ 2 versus < 2 was evaluated by comparing the area under the receiver operating curve (AUROC) and by classification and regression tree (CART) analysis. Among 428 COPD patients, the percentages of patients classified into subgroups A, B, C, and D were 24.5%, 47.2%, 4.2%, and 24.1% based on CAT criteria and 49.3%, 22.4%, 8.9%, and 19.4% based on mMRC criteria, respectively. More than 90% of the patients who met the mMRC criteria for the 'more symptoms group' also met the CAT criteria. AUROC and CART analyses suggested that a CAT score ≥ 15 predicted an mMRC grade ≥ 2 more accurately than the current CAT score criterion. During follow-up, patients with CAT scores of 10 to 14 did not have a different risk of exacerbation versus those with CAT scores < 10, but they did have a lower exacerbation risk compared to those with CAT scores of 15 to 19. A CAT score ≥ 15 is a better indicator for the 'more symptoms group' in the management of COPD patients.

  2. Postural stability in patients with knee osteoarthritis: comparison with controls and evaluation of relationships between postural stability scores and International Classification of Functioning, Disability and Health components.

    PubMed

    Hsieh, Ru-Lan; Lee, Wen-Chung; Lo, Min-Tzu; Liao, Wei-Cheng

    2013-02-01

    To assess the differences in postural stability between patients with knee osteoarthritis and controls without knee osteoarthritis, and to evaluate possible relations between postural stability scores and International Classification of Functioning, Disability and Health (ICF) components. An age-matched, case-controlled trial with a cross-sectional design. A teaching hospital. Patients with knee osteoarthritis (n=73) and age-matched controls (n=60). Data on patients' postural stability and additional health-related variables were collected using various instruments. These included the Hospital Anxiety and Depression Scale, the Multidimensional Fatigue Inventory, the World Health Organization Quality of Life Brief Version, the physical function test (chair-rising time), the Chinese version of the Western Ontario and McMaster Universities Osteoarthritis Index, the Chinese version of the Knee Injury and Osteoarthritis Outcome Score, and the Biodex Stability System. A comparison of postural stability in patients with knee osteoarthritis versus that of controls was performed. The relation between postural stability scores for patients with knee osteoarthritis and ICF components was evaluated. Pearson correlation tests were used to determine the variables that correlated with postural stability among these patients. Patients with knee osteoarthritis displayed lower overall postural stability than controls (scores of 0.7 vs. 0.5, P=.006) and scored lower on the environmental domain of the World Health Organization Quality of Life Brief Version (62.2 vs 66.8, P=.014). For patients with knee osteoarthritis, postural stability was weakly associated with the ICF components of body functions and structures, including pain (r=.33-.34, P=.004), physical fatigue (r=.28, P=.016), and reduced motivation (r=.30, P=.011). Weak to moderate associations between postural stability and the ICF components of activities and participation were found; the relevant ICF variables included

  3. An Accurate and Dynamic Computer Graphics Muscle Model

    NASA Technical Reports Server (NTRS)

    Levine, David Asher

    1997-01-01

    A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.

  4. Height for age z score and cognitive function are associated with Academic performance among school children aged 8-11 years old.

    PubMed

    Haile, Demewoz; Nigatu, Dabere; Gashaw, Ketema; Demelash, Habtamu

    2016-01-01

    Academic achievement of school age children can be affected by several factors such as nutritional status, demographics, and socioeconomic factors. Though evidence about the magnitude of malnutrition is well established in Ethiopia, there is a paucity of evidence about the association of nutritional status with academic performance among the nation's school age children. Hence, this study aimed to determine how nutritional status and cognitive function are associated with academic performance of school children in Goba town, South East Ethiopia. An institution based cross-sectional study was conducted among 131 school age students from primary schools in Goba town enrolled during the 2013/2014 academic year. The nutritional status of students was assessed by anthropometric measurement, while the cognitive assessment was measured by the Kaufman Assessment Battery for Children (KABC-II) and Ravens colored progressive matrices (Raven's CPM) tests. The academic performance of the school children was measured by collecting the preceding semester academic result from the school record. Descriptive statistics, bivariate and multivariable linear regression were used in the statistical analysis. This study found a statistically significant positive association between all cognitive test scores and average academic performance except for number recall (p = 0.12) and hand movements (p = 0.08). The correlation between all cognitive test scores and mathematics score was found positive and statistically significant (p < 0.05). In the multivariable linear regression model, better wealth index was significantly associated with higher mathematics score (ß = 0.63; 95 % CI: 0.12-0.74). Similarly a unit change in height for age z score resulted in 2.11 unit change in mathematics score (ß = 2.11; 95 % CI: 0.002-4.21). A single unit change of wealth index resulted 0.53 unit changes in average score of all academic subjects among school age children (ß = 0

  5. Computer-based personality judgments are more accurate than those made by humans.

    PubMed

    Youyou, Wu; Kosinski, Michal; Stillwell, David

    2015-01-27

    Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy.

  6. [The use of scores in general medicine].

    PubMed

    Huber, Ursula; Rösli, Andreas; Ballmer, Peter E; Rippin, Sarah Jane

    2013-10-01

    Scores are tools to combine complex information into a numerical value. In General Medicine, there are scores to assist in making diagnoses and prognoses, scores to assist therapeutic decision making and to evaluate therapeutic results and scores to help physicians when informing and advising patients. We review six of the scoring systems that have the greatest utility for the General Physician in hospital-based care and in General Practice. The Nutritional Risk Screening (NRS 2002) tool is designed to identify hospital patients in danger of malnutrition. The aim is to improve the nutritional status of these patients. The CURB-65 score predicts 30-day mortality in patients with community acquired pneumonia. Patients with a low score can be considered for home treatment, patients with an elevated score require hospitalisation and those with a high score should be treated as having severe pneumonia; treatment in the intensive care unit should be considered. The IAS-AGLA score of the Working Group on Lipids and Atherosclerosis of the Swiss Society of Cardiology calculates the 10-year risk of a myocardial infarction for people living in Switzerland. The working group makes recommendations for preventative treatment according to the calculated risk status. The Body Mass Index, which is calculated by dividing the body weight in kilograms by the height in meters squared and then divided into weight categories, is used to classify people as underweight, of normal weight, overweight or obese. The prognostic value of this classification is discussed. The Mini-Mental State Examination allows the physician to assess important cognitive functions in a simple and standardised form. The Glasgow Coma Scale is used to classify the level of consciousness in patients with head injury. It can be used for triage and correlates with prognosis.

  7. 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).

  8. 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

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

    2016-06-01

    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. 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. 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. 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. 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. 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 exposures in office workers: a controlled exposure study of green and

  9. Multisystemic Therapy and Functional Family Therapy Compared on their Effectiveness Using the Propensity Score Method.

    PubMed

    Eeren, Hester V; Goossens, Lucas M A; Scholte, Ron H J; Busschbach, Jan J V; van der Rijken, Rachel E A

    2018-01-09

    Multisystemic Therapy (MST) and Functional Family Therapy (FFT) have overlapping target populations and treatment goals. In this study, these interventions were compared on their effectiveness using a quasi-experimental design. Between October, 2009 and June, 2014, outcome data were collected from 697 adolescents (mean age 15.3 (SD 1.48), 61.9% male) assigned to either MST or FFT (422 MST; 275 FFT). Data were gathered during Routine Outcome Monitoring. The primary outcome was externalizing problem behavior (Child Behavior Checklist and Youth Self Report). Secondary outcomes were the proportion of adolescents living at home, engaged in school or work, and who lacked police contact during treatment. Because of the non-random assignment, a propensity score method was used to control for observed pre-treatment differences. Because the risk-need-responsivity (RNR) model guided treatment assignment, effectiveness was also estimated in youth with and without a court order as an indicator of their risk level. Looking at the whole sample, no difference in effect was found with regard to externalizing problems. For adolescents without a court order, effects on externalizing problems were larger after MST. Because many more adolescents with a court order were assigned to MST compared to FFT, the propensity score method could not balance the treatment groups in this subsample. In conclusion, few differences between MST and FFT were found. In line with the RNR model, higher risk adolescents were assigned to the more intensive treatment, namely MST. In the group with lower risk adolescents, this more intensive treatment was more effective in reducing externalizing problems.

  10. Contributions of Hamstring Stiffness to Straight-Leg-Raise and Sit-and-Reach Test Scores.

    PubMed

    Miyamoto, Naokazu; Hirata, Kosuke; Kimura, Noriko; Miyamoto-Mikami, Eri

    2018-02-01

    The passive straight-leg-raise (PSLR) and the sit-and-reach (SR) tests have been widely used to assess hamstring extensibility. However, it remains unclear to what extent hamstring stiffness (a measure of material properties) contributes to PSLR and SR test scores. Therefore, we aimed to clarify the relationship between hamstring stiffness and PSLR and SR scores using ultrasound shear wave elastography. Ninety-eight healthy subjects completed the study. Each subject completed PSLR testing, and classic and modified SR testing of the right leg. Muscle shear modulus of the biceps femoris, semitendinosus, and semimembranosus was quantified as an index of muscle stiffness. The relationships between shear modulus of each muscle and PSLR or SR scores were calculated using Pearson's product-moment correlation coefficients. Shear modulus of the semitendinosus and semimembranosus showed negative correlations with the two PSLR and two SR scores (absolute r value≤0.484). Shear modulus of the biceps femoris was significantly correlated with the PSLR score determined by the examiner and the modified SR score (absolute r value≤0.308). The present findings suggest that PSLR and SR test scores are strongly influenced by factors other than hamstring stiffness and therefore might not accurately evaluate hamstring stiffness. © Georg Thieme Verlag KG Stuttgart · New York.

  11. Studying self-awareness in children: validation of the Questionnaire of Executive Functioning (QEF).

    PubMed

    Geurten, Marie; Catale, Corinne; Geurten, Claire; Wansard, Murielle; Meulemans, Thierry

    2016-05-01

    People with accurate representations of their own cognitive functioning (i.e. cognitive self-awareness) tend to use appropriate strategies to regulate their behavior. Due to the lack of appropriate instruments, few studies have examined the development of this ability among children. This study tested the measurement properties of the self-rating and other-rating forms of the Questionnaire of Executive Functioning (QEF), designed to tap children's knowledge of their executive functioning. Specifically, the construct, convergent, and discriminant validities were investigated and a self-other discrepancy score was computed to assess children's executive self-awareness. Participants were 317 children aged 7-14 years old. Confirmatory factor analyses carried out on the QEF confirmed the eight-factor structure of both versions. There were significant correlations between the QEF and the parent versions of the Behavior Rating Inventory of Executive Function, the Dysexecutive Questionnaire for Children, and the Childhood Executive Functioning Inventory. Both forms of the QEF were able to distinguish between children who had sustained a traumatic brain injury (TBI) and control participants. A statistical difference was observed between the TBI and control groups on this score, suggesting that TBI may trigger self-awareness impairments in children. The good psychometric properties of the two forms of the QEF were established. Furthermore, results of the analyses carried out on the different discrepancy scores seem to indicate that the QEF could help clinicians to detect patients with self-awareness deficits.

  12. 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.

  13. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    PubMed

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

    2009-07-01

    The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

  14. Associations of anatomical measures from MRI with radiographically defined knee osteoarthritis score, pain, and physical functioning.

    PubMed

    Sowers, Maryfran; Karvonen-Gutierrez, Carrie A; Jacobson, Jon A; Jiang, Yebin; Yosef, Matheos

    2011-02-02

    The prevalence of knee osteoarthritis is traditionally based on radiographic findings, but magnetic resonance imaging is now being used to provide better visualization of bone, cartilage, and soft tissues as well as the patellar compartment. The goal of this study was to estimate the prevalences of knee features defined on magnetic resonance imaging in a population and to relate these abnormalities to knee osteoarthritis severity scores based on radiographic findings, physical functioning, and reported knee pain in middle-aged women. Magnetic resonance images of the knee were evaluated for the location and severity of cartilage defects, bone marrow lesions, osteophytes, subchondral cysts, meniscal and/or ligamentous tears, effusion, and synovitis among 363 middle-aged women (724 knees) from the Michigan Study of Women's Health Across the Nation. These findings were related to Kellgren-Lawrence osteoarthritis severity scores from radiographs, self-reported knee pain, self-reported knee injury, perception of physical functioning, and physical performance measures to assess mobility. Radiographs, physical performance assessment, and interviews were undertaken at the 1996 study baseline and again (with the addition of magnetic resonance imaging assessment) at the follow-up visit during 2007 to 2008. The prevalence of moderate-to-severe knee osteoarthritis changed from 3.7% at the baseline assessment to 26.7% at the follow-up visit eleven years later. Full-thickness cartilage defects of the medial, lateral, and patellofemoral compartments were present in 14.5% (105 knees), 4.6% (thirty-three knees), and 26.2% (190 knees), respectively. Synovitis was identified in 24.7% (179) of the knees, and joint effusions were observed in 70% (507 knees); 21.7% (157) of the knees had complex or macerated meniscal tears. Large osteophytes, marked synovitis, macerated meniscal tears, and full-thickness tibial cartilage defects were associated with increased odds of knee pain and with

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

    PubMed

    Ashtawy, Hossam M; Mahapatra, Nihar R

    2015-01-01

    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. 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.

  16. 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

  17. The Zhongshan Score

    PubMed Central

    Zhou, Lin; Guo, Jianming; Wang, Hang; Wang, Guomin

    2015-01-01

    Abstract In the zero ischemia era of nephron-sparing surgery (NSS), a new anatomic classification system (ACS) is needed to adjust to these new surgical techniques. We devised a novel and simple ACS, and compared it with the RENAL and PADUA scores to predict the risk of NSS outcomes. We retrospectively evaluated 789 patients who underwent NSS with available imaging between January 2007 and July 2014. Demographic and clinical data were assessed. The Zhongshan (ZS) score consisted of three parameters. RENAL, PADUA, and ZS scores are divided into three groups, that is, high, moderate, and low scores. For operative time (OT), significant differences were seen between any two groups of ZS score and PADUA score (all P < 0.05). For ZS score, patients with moderate and high scores had longer warm ischemia time (WIT) and greater increase in SCr compared with low score (all P < 0.05). What is more, the differences between moderate and high scores classified by ZS score were borderline but trending toward significance in WIT (P = 0.064) and increase in SCr (P = 0.052). Interestingly, RENAL showed no significant difference between moderate and high complexity in OT, WIT, estimated blood loss, and increase in SCr. Compared with patients with a low score of ZS, those with a high or moderate score had 8.1-fold or 3.3-fold higher risk of surgical complications, respectively (all P < 0.05). As for RENAL score, patients with a high or moderate score had 5.7-fold or 1.9-fold higher risk of surgical complications, respectively (all P < 0.05). Patients with a high or moderate score of PADUA had 2.3-fold or 2.8-fold higher risk of surgical complications, respectively (all P < 0.05). In the ROC curve analysis, ZS score had the greatest AUC for surgical complications (AUC = 0.632) and the conversion to radical nephrectomy (AUC = 0.845) (all P < 0.05). In conclusion, the ability of ZS score to predict the surgical complexity and surgical

  18. Early postoperative repair status after rotator cuff repair cannot be accurately classified using questionnaires of patient function and isokinetic strength evaluation.

    PubMed

    Colliver, Jessica; Wang, Allan; Joss, Brendan; Ebert, Jay; Koh, Eamon; Breidahl, William; Ackland, Timothy

    2016-04-01

    This study investigated if patients with an intact tendon repair or partial-thickness retear early after rotator cuff repair display differences in clinical evaluations and whether early tendon healing can be predicted using these assessments. We prospectively evaluated 60 patients at 16 weeks after arthroscopic supraspinatus repair. Evaluation included the Oxford Shoulder Score, 11-item version of the Disabilities of the Arm, Shoulder and Hand, visual analog scale for pain, 12-item Short Form Health Survey, isokinetic strength, and magnetic resonance imaging (MRI). Independent t tests investigated clinical differences in patients based on the Sugaya MRI rotator cuff classification system (grades 1, 2, or 3). Discriminant analysis determined whether intact repairs (Sugaya grade 1) and partial-thickness retears (Sugaya grades 2 and 3) could be predicted. No differences (P < .05) existed in the clinical or strength measures. Although discriminant analysis revealed the 11-item version of the Disabilities of the Arm, Shoulder and Hand produced a 97% true-positive rate for predicting partial thickness retears, it also produced a 90% false-positive rate whereby it incorrectly predicted a retear in 90% of patients whose repair was intact. The ability to discriminate between groups was enhanced with up to 5 variables entered; however, only 87% of the partial-retear group and 36% of the intact-repair group were correctly classified. No differences in clinical scores existed between patients stratified by the Sugaya MRI classification system at 16 weeks. An intact repair or partial-thickness retear could not be accurately predicted. Our results suggest that correct classification of healing in the early postoperative stages should involve imaging. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2015-01-01

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

  20. Low-dimensional, morphologically accurate models of subthreshold membrane potential

    PubMed Central

    Kellems, Anthony R.; Roos, Derrick; Xiao, Nan; Cox, Steven J.

    2009-01-01

    The accurate simulation of a neuron’s ability to integrate distributed synaptic input typically requires the simultaneous solution of tens of thousands of ordinary differential equations. For, in order to understand how a cell distinguishes between input patterns we apparently need a model that is biophysically accurate down to the space scale of a single spine, i.e., 1 μm. We argue here that one can retain this highly detailed input structure while dramatically reducing the overall system dimension if one is content to accurately reproduce the associated membrane potential at a small number of places, e.g., at the site of action potential initiation, under subthreshold stimulation. The latter hypothesis permits us to approximate the active cell model with an associated quasi-active model, which in turn we reduce by both time-domain (Balanced Truncation) and frequency-domain (ℋ2 approximation of the transfer function) methods. We apply and contrast these methods on a suite of typical cells, achieving up to four orders of magnitude in dimension reduction and an associated speed-up in the simulation of dendritic democratization and resonance. We also append a threshold mechanism and indicate that this reduction has the potential to deliver an accurate quasi-integrate and fire model. PMID:19172386

  1. 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.

  2. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

    PubMed

    Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

  3. MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

    PubMed Central

    Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

  4. The Guy's stone score--grading the complexity of percutaneous nephrolithotomy procedures.

    PubMed

    Thomas, Kay; Smith, Naomi C; Hegarty, Nicholas; Glass, Jonathan M

    2011-08-01

    To report the development and validation of a scoring system, the Guy's stone score, to grade the complexity of percutaneous nephrolithotomy (PCNL). Currently, no standardized method is available to predict the stone-free rate after PCNL. The Guy's stone score was developed through a combination of expert opinion, published data review, and iterative testing. It comprises 4 grades: grade I, solitary stone in mid/lower pole or solitary stone in the pelvis with simple anatomy; grade II, solitary stone in upper pole or multiple stones in a patient with simple anatomy or a solitary stone in a patient with abnormal anatomy; grade III, multiple stones in a patient with abnormal anatomy or stones in a caliceal diverticulum or partial staghorn calculus; grade IV, staghorn calculus or any stone in a patient with spina bifida or spinal injury. It was assessed for reproducibility using the kappa coefficient and validated on a prospective database of 100 PCNL procedures performed in a tertiary stone center. The complications were graded using the modified Clavien score. The clinical outcomes were recorded prospectively and assessed with multivariate analysis. The Guy's stone score was the only factor that significantly and independently predicted the stone-free rate (P = .01). It was found to be reproducible, with good inter-rater agreement (P = .81). None of the other factors tested, including stone burden, operating surgeon, patient weight, age, and comorbidity, correlated with the stone-free rate. The Guy's stone score accurately predicted the stone-free rate after PCNL. It was easy to use and reproducible. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. A Clinical Score to Predict Appendicitis in Older Male Children.

    PubMed

    Kharbanda, Anupam B; Monuteaux, Michael C; Bachur, Richard G; Dudley, Nanette C; Bajaj, Lalit; Stevenson, Michelle D; Macias, Charles G; Mittal, Manoj K; Bennett, Jonathan E; Sinclair, Kelly; Dayan, Peter S

    2017-04-01

    To develop a clinical score to predict appendicitis among older, male children who present to the emergency department with suspected appendicitis. Patients with suspected appendicitis were prospectively enrolled at 9 pediatric emergency departments. A total of 2625 patients enrolled; a subset of 961 male patients, age 8-18 were analyzed in this secondary analysis. Outcomes were determined using pathology, operative reports, and follow-up calls. Clinical and laboratory predictors with <10% missing data and kappa > 0.4 were entered into a multivariable model. Resultant β-coefficients were used to develop a clinical score. Test performance was assessed by calculating the sensitivity, specificity, positive predictive value, negative predictive value, and likelihood ratios. The mean age was 12.2 years; 49.9% (480) had appendicitis, 22.3% (107) had perforation, and the negative appendectomy rate was 3%. In patients with and without appendicitis, overall imaging rates were 68.6% (329) and 84.4% (406), respectively. Variables retained in the model included maximum tenderness in the right lower quadrant, pain with walking/coughing or hopping, and the absolute neutrophil count. A score ≥8.1 had a sensitivity of 25% (95% confidence interval [CI], 20%-29%), specificity of 98% (95% CI, 96%-99%), and positive predictive value of 93% (95% CI, 86%-97%) for ruling in appendicitis. We developed an accurate scoring system for predicting appendicitis in older boys. If validated, the score might allow clinicians to manage a proportion of male patients without diagnostic imaging. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

  6. College Math Assessment: SAT Scores vs. College Math Placement Scores

    ERIC Educational Resources Information Center

    Foley-Peres, Kathleen; Poirier, Dawn

    2008-01-01

    Many colleges and university's use SAT math scores or math placement tests to place students in the appropriate math course. This study compares the use of math placement scores and SAT scores for 188 freshman students. The student's grades and faculty observations were analyzed to determine if the SAT scores and/or college math assessment scores…

  7. A Retrospective Analysis of Post-Stroke Berg Balance Scale Scores: How Should Normal and At-Risk Scores Be Interpreted?

    PubMed Central

    Inness, Elizabeth; McIlroy, William E.; Mansfield, Avril

    2017-01-01

    Purpose: The Berg Balance Scale (BBS) is a performance-based measure of standing balance commonly used by clinicians working with individuals post-stroke. Performance on the BBS can be influenced by compensatory strategies, but measures derived from two force plates can isolate compensatory strategies and thus better indicate balance impairment. This study examined BBS scores that reflect “normal” and disordered balance with respect to dual force-plate measures of standing balance in individuals post-stroke. Methods: BBS and force-plate measures were extracted from 75 patient charts. Individuals were classified by BBS score with respect to (1) age-matched normative values and (2) values that suggested increased risk of falls. Multiple analysis of variance was used to examine the effect of group assignment on force-plate measures of standing balance. Results: Individuals with BBS scores within and below normative values did not differ in force-plate measures. Individuals with BBS scores below the falls risk cutoff loaded their affected leg less than individuals with BBS scores above the cutoff. There were no other differences in force-plate measures between these two groups. Conclusions: BBS scores indicating either normal or disordered balance function are not necessarily associated with normal or disordered quiet standing-balance control measured by two force plates. This finding suggests that the BBS may reflect a capacity for compensation rather than any underlying impairments. PMID:28539694

  8. Rheumatoid arthritis-specific cardiovascular risk scores are not superior to general risk scores: a validation analysis of patients from seven countries.

    PubMed

    Crowson, Cynthia S; Gabriel, Sherine E; Semb, Anne Grete; van Riel, Piet L C M; Karpouzas, George; Dessein, Patrick H; Hitchon, Carol; Pascual-Ramos, Virginia; Kitas, George D

    2017-07-01

    Cardiovascular disease (CVD) risk calculators developed for the general population do not accurately predict CVD events in patients with RA. We sought to externally validate risk calculators recommended for use in patients with RA including the EULAR 1.5 multiplier, the Expanded Cardiovascular Risk Prediction Score for RA (ERS-RA) and QRISK2. Seven RA cohorts from UK, Norway, Netherlands, USA, South Africa, Canada and Mexico were combined. Data on baseline CVD risk factors, RA characteristics and CVD outcomes (including myocardial infarction, ischaemic stroke and cardiovascular death) were collected using standardized definitions. Performance of QRISK2, EULAR multiplier and ERS-RA was compared with other risk calculators [American College of Cardiology/American Heart Association (ACC/AHA), Framingham Adult Treatment Panel III Framingham risk score-Adult Treatment Panel (FRS-ATP) and Reynolds Risk Score] using c-statistics and net reclassification index. Among 1796 RA patients without prior CVD [mean ( s . d .) age: 54.0 (14.0) years, 74% female], 100 developed CVD events during a mean follow-up of 6.9 years (12430 person-years). Estimated CVD risk by ERS-RA [mean ( s . d .) 8.8% (9.8%)] was comparable to FRS-ATP [mean ( s . d .) 9.1% (8.3%)] and Reynolds [mean ( s . d .) 9.2% (12.2%)], but lower than ACC/AHA [mean ( s . d .) 9.8% (12.1%)]. QRISK2 substantially overestimated risk [mean ( s . d .) 15.5% (13.9%)]. Discrimination was not improved for ERS-RA (c-statistic = 0.69), QRISK2 or EULAR multiplier applied to ACC/AHA compared with ACC/AHA (c-statistic = 0.72 for all) or for FRS-ATP (c-statistic = 0.75). The net reclassification index for ERS-RA was low (-0.8% vs ACC/AHA and 2.3% vs FRS-ATP). The QRISK2, EULAR multiplier and ERS-RA algorithms did not predict CVD risk more accurately in patients with RA than CVD risk calculators developed for the general population. © The Author 2017. Published by Oxford University Press on behalf of the British Society for

  9. The association between the metabolic syndrome and metabolic syndrome score and pulmonary function in non-smoking adults.

    PubMed

    Yoon, Hyun; Gi, Mi Young; Cha, Ju Ae; Yoo, Chan Uk; Park, Sang Muk

    2018-03-01

    This study assessed the association of metabolic syndrome and metabolic syndrome score with the predicted forced vital capacity and predicted forced expiratory volume in 1 s (predicted forced expiratory volume in 1 s) values in Korean non-smoking adults. We analysed data obtained from 6684 adults during the 2013-2015 Korean National Health and Nutrition Examination Survey. After adjustment for related variables, metabolic syndrome ( p < 0.001) and metabolic syndrome score ( p < 0.001) were found to be inversely associated with the predicted forced vital capacity and forced expiratory volume in 1 s values. The odds ratios of restrictive pulmonary disease (the predicted forced vital capacity < 80.0% with forced expiratory volume in 1 s/FVC ⩾ 70.0%) by metabolic syndrome score with metabolic syndrome score 0 as a reference group showed no significance for metabolic syndrome score 1 [1.061 (95% confidence interval, 0.755-1.490)] and metabolic syndrome score 2 [1.247 (95% confidence interval, 0.890-1.747)], but showed significant for metabolic syndrome score 3 [1.433 (95% confidence interval, 1.010-2.033)] and metabolic syndrome score ⩾ 4 [1.760 (95% confidence interval, 1.216-2.550)]. In addition, the odds ratio of restrictive pulmonary disease of the metabolic syndrome [1.360 (95% confidence interval, 1.118-1.655)] was significantly higher than those of non-metabolic syndrome. Metabolic syndrome and metabolic syndrome score were inversely associated with the predicted forced vital capacity and forced expiratory volume in 1 s values in Korean non-smoking adults. In addition, metabolic syndrome and metabolic syndrome score were positively associated with the restrictive pulmonary disease.

  10. An examination of ESI triage scoring accuracy in relationship to ED nursing attitudes and experience.

    PubMed

    Martin, Andrew; Davidson, Carolyn L; Panik, Anne; Buckenmyer, Charlotte; Delpais, Paul; Ortiz, Michele

    2014-09-01

    This research was designed to examine if there is a difference in nurse attitudes and experience for those who assign Emergency Severity Index (ESI) scores accurately and those who do not assign ESI scores accurately. Studies that have used ESI scoring discussed the role of experience, but have not specifically addressed how the amount of experience and attitude towards patients in triage affect the triage nurse's decision-making capabilities. A descriptive, exploratory study design was used. Data from 64 nurses and 1,644 triage events at 3 emergency departments was collected. Participants completed demographic data, attitude (Caring Nurse Patient Interaction, CNPI-23) survey, and triage data collection tools during the continuous 8-hour triage shift. Clinical nurse expert raters retrospectively reviewed the charts and assigned an ESI score to be compared with the nurse. Descriptive statistics were used to describe the nurse and Pearson's correlation was used to examine the relationship between experience and attitude. In this study of 64 nurse participants, the ESI score assigned by nurse participants did not differ significantly based on years of experience or CNPI mean score. The Kappa statistic ranged from a high of 0.63 in the nurse participant with 1.00 to 1.99 years of experience to a low of 0.51 in the nurse participant with 15 to 19 years of experience. The nurse participants with an overall mean CNPI-23 score of 106 to 115 achieved the highest agreement compared with a single participant with a CNPI-23 overall mean score of less than 77 who had a Kappa agreement of 0.50. The nurse participants with a CNPI-23 overall mean score between 81 and 92 demonstrated agreement of 0.54 to 0.60. Based on the high level of liability the triage area presents, special consideration needs to be made when deciding which nurse should be assigned to that area. The evidence produced from this study should provide some reassurance to ED managers and nurses alike that nurses

  11. 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.

  12. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

    PubMed

    Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

    2012-06-08

    Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  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. Expressed Vocational Choices and Later Employment Compared with Vocational Preference Inventory and Kuder Preference Record-Vocational Scores

    ERIC Educational Resources Information Center

    Wiggins, J. D.; Weslander, Darrell

    1977-01-01

    Expressed vocational choices were more predictive of employment status four years after high school graduation for males than were scores on either the Vocational Preference Inventory or the Kuder Preference Record--Vocational. Predictions for males were more accurate than for females on all measures. (Author)

  15. Detection and Automated Scoring of Dicentric Chromosomes in Nonstimulated Lymphocyte Prematurely Condensed Chromosomes After Telomere and Centromere Staining

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

    M'kacher, Radhia; El Maalouf, Elie; Laboratoire Modélisation Intelligence Processus Systèmes

    Purpose: To combine telomere and centromere (TC) staining of premature chromosome condensation (PCC) fusions to identify dicentrics, centric rings, and acentric chromosomes, making possible the realization of a dose–response curve and automation of the process. Methods and Materials: Blood samples from healthy donors were exposed to {sup 60}Co irradiation at varying doses up to 8 Gy, followed by a repair period of 8 hours. Premature chromosome condensation fusions were carried out, and TC staining using peptide nucleic acid probes was performed. Chromosomal aberration (CA) scoring was carried out manually and automatically using PCC-TCScore software, developed in our laboratory. Results: Wemore » successfully optimized the hybridization conditions and image capture parameters, to increase the sensitivity and effectiveness of CA scoring. Dicentrics, centric rings, and acentric chromosomes were rapidly and accurately detected, leading to a linear-quadratic dose–response curve by manual scoring at up to 8 Gy. Using PCC-TCScore software for automatic scoring, we were able to detect 95% of dicentrics and centric rings. Conclusion: The introduction of TC staining to the PCC fusion technique has made possible the rapid scoring of unstable CAs, including dicentrics, with a level of accuracy and ease not previously possible. This new approach can be used for biological dosimetry in radiation emergency medicine, where the rapid and accurate detection of dicentrics is a high priority using automated scoring. Because there is no culture time, this new approach can also be used for the follow-up of patients treated by genotoxic therapy, creating the possibility to perform the estimation of induced chromosomal aberrations immediately after the blood draw.« less

  16. Accurate Binding Free Energy Predictions in Fragment Optimization.

    PubMed

    Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

    2015-11-23

    Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

  17. Decision making under internal uncertainty: the case of multiple-choice tests with different scoring rules.

    PubMed

    Bereby-Meyer, Yoella; Meyer, Joachim; Budescu, David V

    2003-02-01

    This paper assesses framing effects on decision making with internal uncertainty, i.e., partial knowledge, by focusing on examinees' behavior in multiple-choice (MC) tests with different scoring rules. In two experiments participants answered a general-knowledge MC test that consisted of 34 solvable and 6 unsolvable items. Experiment 1 studied two scoring rules involving Positive (only gains) and Negative (only losses) scores. Although answering all items was the dominating strategy for both rules, the results revealed a greater tendency to answer under the Negative scoring rule. These results are in line with the predictions derived from Prospect Theory (PT) [Econometrica 47 (1979) 263]. The second experiment studied two scoring rules, which allowed respondents to exhibit partial knowledge. Under the Inclusion-scoring rule the respondents mark all answers that could be correct, and under the Exclusion-scoring rule they exclude all answers that might be incorrect. As predicted by PT, respondents took more risks under the Inclusion rule than under the Exclusion rule. The results illustrate that the basic process that underlies choice behavior under internal uncertainty and especially the effect of framing is similar to the process of choice under external uncertainty and can be described quite accurately by PT. Copyright 2002 Elsevier Science B.V.

  18. Lowering risk score profile during PCI in multiple vessel disease is associated with low adverse events: The ERACI risk score.

    PubMed

    Rodriguez, Alfredo E; Fernandez-Pereira, Carlos; Mieres, Juan; Pavlovsky, Hernan; Del Pozo, Juan; Rodriguez-Granillo, Alfredo M; Antoniucci, David

    2018-02-13

    In recent years angiographic risk scores have been introduced in clinical practice to stratify different levels of risk after percutaneous coronary interventions (PCI). The SYNTAX score included all intermediate lesions in vessels ≥1.5 mm, consequently, multiple stent implantation was required. Four years ago, we built a new angiographic score in order to guide PCI strategy avoiding stent deployment both in intermediate stenosis as in small vessels, therefore these were not scored (ERACI risk score). The purpose of this mini review is to validate the strategy of PCI guided by this scoring, taking into account long term follow up outcomes of two observational and prospective registries where this policy was used. With this new risk score we have modified risk profile of our patient's candidates for PCI or coronary artery bypass surgery lowering the risk and <20% of them are now included anatomically as high risk for PCI. The simple exclusion of small vessels and intermediate stenosis from the revascularization approach resulted in clinical outcome comparable with the one of fractional flow reserve guided revascularization. Low events rate at late follow up observed in both studies was also in agreement with guided PCI by functional lesion assessment observed by Syntax II registry, where investigators found lower events rate in spite of a few number of stents implanted per patient. use of ERACI risk scores may significantly reclassify patients into a lower risk category and be associated with low adverse events rate. Copyright © 2018. Published by Elsevier Inc.

  19. [Cleft lip, alveolar and palate sequelae. Proposal of new alveolar score by the Alveolar Cleft Score (ACS) classification].

    PubMed

    Molé, C; Simon, E

    2015-06-01

    The management of cleft lip, alveolar and palate sequelae remains problematic today. To optimize it, we tried to establish a new clinical index for diagnostic and prognostic purposes. Seven tissue indicators, that we consider to be important in the management of alveolar sequelae, are listed by assigning them individual scores. The final score, obtained by adding together the individual scores, can take a low, high or maximum value. We propose a new classification (ACS: Alveolar Cleft Score) that guides the therapeutic team to a prognosis approach, in terms of the recommended surgical and prosthetic reconstruction, the type of medical care required, and the preventive and supportive therapy to establish. Current studies are often only based on a standard radiological evaluation of the alveolar bone height at the cleft site. However, the gingival, the osseous and the cellular areas bordering the alveolar cleft sequelae induce many clinical parameters, which should be reflected in the morphological diagnosis, to better direct the surgical indications and the future prosthetic requirements, and to best maintain successful long term aesthetic and functional results. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  20. Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

    PubMed

    Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

    2015-09-01

    Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need

  1. Accurately Mapping M31's Microlensing Population

    NASA Astrophysics Data System (ADS)

    Crotts, Arlin

    2004-07-01

    We propose to augment an existing microlensing survey of M31 with source identifications provided by a modest amount of ACS {and WFPC2 parallel} observations to yield an accurate measurement of the masses responsible for microlensing in M31, and presumably much of its dark matter. The main benefit of these data is the determination of the physical {or "einstein"} timescale of each microlensing event, rather than an effective {"FWHM"} timescale, allowing masses to be determined more than twice as accurately as without HST data. The einstein timescale is the ratio of the lensing cross-sectional radius and relative velocities. Velocities are known from kinematics, and the cross-section is directly proportional to the {unknown} lensing mass. We cannot easily measure these quantities without knowing the amplification, hence the baseline magnitude, which requires the resolution of HST to find the source star. This makes a crucial difference because M31 lens m ass determinations can be more accurate than those towards the Magellanic Clouds through our Galaxy's halo {for the same number of microlensing events} due to the better constrained geometry in the M31 microlensing situation. Furthermore, our larger survey, just completed, should yield at least 100 M31 microlensing events, more than any Magellanic survey. A small amount of ACS+WFPC2 imaging will deliver the potential of this large database {about 350 nights}. For the whole survey {and a delta-function mass distribution} the mass error should approach only about 15%, or about 6% error in slope for a power-law distribution. These results will better allow us to pinpoint the lens halo fraction, and the shape of the halo lens spatial distribution, and allow generalization/comparison of the nature of halo dark matter in spiral galaxies. In addition, we will be able to establish the baseline magnitude for about 50, 000 variable stars, as well as measure an unprecedentedly deta iled color-magnitude diagram and luminosity

  2. Exploring a Source of Uneven Score Equity across the Test Score Range

    ERIC Educational Resources Information Center

    Huggins-Manley, Anne Corinne; Qiu, Yuxi; Penfield, Randall D.

    2018-01-01

    Score equity assessment (SEA) refers to an examination of population invariance of equating across two or more subpopulations of test examinees. Previous SEA studies have shown that score equity may be present for examinees scoring at particular test score ranges but absent for examinees scoring at other score ranges. No studies to date have…

  3. Value of Nephrometry Score Constituents on Perioperative Outcomes and Split Renal Function in Patients Undergoing Minimally Invasive Partial Nephrectomy.

    PubMed

    Watts, Kara L; Ghosh, Propa; Stein, Solomon; Ghavamian, Reza

    2017-01-01

    To assess the relationship between individual nephrometry score (NS) constituents (RENAL) on perioperative outcomes and renal function of the surgical kidney in patients undergoing laparoscopic partial nephrectomy or robotic-assisted partial nephrectomy. Two hundred forty-five patients who underwent laparoscopic partial nephrectomy or robotic-assisted partial nephrectomy between 2005 and 2014 were retrospectively reviewed. Each renal mass' NS was calculated from preoperative computed tomography imaging. Multivariate regression analysis was used to evaluate the effect of NS variables on perioperative outcomes and change in overall renal function (as estimated by glomerular filtration rate) from preoperative to 1-year postoperative. A cohort analysis assessed the effect of NS variables on change in split renal function of the surgical kidney from pre- to postoperative based on nuclear medicine renal scintigraphy. Tumor radius (R), endophytic nature (E), and nearness to collecting system (N) variables significantly and incrementally predicted a longer operative time and warm ischemia time. Overall renal function based on glomerular filtration rate was not affected by any NS variable. However, percent function of the surgical kidney by renal scintigraphy significantly decreased postoperatively as R and E values increased. R, E, and N were associated with significant changes in warm ischemia time and operative time. R and E were associated with a significant decrease in split renal function of the surgical kidney at 1 year after surgery but not with overall renal function. R, E, and N are the NS constituents most relevant to perioperative outcomes and postoperative differential renal function after partial nephrectomy. Copyright © 2016. Published by Elsevier Inc.

  4. 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.

  5. Clinical scoring system in the evaluation of adult pharyngitis.

    PubMed

    Seppälä, H; Lahtonen, R; Ziegler, T; Meurman, O; Hakkarainen, K; Miettinen, A; Arstila, P; Eskola, J; Saikku, P; Huovinen, P

    1993-03-01

    To compare results of a clinical scoring system for diagnosis of group A streptococcal pharyngitis with microbiologic results, when several different pharyngeal pathogens were tested simultaneously. Evaluation of clinical manifestations of 106 adult patients with pharyngitis of different microbial origin. General private practice; Health Center Pulssi, Turku, Finland. Adult patients whose chief complaints were sore throats. A symptom score that was assigned to each patient according to the total number of certain signs and symptoms that are postulated to increase the probability of group A streptococcal pharyngitis and blood measurements for infection. The highest symptom scores, 3 and 4, were found in 21 patients. These patients had pharyngitis due to group A streptococcus (four patients), group C streptococcus (four patients), group G streptococcus (two patients), group F streptococcus, Mycoplasma pneumoniae, Chlamydia pneumoniae, influenza A virus, influenza B virus, herpes simplex type 1 virus (two patients), and coxsackie B4 virus. No pathogen could be identified from three of the 21 patients. The C-reactive protein values and the leukocyte counts were raised significantly more often in streptococcal infections than in infections of other origin; the P values were .00016 and .028, respectively. Use of a clinical scoring system alone for diagnosis of pharyngitis may lead to improper use of anti-microbial agents. There is a need for accurate microbiologic diagnostic procedures in general practice to determine proper treatment of pharyngitis as well as to test the effect of antibacterial and, in the future, antiviral treatment in respiratory tract infections.

  6. Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1

    PubMed Central

    Vangone, A.; Rodrigues, J. P. G. L. M.; Xue, L. C.; van Zundert, G. C. P.; Geng, C.; Kurkcuoglu, Z.; Nellen, M.; Narasimhan, S.; Karaca, E.; van Dijk, M.; Melquiond, A. S. J.; Visscher, K. M.; Trellet, M.; Kastritis, P. L.

    2016-01-01

    ABSTRACT Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community‐wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP‐CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets – a top‐ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico‐chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center‐of‐mass and symmetry restrained protocol, or on a template‐based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417–423. © 2016 Wiley Periodicals, Inc. PMID:27802573

  7. Accurate phase measurements for thick spherical objects using optical quadrature microscopy

    NASA Astrophysics Data System (ADS)

    Warger, William C., II; DiMarzio, Charles A.

    2009-02-01

    In vitro fertilization (IVF) procedures have resulted in the birth of over three million babies since 1978. Yet the live birth rate in the United States was only 34% in 2005, with 32% of the successful pregnancies resulting in multiple births. These multiple pregnancies were directly attributed to the transfer of multiple embryos to increase the probability that a single, healthy embryo was included. Current viability markers used for IVF, such as the cell number, symmetry, size, and fragmentation, are analyzed qualitatively with differential interference contrast (DIC) microscopy. However, this method is not ideal for quantitative measures beyond the 8-cell stage of development because the cells overlap and obstruct the view within and below the cluster of cells. We have developed the phase-subtraction cell-counting method that uses the combination of DIC and optical quadrature microscopy (OQM) to count the number of cells accurately in live mouse embryos beyond the 8-cell stage. We have also created a preliminary analysis to measure the cell symmetry, size, and fragmentation quantitatively by analyzing the relative dry mass from the OQM image in conjunction with the phase-subtraction count. In this paper, we will discuss the characterization of OQM with respect to measuring the phase accurately for spherical samples that are much larger than the depth of field. Once fully characterized and verified with human embryos, this methodology could provide the means for a more accurate method to score embryo viability.

  8. Accurate indel prediction using paired-end short reads

    PubMed Central

    2013-01-01

    Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/. PMID:23442375

  9. Functional MRI evidence for the decline of word retrieval and generation during normal aging.

    PubMed

    Baciu, M; Boudiaf, N; Cousin, E; Perrone-Bertolotti, M; Pichat, C; Fournet, N; Chainay, H; Lamalle, L; Krainik, A

    2016-02-01

    This fMRI study aimed to explore the effect of normal aging on word retrieval and generation. The question addressed is whether lexical production decline is determined by a direct mechanism, which concerns the language operations or is rather indirectly induced by a decline of executive functions. Indeed, the main hypothesis was that normal aging does not induce loss of lexical knowledge, but there is only a general slowdown in retrieval mechanisms involved in lexical processing, due to possible decline of the executive functions. We used three tasks (verbal fluency, object naming, and semantic categorization). Two groups of participants were tested (Young, Y and Aged, A), without cognitive and psychiatric impairment and showing similar levels of vocabulary. Neuropsychological testing revealed that older participants had lower executive function scores, longer processing speeds, and tended to have lower verbal fluency scores. Additionally, older participants showed higher scores for verbal automatisms and overlearned information. In terms of behavioral data, older participants performed as accurate as younger adults, but they were significantly slower for the semantic categorization and were less fluent for verbal fluency task. Functional MRI analyses suggested that older adults did not simply activate fewer brain regions involved in word production, but they actually showed an atypical pattern of activation. Significant correlations between the BOLD (Blood Oxygen Level Dependent) signal of aging-related (A > Y) regions and cognitive scores suggested that this atypical pattern of the activation may reveal several compensatory mechanisms (a) to overcome the slowdown in retrieval, due to the decline of executive functions and processing speed and (b) to inhibit verbal automatic processes. The BOLD signal measured in some other aging-dependent regions did not correlate with the behavioral and neuropsychological scores, and the overactivation of these uncorrelated

  10. Predictive accuracy of combined genetic and environmental risk scores.

    PubMed

    Dudbridge, Frank; Pashayan, Nora; Yang, Jian

    2018-02-01

    The substantial heritability of most complex diseases suggests that genetic data could provide useful risk prediction. To date the performance of genetic risk scores has fallen short of the potential implied by heritability, but this can be explained by insufficient sample sizes for estimating highly polygenic models. When risk predictors already exist based on environment or lifestyle, two key questions are to what extent can they be improved by adding genetic information, and what is the ultimate potential of combined genetic and environmental risk scores? Here, we extend previous work on the predictive accuracy of polygenic scores to allow for an environmental score that may be correlated with the polygenic score, for example when the environmental factors mediate the genetic risk. We derive common measures of predictive accuracy and improvement as functions of the training sample size, chip heritabilities of disease and environmental score, and genetic correlation between disease and environmental risk factors. We consider simple addition of the two scores and a weighted sum that accounts for their correlation. Using examples from studies of cardiovascular disease and breast cancer, we show that improvements in discrimination are generally small but reasonable degrees of reclassification could be obtained with current sample sizes. Correlation between genetic and environmental scores has only minor effects on numerical results in realistic scenarios. In the longer term, as the accuracy of polygenic scores improves they will come to dominate the predictive accuracy compared to environmental scores. © 2017 WILEY PERIODICALS, INC.

  11. Predictive accuracy of combined genetic and environmental risk scores

    PubMed Central

    Pashayan, Nora; Yang, Jian

    2017-01-01

    ABSTRACT The substantial heritability of most complex diseases suggests that genetic data could provide useful risk prediction. To date the performance of genetic risk scores has fallen short of the potential implied by heritability, but this can be explained by insufficient sample sizes for estimating highly polygenic models. When risk predictors already exist based on environment or lifestyle, two key questions are to what extent can they be improved by adding genetic information, and what is the ultimate potential of combined genetic and environmental risk scores? Here, we extend previous work on the predictive accuracy of polygenic scores to allow for an environmental score that may be correlated with the polygenic score, for example when the environmental factors mediate the genetic risk. We derive common measures of predictive accuracy and improvement as functions of the training sample size, chip heritabilities of disease and environmental score, and genetic correlation between disease and environmental risk factors. We consider simple addition of the two scores and a weighted sum that accounts for their correlation. Using examples from studies of cardiovascular disease and breast cancer, we show that improvements in discrimination are generally small but reasonable degrees of reclassification could be obtained with current sample sizes. Correlation between genetic and environmental scores has only minor effects on numerical results in realistic scenarios. In the longer term, as the accuracy of polygenic scores improves they will come to dominate the predictive accuracy compared to environmental scores. PMID:29178508

  12. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2002-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  13. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2003-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  14. Predicting 30-Day Hospital Readmissions in Acute Myocardial Infarction: The AMI "READMITS" (Renal Function, Elevated Brain Natriuretic Peptide, Age, Diabetes Mellitus, Nonmale Sex, Intervention with Timely Percutaneous Coronary Intervention, and Low Systolic Blood Pressure) Score.

    PubMed

    Nguyen, Oanh Kieu; Makam, Anil N; Clark, Christopher; Zhang, Song; Das, Sandeep R; Halm, Ethan A

    2018-04-17

    Readmissions after hospitalization for acute myocardial infarction (AMI) are common. However, the few currently available AMI readmission risk prediction models have poor-to-modest predictive ability and are not readily actionable in real time. We sought to develop an actionable and accurate AMI readmission risk prediction model to identify high-risk patients as early as possible during hospitalization. We used electronic health record data from consecutive AMI hospitalizations from 6 hospitals in north Texas from 2009 to 2010 to derive and validate models predicting all-cause nonelective 30-day readmissions, using stepwise backward selection and 5-fold cross-validation. Of 826 patients hospitalized with AMI, 13% had a 30-day readmission. The first-day AMI model (the AMI "READMITS" score) included 7 predictors: renal function, elevated brain natriuretic peptide, age, diabetes mellitus, nonmale sex, intervention with timely percutaneous coronary intervention, and low systolic blood pressure, had an optimism-corrected C-statistic of 0.73 (95% confidence interval, 0.71-0.74) and was well calibrated. The full-stay AMI model, which included 3 additional predictors (use of intravenous diuretics, anemia on discharge, and discharge to postacute care), had an optimism-corrected C-statistic of 0.75 (95% confidence interval, 0.74-0.76) with minimally improved net reclassification and calibration. Both AMI models outperformed corresponding multicondition readmission models. The parsimonious AMI READMITS score enables early prospective identification of high-risk AMI patients for targeted readmissions reduction interventions within the first 24 hours of hospitalization. A full-stay AMI readmission model only modestly outperformed the AMI READMITS score in terms of discrimination, but surprisingly did not meaningfully improve reclassification. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

  15. 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.

  16. Knowing the Score

    ERIC Educational Resources Information Center

    Strouse, Lewis H.

    2009-01-01

    Before rehearsals begin, conductors need to thoroughly study the score. What elements go into a comprehensive score preparation? To learn music scores efficiently, having a detailed and systematic study method helps. The author has developed a score preparation guide that works for directors of bands, choruses, and orchestras, even when there's…

  17. A Prediction Model for Functional Outcomes in Spinal Cord Disorder Patients Using Gaussian Process Regression.

    PubMed

    Lee, Sunghoon Ivan; Mortazavi, Bobak; Hoffman, Haydn A; Lu, Derek S; Li, Charles; Paak, Brian H; Garst, Jordan H; Razaghy, Mehrdad; Espinal, Marie; Park, Eunjeong; Lu, Daniel C; Sarrafzadeh, Majid

    2016-01-01

    Predicting the functional outcomes of spinal cord disorder patients after medical treatments, such as a surgical operation, has always been of great interest. Accurate posttreatment prediction is especially beneficial for clinicians, patients, care givers, and therapists. This paper introduces a prediction method for postoperative functional outcomes by a novel use of Gaussian process regression. The proposed method specifically considers the restricted value range of the target variables by modeling the Gaussian process based on a truncated Normal distribution, which significantly improves the prediction results. The prediction has been made in assistance with target tracking examinations using a highly portable and inexpensive handgrip device, which greatly contributes to the prediction performance. The proposed method has been validated through a dataset collected from a clinical cohort pilot involving 15 patients with cervical spinal cord disorder. The results show that the proposed method can accurately predict postoperative functional outcomes, Oswestry disability index and target tracking scores, based on the patient's preoperative information with a mean absolute error of 0.079 and 0.014 (out of 1.0), respectively.

  18. [The diagnostic value of ultrasonic elastography and ultrasonography comprehensive score in cervical lesions].

    PubMed

    Lu, R; Xiao, Y

    2017-07-18

    Objective: To evaluate the clinical value of ultrasonic elastography and ultrasonography comprehensive scoring method in the diagnosis of cervical lesions. Methods: A total of 116 patients were selected from the Department of Gynecology of the first hospital affiliated with Central South University from March 2014 to September 2015.All of the lesions were preoperatively examined by Doppler Ultrasound and elastography.The elasticity score was determined by a 5-point scoring method. Calculation of the strain ratio was based on a comparison of the average strain measured in the lesion with the adjacent tissue of the same depth, size, and shape.All these ultrasonic parameters were quantified, added, and arrived at ultrasonography comprehensive scores.To use surgical pathology as the gold standard, the sensitivity, specificity, accuracy of Doppler Ultrasound, elasticity score and strain ratio methods and ultrasonography comprehensive scoring method were comparatively analyzed. Results: (1) The sensitivity, specificity, and accuracy of Doppler Ultrasound in diagnosing cervical lesions were 82.89% (63/76), 85.0% (34/40), and 83.62% (97/116), respectively.(2) The sensitivity, specificity, and accuracy of the elasticity score method were 77.63% (59/76), 82.5% (33/40), and 79.31% (92/116), respectively; the sensitivity, specificity, and accuracy of the strain ratio measure method were 84.21% (64/76), 87.5% (35/40), and 85.34% (99/116), respectively.(3) The sensitivity, specificity, and accuracy of ultrasonography comprehensive scoring method were 90.79% (69/76), 92.5% (37/40), and 91.38% (106/116), respectively. Conclusion: (1) It was obvious that ultrasonic elastography had certain diagnostic value in cervical lesions. Strain ratio measurement can be more objective than elasticity score method.(2) The combined application of ultrasonography comprehensive scoring method, ultrasonic elastography and conventional sonography was more accurate than single parameter.

  19. Association of Apgar scores with death and neurologic disability

    PubMed Central

    Ehrenstein, Vera

    2009-01-01

    Apgar score was devised with the aim to standardize the assessment of newborns. It has been used worldwide to evaluate infants’ condition immediately after birth, to determine their need for resuscitation, and to evaluate the effectiveness of resuscitation. Apgar score was never intended for prediction of outcome beyond the immediate postnatal period; however, since low scores correlate with prenatal and perinatal adversities, multiple studies have examined the relation between the value of Apgar score and duration of low (<7) Apgar score and subsequent death or neurologic disability. This article reviews such studies. The author concludes that the overall evidence shows consistent association of low Apgar scores with increased risks of neonatal and infant death and with neurologic disability, including cerebral palsy, epilepsy, and cognitive impairment. Dose-response patterns have been shown for the value of Apgar score and duration of low score and the outcomes of mortality and neurologic disability. The association of Apgar score <7 at five minutes with increased risks of neurologic disability seems to persist many years postnatally. Some corresponding relative risk estimates are large (eg, four to seven for epilepsy or more than 20 for cerebral palsy), while others are modest (eg, 1.33 for impaired cognitive function). The absolute risks, however, are low (<5% in for most neurologic conditions), and majority of surviving babies with low Apgar scores grow up without disability. The low magnitude of absolute risks makes Apgar score a poor clinical predictor of long-term outcome. Nevertheless, the observed associations point to the importance of fetal and perinatal periods for neurodevelopment. PMID:20865086

  20. Upper limb motor function in young adults with spina bifida and hydrocephalus

    PubMed Central

    Salman, M. S.; Jewell, D.; Hetherington, R.; Spiegler, B. J.; MacGregor, D. L.; Drake, J. M.; Humphreys, R. P.; Gentili, F.

    2011-01-01

    Objective The objective of the study was to measure upper limb motor function in young adults with spina bifida meningomyelocele (SBM) and typically developing age peers. Method Participants were 26 young adults with SBM, with a Verbal or Performance IQ score of at least 70 on the Wechsler scales, and 27 age- and gender-matched controls. Four upper limb motor function tasks were performed under four different visual and cognitive challenge conditions. Motor independence was assessed by questionnaire. Results Fewer SBM than control participants obtained perfect posture and rebound scores. The SBM group performed less accurately and was more disrupted by cognitive challenge than controls on limb dysmetria tasks. The SBM group was slower than controls on the diadochokinesis task. Adaptive motor independence was related to one upper limb motor task, arm posture, and upper rather than lower spinal lesions were associated with less motor independence. Conclusions Young adults with SBM have significant limitations in upper limb function and are more disrupted by some challenges while performing upper limb motor tasks. Within the group of young adults with SBM, upper spinal lesions compromise motor independence more than lower spinal lesions. PMID:19672605

  1. Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

    PubMed

    Sarti, Edoardo; Gladich, Ivan; Zamuner, Stefano; Correia, Bruno E; Laio, Alessandro

    2016-09-01

    The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Computer-based personality judgments are more accurate than those made by humans

    PubMed Central

    Youyou, Wu; Kosinski, Michal; Stillwell, David

    2015-01-01

    Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507

  3. SKATE: a docking program that decouples systematic sampling from scoring.

    PubMed

    Feng, Jianwen A; Marshall, Garland R

    2010-11-15

    SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in-house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 A RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross-docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin-dependent kinase. 2010 Wiley Periodicals, Inc.

  4. How Accurately Can the Google Web Speech API Recognize and Transcribe Japanese L2 English Learners' Oral Production?

    ERIC Educational Resources Information Center

    Ashwell, Tim; Elam, Jesse R.

    2017-01-01

    The ultimate aim of our research project was to use the Google Web Speech API to automate scoring of elicited imitation (EI) tests. However, in order to achieve this goal, we had to take a number of preparatory steps. We needed to assess how accurate this speech recognition tool is in recognizing native speakers' production of the test items; we…

  5. Functional connectivity in autosomal dominant and late-onset Alzheimer disease.

    PubMed

    Thomas, Jewell B; Brier, Matthew R; Bateman, Randall J; Snyder, Abraham Z; Benzinger, Tammie L; Xiong, Chengjie; Raichle, Marcus; Holtzman, David M; Sperling, Reisa A; Mayeux, Richard; Ghetti, Bernardino; Ringman, John M; Salloway, Stephen; McDade, Eric; Rossor, Martin N; Ourselin, Sebastien; Schofield, Peter R; Masters, Colin L; Martins, Ralph N; Weiner, Michael W; Thompson, Paul M; Fox, Nick C; Koeppe, Robert A; Jack, Clifford R; Mathis, Chester A; Oliver, Angela; Blazey, Tyler M; Moulder, Krista; Buckles, Virginia; Hornbeck, Russ; Chhatwal, Jasmeer; Schultz, Aaron P; Goate, Alison M; Fagan, Anne M; Cairns, Nigel J; Marcus, Daniel S; Morris, John C; Ances, Beau M

    2014-09-01

    Autosomal dominant Alzheimer disease (ADAD) is caused by rare genetic mutations in 3 specific genes in contrast to late-onset Alzheimer disease (LOAD), which has a more polygenetic risk profile. To assess the similarities and differences in functional connectivity changes owing to ADAD and LOAD. We analyzed functional connectivity in multiple brain resting state networks (RSNs) in a cross-sectional cohort of participants with ADAD (n = 79) and LOAD (n = 444), using resting-state functional connectivity magnetic resonance imaging at multiple international academic sites. For both types of AD, we quantified and compared functional connectivity changes in RSNs as a function of dementia severity measured by the Clinical Dementia Rating Scale. In ADAD, we qualitatively investigated functional connectivity changes with respect to estimated years from onset of symptoms within 5 RSNs. A decrease in functional connectivity with increasing Clinical Dementia Rating scores were similar for both LOAD and ADAD in multiple RSNs. Ordinal logistic regression models constructed in one type of Alzheimer disease accurately predicted clinical dementia rating scores in the other, further demonstrating the similarity of functional connectivity loss in each disease type. Among participants with ADAD, functional connectivity in multiple RSNs appeared qualitatively lower in asymptomatic mutation carriers near their anticipated age of symptom onset compared with asymptomatic mutation noncarriers. Resting-state functional connectivity magnetic resonance imaging changes with progressing AD severity are similar between ADAD and LOAD. Resting-state functional connectivity magnetic resonance imaging may be a useful end point for LOAD and ADAD therapy trials. Moreover, the disease process of ADAD may be an effective model for the LOAD disease process.

  6. Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

    PubMed

    Li, Fuyi; Li, Chen; Marquez-Lago, Tatiana T; Leier, André; Akutsu, Tatsuya; Purcell, Anthony W; Smith, A Ian; Lithgow, Trevor; Daly, Roger J; Song, Jiangning; Chou, Kuo-Chen

    2018-06-27

    Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary data are available at Bioinformatics online.

  7. Tomosynthesis can facilitate accurate measurement of joint space width under the condition of the oblique incidence of X-rays in patients with rheumatoid arthritis.

    PubMed

    Ono, Yohei; Kashihara, Rina; Yasojima, Nobutoshi; Kasahara, Hideki; Shimizu, Yuka; Tamura, Kenichi; Tsutsumi, Kaori; Sutherland, Kenneth; Koike, Takao; Kamishima, Tamotsu

    2016-06-01

    Accurate evaluation of joint space width (JSW) is important in the assessment of rheumatoid arthritis (RA). In clinical radiography of bilateral hands, the oblique incidence of X-rays is unavoidable, which may cause perceptional or measurement error of JSW. The objective of this study was to examine whether tomosynthesis, a recently developed modality, can facilitate a more accurate evaluation of JSW than radiography under the condition of oblique incidence of X-rays. We investigated quantitative errors derived from the oblique incidence of X-rays by imaging phantoms simulating various finger joint spaces using radiographs and tomosynthesis images. We then compared the qualitative results of the modified total Sharp score of a total of 320 joints from 20 patients with RA between these modalities. A quantitative error was prominent when the location of the phantom was shifted along the JSW direction. Modified total Sharp scores of tomosynthesis images were significantly higher than those of radiography, that is to say JSW was regarded as narrower in tomosynthesis than in radiography when finger joints were located where the oblique incidence of X-rays is expected in the JSW direction. Tomosynthesis can facilitate accurate evaluation of JSW in finger joints of patients with RA, even with oblique incidence of X-rays. Accurate evaluation of JSW is necessary for the management of patients with RA. Through phantom and clinical studies, we demonstrate that tomosynthesis may achieve more accurate evaluation of JSW.

  8. Higher burnout scores in paediatric residents are associated with increased brain activity during attentional functional magnetic resonance imaging task.

    PubMed

    de Andrade, Anarella Penha Meirelles; Amaro, Edson; Farhat, Sylvia Costa Lima; Schvartsman, Claudio

    2016-06-01

    Burnout syndrome is common in healthcare workers. We evaluated its prevalence in paediatric residents and investigated its influence on cerebral function correlations, using functional magnetic resonance imaging (MRI), when they carried out an attentional paradigm. This cross-sectional descriptive study involved 28 residents from the Department of Paediatrics at the University of São Paulo. The functional MRI was carried out while the residents completed the Stroop colour word task paradigm to investigate their attentional task performance. The Maslach Burnout Inventory (MBI) was applied, and stress was assessed using the Lipp Inventory of Stress Symptoms for Adults and by a visual analogue mood scale. The MBI subscales of depersonalisation and emotional exhaustion indicated that 53.1% of the residents had moderate or high burnout syndrome. The whole-brain multivariate analysis showed positive correlations between the blood oxygenation level dependent effect and the MBI depersonalisation and emotional exhaustion indices in the dorsolateral prefrontal cortex, which controls for anxiety. Increased brain activation during an attention task, measured using functional MRI, was associated with higher burnout scores in paediatric residents. This study provides a biological basis for the implementation of measures to reduce burnout syndrome at the start of residency training programmes. ©2016 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

  9. 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

  10. The analytical validation of the Oncotype DX Recurrence Score assay

    PubMed Central

    Baehner, Frederick L

    2016-01-01

    In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i.e., how likely the test is to significantly improve patient outcomes). In considering the use of these assays, clinicians often focus primarily on the clinical validity/utility; however, the analytical validity of an assay (e.g., its accuracy, reproducibility, and standardisation) should also be evaluated and carefully considered. This review focuses on the rigorous analytical validation and performance of the Oncotype DX® Breast Cancer Assay, which is performed at the Central Clinical Reference Laboratory of Genomic Health, Inc. The assay process includes tumour tissue enrichment (if needed), RNA extraction, gene expression quantitation (using a gene panel consisting of 16 cancer genes plus 5 reference genes and quantitative real-time RT-PCR), and an automated computer algorithm to produce a Recurrence Score® result (scale: 0–100). This review presents evidence showing that the Recurrence Score result reported for each patient falls within a tight clinically relevant confidence interval. Specifically, the review discusses how the development of the assay was designed to optimise assay performance, presents data supporting its analytical validity, and describes the quality control and assurance programmes that ensure optimal test performance over time. PMID:27729940

  11. The analytical validation of the Oncotype DX Recurrence Score assay.

    PubMed

    Baehner, Frederick L

    2016-01-01

    In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i.e., how likely the test is to significantly improve patient outcomes). In considering the use of these assays, clinicians often focus primarily on the clinical validity/utility; however, the analytical validity of an assay (e.g., its accuracy, reproducibility, and standardisation) should also be evaluated and carefully considered. This review focuses on the rigorous analytical validation and performance of the Oncotype DX ® Breast Cancer Assay, which is performed at the Central Clinical Reference Laboratory of Genomic Health, Inc. The assay process includes tumour tissue enrichment (if needed), RNA extraction, gene expression quantitation (using a gene panel consisting of 16 cancer genes plus 5 reference genes and quantitative real-time RT-PCR), and an automated computer algorithm to produce a Recurrence Score ® result (scale: 0-100). This review presents evidence showing that the Recurrence Score result reported for each patient falls within a tight clinically relevant confidence interval. Specifically, the review discusses how the development of the assay was designed to optimise assay performance, presents data supporting its analytical validity, and describes the quality control and assurance programmes that ensure optimal test performance over time.

  12. Management of heart failure in the new era: the role of scores.

    PubMed

    Mantegazza, Valentina; Badagliacca, Roberto; Nodari, Savina; Parati, Gianfranco; Lombardi, Carolina; Di Somma, Salvatore; Carluccio, Erberto; Dini, Frank Lloyd; Correale, Michele; Magrì, Damiano; Agostoni, Piergiuseppe

    2016-08-01

    Heart failure is a widespread syndrome involving several organs, still characterized by high mortality and morbidity, and whose clinical course is heterogeneous and hardly predictable.In this scenario, the assessment of heart failure prognosis represents a fundamental step in clinical practice. A single parameter is always unable to provide a very precise prognosis. Therefore, risk scores based on multiple parameters have been introduced, but their clinical utility is still modest. In this review, we evaluated several prognostic models for acute, right, chronic, and end-stage heart failure based on multiple parameters. In particular, for chronic heart failure we considered risk scores essentially based on clinical evaluation, comorbidities analysis, baroreflex sensitivity, heart rate variability, sleep disorders, laboratory tests, echocardiographic imaging, and cardiopulmonary exercise test parameters. What is at present established is that a single parameter is not sufficient for an accurate prediction of prognosis in heart failure because of the complex nature of the disease. However, none of the scoring systems available is widely used, being in some cases complex, not user-friendly, or based on expensive or not easily available parameters. We believe that multiparametric scores for risk assessment in heart failure are promising but their widespread use needs to be experienced.

  13. Intelligibility in microbial complex systems: Wittgenstein and the score of life.

    PubMed

    Baquero, Fernando; Moya, Andrés

    2012-01-01

    Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the "score of life" metaphor is more accurate to express the complexity of living systems than the classic "book of life." Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life.

  14. Prevalence of overestimation or underestimation of the functional capacity using MRC score as compared to 6-minute walk test in patients with cardio-respiratory disorders.

    PubMed

    Callens, Etienne; Graba, Sémia; Essalhi, Mohamed; Gillet-Juvin, Karine; Chevalier-Bidaud, Brigitte; Chenu, Romain; Mahut, Bruno; Delclaux, Christophe

    2014-09-01

    The first objective of our study was to assess whether patients diagnosed with cardio-respiratory disorders report overestimation or underestimation on recall (Medical Research Council (MRC) dyspnea scale) of their true functional capacity (walked distance during a 6-minute walk test (6MWT)). The second objective was to assess whether the measurement of breathlessness at the end of a 6MWT (Borg score) may help to identify dyspneic patients on recall. The 6MWTs of 746 patients aged from 40 to 80 years who were diagnosed with either chronic obstructive pulmonary disease (COPD, n = 355), diffuse parenchymal lung disease (n = 140), pulmonary vascular diseases (n = 188) or congestive heart failure (n = 63) were selected from a prospective Clinical Database Warehouse. The percentage of patients who overestimated (MRC ≤ 2 with distance < lower limit of normal (LLN), 61/746, 8%; 95% confidence interval (CI): 6 to 10%) or underestimated (MRC > 2 with distance ≥LLN, 121/746, 16%; 95%CI: 14 to 19%) on recall their capacity was elevated. The overestimation seemed related to self-limitation, while the underestimation seemed related to patients who "work through" their breathing discomfort. These two latter groups of patients were mainly diagnosed with COPD. A Borg dyspnea score >3 (upper limit of normal) at the end of the 6MWT had 84% specificity for the prediction of a MRC score >1. Almost one fourth of patients suffering from cardio-pulmonary disorders overestimate or underestimate on recall their true functional capacity. An elevated Borg dyspnea score at the end of the 6MWT has a good specificity to predict dyspnea on recall.

  15. Within-patient temporal variance in MELD score and impact on survival prediction after TIPS creation.

    PubMed

    Gaba, Ron C; Shah, Kruti D; Couture, Patrick M; Parvinian, Ahmad; Minocha, Jeet; Knuttinen, M Grace; Bui, James T

    2013-01-01

    To assess within-patient temporal variability in Model for End Stage Liver Disease (MELD) scores and impact on outcome prognostication after transjugular intrahepatic portosystemic shunt (TIPS) creation. In this single institution retrospective study, MELD score was calculated in 68 patients (M:F = 42:26, mean age 55 years) at 4 pre-procedure time points (1, 2-6, 7-14, and 15-35 days) before TIPS creation. Medical record review was used to identify 30- and 90-day clinical outcomes. Within-patient variability in pre-procedure MELD scores was assessed using repeated measures analysis of variance, and the ability of MELD scores at different time points to predict post-TIPS mortality was evaluated by comparing area under receiver operating characteristic (AUROC) curves. TIPS were successfully created for ascites (n = 30), variceal hemorrhage (n = 29), hepatic hydrothorax (n = 8), and portal vein thrombosis (n = 1). Pre-TIPS MELD scores showed significant (P = 0.032) within-subject variance that approached ± 18.5%. Higher MELD scores demonstrated greater variability in sequential scores as compared to lower MELD scores. Overall 30- and 90-day patient mortality was 22% (15/67) and 38% (24/64). AUROC curves showed that most recent MELD scores performed on the day of TIPS had superior predictive capacity for 30- (0.876, P = 0.037) and 90-day (0.805 P = 0.020) mortality compared to MELD scores performed 2-6 or 7-14 days prior. In conclusion, MELD scores show within-patient variability over time, and scores calculated on the day of TIPS most accurately predict risk and should be used for patient selection and counseling.

  16. Evaluating the Effects of Differences in Group Abilities on the Tucker and the Levine Observed-Score Methods for Common-Item Nonequivalent Groups Equating. ACT Research Report Series 2010-1

    ERIC Educational Resources Information Center

    Chen, Hanwei; Cui, Zhongmin; Zhu, Rongchun; Gao, Xiaohong

    2010-01-01

    The most critical feature of a common-item nonequivalent groups equating design is that the average score difference between the new and old groups can be accurately decomposed into a group ability difference and a form difficulty difference. Two widely used observed-score linear equating methods, the Tucker and the Levine observed-score methods,…

  17. A Comparison of Presentation Levels to Maximize Word Recognition Scores

    PubMed Central

    Guthrie, Leslie A.; Mackersie, Carol L.

    2010-01-01

    Background While testing suprathreshold word recognition at multiple levels is considered best practice, studies on practice patterns do not suggest that this is common practice. Audiologists often test at a presentation level intended to maximize recognition scores, but methods for selecting this level are not well established for a wide range of hearing losses. Purpose To determine the presentation level methods that resulted in maximum suprathreshold phoneme-recognition scores while avoiding loudness discomfort. Research Design Performance-intensity functions were obtained for 40 participants with sensorineural hearing loss using the Computer-Assisted Speech Perception Assessment. Participants had either gradually sloping (mild, moderate, moderately severe/severe) or steeply sloping losses. Performance-intensity functions were obtained at presentation levels ranging from 10 dB above the SRT to 5 dB below the UCL (uncomfortable level). In addition, categorical loudness ratings were obtained across a range of intensities using speech stimuli. Scores obtained at UCL – 5 dB (maximum level below loudness discomfort) were compared to four alternative presentation-level methods. The alternative presentation-level methods included sensation level (SL; 2 kHz reference, SRT reference), a fixed-level (95 dB SPL) method, and the most comfortable loudness level (MCL). For the SL methods, scores used in the analysis were selected separately for the SRT and 2 kHz references based on several criteria. The general goal was to choose levels that represented asymptotic performance while avoiding loudness discomfort. The selection of SLs varied across the range of hearing losses. Results Scores obtained using the different presentation-level methods were compared to scores obtained using UCL – 5 dB. For the mild hearing loss group, the mean phoneme scores were similar for all presentation levels. For the moderately severe/severe group, the highest mean score was obtained using

  18. Open-Source Logic-Based Automated Sleep Scoring Software using Electrophysiological Recordings in Rats

    PubMed Central

    Gross, Brooks A.; Walsh, Christine M.; Turakhia, Apurva A.; Booth, Victoria; Mashour, George; Poe, Gina R.

    2009-01-01

    Manual state scoring of physiological recordings in sleep studies is time-consuming, resulting in a data backlog, research delays and increased personnel costs. We developed MATLAB-based software to automate scoring of sleep/waking states in rats, potentially extendable to other animals, from a variety of recording systems. The software contains two programs, Sleep Scorer and Auto-Scorer, for manual and automated scoring. Auto-Scorer is a logic-based program that displays power spectral densities of an electromyographic signal and σ, δ, and θ frequency bands of an electroencephalographic signal, along with the δ/θ ratio and σ ×θ, for every epoch. The user defines thresholds from the training file state definitions which the Auto-Scorer uses with logic to discriminate the state of every epoch in the file. Auto-Scorer was evaluated by comparing its output to manually scored files from 6 rats under 2 experimental conditions by 3 users. Each user generated a training file, set thresholds, and autoscored the 12 files into 4 states (waking, non-REM, transition-to-REM, and REM sleep) in ¼ the time required to manually score the file. Overall performance comparisons between Auto-Scorer and manual scoring resulted in a mean agreement of 80.24 +/− 7.87%, comparable to the average agreement among 3 manual scorers (83.03 +/− 4.00%). There was no significant difference between user-user and user-Auto-Scorer agreement ratios. These results support the use of our open-source Auto-Scorer, coupled with user review, to rapidly and accurately score sleep/waking states from rat recordings. PMID:19615408

  19. The BIG Score and Prediction of Mortality in Pediatric Blunt Trauma.

    PubMed

    Davis, Adrienne L; Wales, Paul W; Malik, Tahira; Stephens, Derek; Razik, Fathima; Schuh, Suzanne

    2015-09-01

    To examine the association between in-hospital mortality and the BIG (composed of the base deficit [B], International normalized ratio [I], Glasgow Coma Scale [G]) score measured on arrival to the emergency department in pediatric blunt trauma patients, adjusted for pre-hospital intubation, volume administration, and presence of hypotension and head injury. We also examined the association between the BIG score and mortality in patients requiring admission to the intensive care unit (ICU). A retrospective 2001-2012 trauma database review of patients with blunt trauma ≤ 17 years old with an Injury Severity score ≥ 12. Charts were reviewed for in-hospital mortality, components of the BIG score upon arrival to the emergency department, prehospital intubation, crystalloids ≥ 20 mL/kg, presence of hypotension, head injury, and disposition. 50/621 (8%) of the study patients died. Independent mortality predictors were the BIG score (OR 11, 95% CI 6-25), prior fluid bolus (OR 3, 95% CI 1.3-9), and prior intubation (OR 8, 95% CI 2-40). The area under the receiver operating characteristic curve was 0.95 (CI 0.93-0.98), with the optimal BIG cutoff of 16. With BIG <16, death rate was 3/496 (0.006, 95% CI 0.001-0.007) vs 47/125 (0.38, 95% CI 0.15-0.7) with BIG ≥ 16, (P < .0001). In patients requiring admission to the ICU, the BIG score remained predictive of mortality (OR 14.3, 95% CI 7.3-32, P < .0001). The BIG score accurately predicts mortality in a population of North American pediatric patients with blunt trauma independent of pre-hospital interventions, presence of head injury, and hypotension, and identifies children with a high probability of survival (BIG <16). The BIG score is also associated with mortality in pediatric patients with trauma requiring admission to the ICU. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Physical models have gender-specific effects on student understanding of protein structure-function relationships.

    PubMed

    Forbes-Lorman, Robin M; Harris, Michelle A; Chang, Wesley S; Dent, Erik W; Nordheim, Erik V; Franzen, Margaret A

    2016-07-08

    Understanding how basic structural units influence function is identified as a foundational/core concept for undergraduate biological and biochemical literacy. It is essential for students to understand this concept at all size scales, but it is often more difficult for students to understand structure-function relationships at the molecular level, which they cannot as effectively visualize. Students need to develop accurate, 3-dimensional mental models of biomolecules to understand how biomolecular structure affects cellular functions at the molecular level, yet most traditional curricular tools such as textbooks include only 2-dimensional representations. We used a controlled, backward design approach to investigate how hand-held physical molecular model use affected students' ability to logically predict structure-function relationships. Brief (one class period) physical model use increased quiz score for females, whereas there was no significant increase in score for males using physical models. Females also self-reported higher learning gains in their understanding of context-specific protein function. Gender differences in spatial visualization may explain the gender-specific benefits of physical model use observed. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 44(4):326-335, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.