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Sample records for function tests predict

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

    PubMed

    Deckel, A W

    1999-02-01

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

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

    PubMed

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

    2012-06-01

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

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

    PubMed

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

    2012-06-01

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

  4. [Common prediction equations of respiratory function tests from children to adults in Japan].

    PubMed

    Tamura, Gen; Aizawa, Hisamichi; Nagai, Atsushi; Inoue, Hiroshi

    2007-07-01

    In order to make common prediction equations of respiratory function tests (RFTs) from children to adults in Japan, we combined data of RFTs accumulated for "Reference values of spirogram and arterial blood gas levels in Japanese" reported in 2001 at the Japanese Respiratory Society congress and those for "An attempt to establish reference vales of respiratory function tests for Japanese children and adolescents" reported in 2006 from the Tohoku district. We then conducted multiple regression analysis on forced vital capacity, forced expiratory volume in 1 second (FEV1), V50, V25, and Gaensler's FEV1%, since they were measured under the same condition in the both reports. With all the combinations of 5 dependent variables (age, height, age2, height2, and age x height), multiple regression analysis was performed for each RFT. Judging by both evaluation indices of adjusted R-square and Mallows's Cp statistic, the equation using 4 dependent variables of age, height, age2, and age x height demonstrated roughly high efficiency for all RFTs. Therefore, we decided the equation excluding a dependent variable of height2 as common prediction equations for all RFTs and demonstrated the prediction equation for each RFT by sex.

  5. Pulmonary Function Tests Do Not Predict Pulmonary Complications After Thoracoscopic Lobectomy

    PubMed Central

    Berry, Mark F.; Villamizar-Ortiz, Nestor R.; Tong, Betty C.; Burfeind, William R.; Harpole, David H.; D’Amico, Thomas A.; Onaitis, Mark W.

    2011-01-01

    BACKGROUND Pulmonary function tests (PFTs) predict respiratory complications and mortality after lung resection via thoracotomy. We sought to determine the impact of PFTs upon complications after thoracoscopic lobectomy. METHODS A model for morbidity including published preoperative risk factors and surgical approach was developed by multivariable logistic regression. All patients who underwent lobectomy for primary lung cancer between December, 1999 and October, 2007 with preoperative forced expiratory volume in 1 second (FEV1) or diffusion capacity to carbon monoxide (DLCO) ≤ 60% predicted were reviewed. Preoperative, histopathologic, perioperative, and outcome variables were assessed using standard descriptive statistics. Pulmonary complications were defined as atelectasis requiring bronchoscopy, pneumonia, reintubation, and tracheostomy. RESULTS During the study period, 340 patients (median age 67) with DLCO or FEV1 ≤ 60% (mean % predicted FEV1 55±1, mean % predicted DLCO 61±1) underwent lobectomy (173 thoracoscopy, 167 thoracotomy). Operative mortality was 5% (17 patients) and overall morbidity was 48% (164 patients). At least one pulmonary complication occurred in 57 patients (17%). Significant predictors of pulmonary complications by multivariable analysis for all patients included DLCO (odds ratio 1.03, p=0.003), FEV1 (odds ratio 1.04, p=0.003) and thoracotomy as surgical approach (odds ratio 3.46,p=0.0007). When patients were analyzed according to operative approach, DLCO and FEV1 remained significant predictors of pulmonary morbidity for patients undergoing thoracotomy but not thoracoscopy. CONCLUSIONS In patients with impaired pulmonary function, preoperative pulmonary function tests are predictors of pulmonary complications when lobectomy for lung cancer is performed via thoracotomy but not via thoracoscopy. PMID:20338305

  6. Use of respiratory function tests to predict survival in amyotrophic lateral sclerosis.

    PubMed

    Baumann, Fusun; Henderson, Robert D; Morrison, Stephen C; Brown, Michael; Hutchinson, N; Douglas, James A; Robinson, Peter J; McCombe, Pamela A

    2010-01-01

    Respiratory function tests (RFTs) are commonly used as a measure of progression in ALS. This study assessed the ability of various RFTs to predict survival in ALS patients. Subjects with ALS had one or more measurements of seated and supine FVC, maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP). Kaplan-Meier (KM) analysis was used to determine whether patients with abnormal RFTs had shorter survival than those with normal RFTs. The sensitivity and specificity of RFTs as predictors of two-year survival were calculated from receiver operating characteristic (ROC) curves. With KM analysis, subjects with abnormal values of seated FVC, supine FVC, MIP and MEP had significantly reduced survival compared to subjects with normal values. With ROC curves, a normal supine FVC was highly predictive for two-year survival and had superior sensitivity over seated FVC. Slower rates of decline in seated or supine FVC were strong predictors of two-year survival. Our study demonstrates that respiratory function measurements are useful to predict survival in ALS patients. We show that measurements of FVC in the supine position are worth including in the assessment of respiratory function in ALS.

  7. Prediction of glass durability as a function of glass composition and test conditions: Thermodynamics and kinetics

    SciTech Connect

    Jantzen, C M

    1988-01-01

    The long-term durability of nuclear waste glasses can be predicted by comparing their performance to natural and ancient glasses. Glass durability is a function of the kinetic and thermodynamic stability of glass in solution. The relationship between the kinetic and thermodynamic aspects of glass durability can be understood when the relative contributions of glass composition and imposed test conditions are delineated. Glass durability has been shown to be a function of the thermodynamic hydration free energy which can be calculated from the glass composition. Hydration thermodynamics also furnishes a quantitative frame of reference to understand how various test parameters affect glass durability. Linear relationships have been determined between the logarithmic extent of hydration and the calculated hydration free energy for several different test geometries. Different test conditions result in different kinetic reactivity parameters such as the exposed glass surface area (SA), the leachant solution volume (V), and the length of time that the glass is in the leachant (t). Leachate concentrations are known to be a function of the kinetic test parameter (SAV)t. The relative durabilities of glasses, including pure silica, obsidians, nuclear waste glasses, medieval window glasses, and frit glasses define a plane in three dimensional ..delta..G/sub hyd/-concentration-(SAV)t space. At constant kinetic conditions, e.g., test geometry and test duration, the three dimensional plane is intersected at constant (SAV)t and the ..delta..G/sub hyd/-concentration plots have similar slopes. The slope represents the natural logarithm of the theoretical slope, (12.303 RT), for the rate of glass dissolution. 53 refs., 4 figs.

  8. [Prediction of G-load (Gz) tolerance based on various functional tests].

    PubMed

    Suvorov, P M; Karlov, V N; Sidorova, K A

    1996-01-01

    The purpose of the present study was to analyze and sum up the data on the methods of predicting g-tolerance (+Gz) utilizing various functional tests within the program of medical flight certification. The study involved 478 fighter pilots who were examined at the Central Military Scientific/Research Aviation Hospital. The age of examinates varied from 25 to 50 years (35 yr. on the average). Along with healthy subjects there were also pilots with the history of vascular-autonomous instability, anamnesis of syncope, myocardiodystrophy, myocardiac and atherosclerotic cardiosclerosis, and some other disorders. As a result, a correlation was established between the tolerance of lower body negative pressure at -50 mm Hg and standing tests. No link was noted between tolerance of the subjects to moderate hypoxia (H = 5,000 m for 30 minutes) and +Gz-loads at 3 and 5 units for 30 seconds. Neither was there evidence of correlation between tolerance of standing tests including their modifications and g-loads. Pearson association coefficient ra = 0.01. Comparison of the tolerance to +Gz at 3, 5, and 6 units without the anti-gravity suit and static loads at 120, 160, 200, and 240 kg/s during 30 seconds each gave an agreement of 67%. However, the statoergometry test revealed a poor tolerance of static loads only in 17.2% out of 29 pilots with low g-loads tolerance. Hence, the association coefficient appeared to be equal to 0.06 denying any predictive link. This absence of reliable predictive correlation between the tests in use was extenuated by different physiological mechanisms of adaptation.

  9. [Prediction of G-load (Gz) tolerance based on various functional tests].

    PubMed

    Suvorov, P M; Karlov, V N; Sidorova, K A

    1996-01-01

    The purpose of the present study was to analyze and sum up the data on the methods of predicting g-tolerance (+Gz) utilizing various functional tests within the program of medical flight certification. The study involved 478 fighter pilots who were examined at the Central Military Scientific/Research Aviation Hospital. The age of examinates varied from 25 to 50 years (35 yr. on the average). Along with healthy subjects there were also pilots with the history of vascular-autonomous instability, anamnesis of syncope, myocardiodystrophy, myocardiac and atherosclerotic cardiosclerosis, and some other disorders. As a result, a correlation was established between the tolerance of lower body negative pressure at -50 mm Hg and standing tests. No link was noted between tolerance of the subjects to moderate hypoxia (H = 5,000 m for 30 minutes) and +Gz-loads at 3 and 5 units for 30 seconds. Neither was there evidence of correlation between tolerance of standing tests including their modifications and g-loads. Pearson association coefficient ra = 0.01. Comparison of the tolerance to +Gz at 3, 5, and 6 units without the anti-gravity suit and static loads at 120, 160, 200, and 240 kg/s during 30 seconds each gave an agreement of 67%. However, the statoergometry test revealed a poor tolerance of static loads only in 17.2% out of 29 pilots with low g-loads tolerance. Hence, the association coefficient appeared to be equal to 0.06 denying any predictive link. This absence of reliable predictive correlation between the tests in use was extenuated by different physiological mechanisms of adaptation. PMID:8974598

  10. Impairment in occupational functioning and adult ADHD: the predictive utility of executive function (EF) ratings versus EF tests.

    PubMed

    Barkley, Russell A; Murphy, Kevin R

    2010-05-01

    Attention deficit hyperactivity disorder (ADHD) is associated with deficits in executive functioning (EF). ADHD in adults is also associated with impairments in major life activities, particularly occupational functioning. We investigated the extent to which EF deficits assessed by both tests and self-ratings contributed to the degree of impairment in 11 measures involving self-reported occupational problems, employer reported workplace adjustment, and clinician rated occupational adjustment. Three groups of adults were recruited as a function of their severity of ADHD: ADHD diagnosis (n = 146), clinical controls self-referring for ADHD but not diagnosed with it (n = 97), and community controls (n = 109). Groups were combined and regression analyses revealed that self-ratings of EF were significantly predictive of impairments in all 11 measures of occupational adjustment. Although several tests of EF also did so, they contributed substantially less than did the EF ratings, particularly when analyzed jointly with the ratings. We conclude that EF deficits contribute to the impairments in occupational functioning that occur in conjunction with adult ADHD. Ratings of EF in daily life contribute more to such impairments than do EF tests, perhaps because, as we hypothesize, each assesses a different level in the hierarchical organization of EF as a meta-construct.

  11. Predictive Effects of Lung function test on Postoperative Pneumonia in Squamous Esophageal Cancer.

    PubMed

    Wei, Ran; Dong, Wei; Shen, Hongchang; Ni, Yang; Zhang, Tiehong; Wang, Yibing; Du, Jiajun

    2016-01-01

    Pulmonary function tests had prospective implications for postoperative pneumonia, which occurred frequently after esophagectomy. Understanding factors that were associated with pulmonary infection may help in patient selection and postoperative management. We performed a retrospective review of 2 independent cohorts including 216 patients who underwent esophagectomy between November 2011 and May 2014, aiming at identifying predictors of primary pneumonia. Univariate analysis was used to identify potential covariates for the development of primary pneumonia. Adjustments for multiple comparisons were made using False Discovery Rate (FDR) (Holm-Bonferroni method). Multivariable logistic regression analysis was used to identify independent predictors and construct a regression model based on a training cohort (n = 166) and then the regression model was validated using an independent cohort (n = 50). It showed that low PEF (hazard ratio 0.97, P = 0.009) was independent risk factors for the development of primary pneumonia in multivariate analyses and had a predictive effect for primary pneumonia (AUC = 0.691 and 0.851 for training and validation data set, respectively). Therefore, PEF has clinical value in predicting postoperative pneumonia after esophagectomy and it may serve as an indicator of preoperative lung function training. PMID:27004739

  12. Utility of preoperative in vitro platelet function tests for predicting bleeding risk in patients undergoing functional endoscopic sinus surgery

    PubMed Central

    Lee, A-Jin; Kim, Sang-Gyung

    2016-01-01

    Background It is necessary to predict the bleeding risk in patients undergoing functional endoscopic sinus surgery (FESS). To evaluate the adequacy of primary hemostasis, preoperative hemostatic screening tests are used. In the present study, we determined whether there is a positive correlation between prolonged closure time (CT) with collagen/epinephrine (CT-epi), prothrombin time (PT), international normalized ratio (INR), activated partial thromboplastin time (aPTT) and bleeding during FESS. Patients and methods We reviewed the medical records of 90 patients without bleeding histories who had undergone FESS from March 2013 to June 2014. More than 200 mL of blood loss was defined as moderate bleeding during surgery. With respect to bleeding during surgery, we determined the sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of CT-epi, PT, INR and aPTT. Results Of the 90 patients, 17 (18.9%) patients had preoperative prolonged CT values and three (17.6%) patients had bleeding. In comparison, five (6.8%) of the 73 (81.1%) patients who had undergone FESS with preoperative normal PFA values experienced bleeding (P=0.171). On the other hand, patients with prolonged PT values (2, 2.2%), prolonged INR values (3, 3.3%) or prolonged PTT values (1, 1.1%) had no bleeding episode. Preoperative CT had low sensitivity (44.4%) and PPV (23.5%). Conclusion During preoperative period, the hemostatic screening may not be helpful to detect the bleeding tendency in adult patients undergoing FESS. Routine measurement of CT-epi, PT, INR and aPTT for preoperative screening may not be recommended for FESS patients. PMID:27799837

  13. Prediction of psychological functioning one year after the predictive test for Huntington's disease and impact of the test result on reproductive decision making.

    PubMed

    Decruyenaere, M; Evers-Kiebooms, G; Boogaerts, A; Cassiman, J J; Cloostermans, T; Demyttenaere, K; Dom, R; Fryns, J P; Van den Berghe, H

    1996-09-01

    For people at risk for Huntington's disease, the anxiety and uncertainty about the future may be very burdensome and may be an obstacle to personal decision making about important life issues, for example, procreation. For some at risk persons, this situation is the reason for requesting predictive DNA testing. The aim of this paper is two-fold. First, we want to evaluate whether knowing one's carrier status reduces anxiety and uncertainty and whether it facilitates decision making about procreation. Second, we endeavour to identify pretest predictors of psychological adaptation one year after the predictive test (psychometric evaluation of general anxiety, depression level, and ego strength). The impact of the predictive test result was assessed in 53 subjects tested, using pre- and post-test psychometric measurement and self-report data of follow up interviews. Mean anxiety and depression levels were significantly decreased one year after a good test result; there was no significant change in the case of a bad test result. The mean personality profile, including ego strength, remained unchanged one year after the test. The study further shows that the test result had a definite impact on reproductive decision making. Stepwise multiple regression analyses were used to select the best predictors of the subject's post-test reactions. The results indicate that a careful evaluation of pretest ego strength, depression level, and coping strategies may be helpful in predicting post-test reactions, independently of the carrier status. Test result (carrier/ non-carrier), gender, and age did not significantly contribute to the prediction. About one third of the variance of post-test anxiety and depression level and more than half of the variance of ego strength was explained, implying that other psychological or social aspects should also be taken into account when predicting individual post-test reactions.

  14. Functional test of pedotransfer functions to predict water flow and solute transport with the dual-permeability model MACRO

    NASA Astrophysics Data System (ADS)

    Moeys, J.; Larsbo, M.; Bergström, L.; Brown, C. D.; Coquet, Y.; Jarvis, N. J.

    2012-02-01

    Estimating pesticide leaching risks at the regional scale requires the ability to completely parameterise a pesticide fate model using only survey data, such as soil and land-use maps. Such parameterisation usually rely on a set of lookup tables and (pedo)transfer functions, relating elementary soil and site properties to model parameters. The aim of this paper is to describe and test a complete set of parameter estimation algorithms developed for the pesticide fate model MACRO, which accounts for preferential flow in soil macropores. We used tracer monitoring data from 16 lysimeter studies, carried out in three European countries, to evaluate the ability of MACRO and this "blind parameterisation" scheme to reproduce measured solute leaching at the base of each lysimeter. We focused on the prediction of early tracer breakthrough due to preferential flow, because this is critical for pesticide leaching. We then calibrated a selected number of parameters in order to assess to what extent the prediction of water and solute leaching could be improved. Our results show that water flow was generally reasonably well predicted (median model efficiency, ME, of 0.42). Although the general pattern of solute leaching was reproduced well by the model, the overall model efficiency was low (median ME = -0.26) due to errors in the timing and magnitude of some peaks. Preferential solute leaching at early pore volumes was also systematically underestimated. Nonetheless, the ranking of soils according to solute loads at early pore volumes was reasonably well estimated (concordance correlation coefficient, CCC, between 0.54 and 0.72). Moreover, we also found that ignoring macropore flow leads to a significant deterioration in the ability of the model to reproduce the observed leaching pattern, and especially the early breakthrough in some soils. Finally, the calibration procedure showed that improving the estimation of solute transport parameters is probably more important than the

  15. Functional test of pedotransfer functions to predict water flow and solute transport with the dual-permeability model MACRO

    NASA Astrophysics Data System (ADS)

    Moeys, J.; Larsbo, M.; Bergström, L.; Brown, C. D.; Coquet, Y.; Jarvis, N. J.

    2012-07-01

    Estimating pesticide leaching risks at the regional scale requires the ability to completely parameterise a pesticide fate model using only survey data, such as soil and land-use maps. Such parameterisations usually rely on a set of lookup tables and (pedo)transfer functions, relating elementary soil and site properties to model parameters. The aim of this paper is to describe and test a complete set of parameter estimation algorithms developed for the pesticide fate model MACRO, which accounts for preferential flow in soil macropores. We used tracer monitoring data from 16 lysimeter studies, carried out in three European countries, to evaluate the ability of MACRO and this "blind parameterisation" scheme to reproduce measured solute leaching at the base of each lysimeter. We focused on the prediction of early tracer breakthrough due to preferential flow, because this is critical for pesticide leaching. We then calibrated a selected number of parameters in order to assess to what extent the prediction of water and solute leaching could be improved. Our results show that water flow was generally reasonably well predicted (median model efficiency, ME, of 0.42). Although the general pattern of solute leaching was reproduced well by the model, the overall model efficiency was low (median ME = -0.26) due to errors in the timing and magnitude of some peaks. Preferential solute leaching at early pore volumes was also systematically underestimated. Nonetheless, the ranking of soils according to solute loads at early pore volumes was reasonably well estimated (concordance correlation coefficient, CCC, between 0.54 and 0.72). Moreover, we also found that ignoring macropore flow leads to a significant deterioration in the ability of the model to reproduce the observed leaching pattern, and especially the early breakthrough in some soils. Finally, the calibration procedure showed that improving the estimation of solute transport parameters is probably more important than the

  16. Prospective prediction of post-radiation therapy lung function using quantitative lung scans and pulmonary function testing

    SciTech Connect

    Rubenstein, J.H.; Richter, M.P.; Moldofsky, P.J.; Solin, L.J.

    1988-07-01

    Surgeons have made use of quantitative perfusion lung scanning (QS) and forced expiratory volume in one second (FEV1) to predict a patient's ability to tolerate lung resection. In this study QS and FEV1 were used to predict prospectively pulmonary function following lung irradiation (XRT). Twenty-two patients have had QS and FEV1 determined before XRT and at planned intervals post-XRT. Serial determination of lung function post-XRT allows comment on the temporal nature of the XRT effect on lung function. Seventeen patients had QS and FEV1 determined at an interval of 2-6 months post-irradiation with a drop in the groups mean FEV1 from 1.91 to 1.87L. or 2% during that interval. In the interval from 6-12 months post-XRT, 13 patients had studies with the groups mean FEV1 dropping from 1.79 to 1.58L or 12% of the original. In the interval from 12-18 months, 6 patients had a decline in mean FEV1 from 1.73 to 1.56L. or 10% of the original. In 22 patients a predicted final FEV1 was compared with a measured value at an interval from XRT. Fourteen of these determinations were at intervals greater than 6 months from the start of XRT and 6 at intervals of greater than 1 year. FEV1 was seen to drop during the follow-up intervals toward the predicted value. In only 2 patients did the final FEV1 drop below the predicted FEV1 and never by more than 0.12L. (6%). In summary, a method for predicting post-XRT pulmonary function using QS and FEV1 is described. Serial follow-up revealed a latent period followed by a late phase where FEV1 fell toward, but not significantly below, the predicted value. Such a determination can be of value in formulating a treatment plan for patients with significantly diminished pulmonary function.

  17. Optimizing cross-sectional prediction of social functioning in youth referred for neuropsychological testing.

    PubMed

    Lerner, Matthew D; Potthoff, Lauren M; Hunter, Scott J

    2015-01-01

    The current study aimed to establish a fine-grained, efficient characterization of the concurrent neuropsychological contributions to social functioning in neuropsychologically-referred youth. A secondary aim was to demonstrate a useful statistic approach for such investigations (Partial Least Squares Regression; PLSR), which is underutilized in this field. Forty-five participants (70 - 164 months; Mage = 110.89; 34 male) were recruited from a large neuropsychological assessment clinic. Participants completed subtests from the NEPSY-II focusing on neuropsychological constructs that have been linked to social functioning (affect decoding, social memory, motor skills, visuomotor skills, response inhibition, attention and set-shifting, and verbal comprehension). Mothers completed the BASC-2, from which Atypicality and Social Skills scales were analyzed. PLSR revealed that difficulty with social memory, sensorimotor integration, and the ability to attend to and accurately discriminate auditory stimuli combine to best predict atypical or "odd" behavior. In terms of social skills, two factors emerged. The first factor indicated that, counterintuitively, greater emotional perception, visuospatial perception, ability to attend to and accurately discriminate auditory stimuli, and understand instructions was related to poorer social skills. The second factor indicated that a pattern of better facial memory, and sensorimotor ability (execution & integration) characterized a distinct profile of greater social ability. PLSR results were compared to traditional OLS and Backwards Stepwise regression approaches to demonstrate utility. Results also suggested that these findings were consistent across age, gender, and diagnostic group, indicating common neuropsychological substrates of social functioning in this sample of referred youth. Overall, this study provides the first characterization of optimized combinations of neuropsychological variables in predicting social functioning

  18. Optimizing Cross-Sectional Prediction of Social Functioning in Youth Referred for Neuropsychological Testing

    PubMed Central

    Lerner, Matthew D.; Potthoff, Lauren M.; Hunter, Scott J.

    2015-01-01

    The current study aimed to establish a fine-grained, efficient characterization of the concurrent neuropsychological contributions to social functioning in neuropsychologically-referred youth. A secondary aim was to demonstrate a useful statistic approach for such investigations (Partial Least Squares Regression; PLSR), which is underutilized in this field. Forty-five participants (70 – 164 months; Mage = 110.89; 34 male) were recruited from a large neuropsychological assessment clinic. Participants completed subtests from the NEPSY-II focusing on neuropsychological constructs that have been linked to social functioning (affect decoding, social memory, motor skills, visuomotor skills, response inhibition, attention and set-shifting, and verbal comprehension). Mothers completed the BASC-2, from which Atypicality and Social Skills scales were analyzed. PLSR revealed that difficulty with social memory, sensorimotor integration, and the ability to attend to and accurately discriminate auditory stimuli combine to best predict atypical or “odd” behavior. In terms of social skills, two factors emerged. The first factor indicated that, counterintuitively, greater emotional perception, visuospatial perception, ability to attend to and accurately discriminate auditory stimuli, and understand instructions was related to poorer social skills. The second factor indicated that a pattern of better facial memory, and sensorimotor ability (execution & integration) characterized a distinct profile of greater social ability. PLSR results were compared to traditional OLS and Backwards Stepwise regression approaches to demonstrate utility. Results also suggested that these findings were consistent across age, gender, and diagnostic group, indicating common neuropsychological substrates of social functioning in this sample of referred youth. Overall, this study provides the first characterization of optimized combinations of neuropsychological variables in predicting social

  19. Psychometric properties and convergent and predictive validity of an executive function test battery for two-year-olds

    PubMed Central

    Mulder, Hanna; Hoofs, Huub; Verhagen, Josje; van der Veen, Ineke; Leseman, Paul P. M.

    2014-01-01

    Executive function (EF) is an important predictor of numerous developmental outcomes, such as academic achievement and behavioral adjustment. Although a plethora of measurement instruments exists to assess executive function in children, only few of these are suitable for toddlers, and even fewer have undergone psychometric evaluation. The present study evaluates the psychometric properties and validity of an assessment battery for measuring EF in two-year-olds. A sample of 2437 children were administered the assessment battery at a mean age of 2;4 years (SD = 0;3 years) in a large-scale field study. Measures of both hot EF (snack and gift delay tasks) and cool EF (six boxes, memory for location, and visual search task) were included. Confirmatory Factor Analyses showed that a two-factor hot and cool EF model fitted the data better than a one-factor model. Measurement invariance was supported across groups differing in age, gender, socioeconomic status (SES), home language, and test setting. Criterion and convergent validity were evaluated by examining relationships between EF and age, gender, SES, home language, and parent and teacher reports of children's attention and inhibitory control. Predictive validity of the test battery was investigated by regressing children's pre-academic skills and behavioral problems at age three on the latent hot and cool EF factors at age 2 years. The test battery showed satisfactory psychometric quality and criterion, convergent, and predictive validity. Whereas cool EF predicted both pre-academic skills and behavior problems 1 year later, hot EF predicted behavior problems only. These results show that EF can be assessed with psychometrically sound instruments in children as young as 2 years, and that EF tasks can be reliably applied in large scale field research. The current instruments offer new opportunities for investigating EF in early childhood, and for evaluating interventions targeted at improving EF from a young age. PMID

  20. Psychometric properties and convergent and predictive validity of an executive function test battery for two-year-olds.

    PubMed

    Mulder, Hanna; Hoofs, Huub; Verhagen, Josje; van der Veen, Ineke; Leseman, Paul P M

    2014-01-01

    Executive function (EF) is an important predictor of numerous developmental outcomes, such as academic achievement and behavioral adjustment. Although a plethora of measurement instruments exists to assess executive function in children, only few of these are suitable for toddlers, and even fewer have undergone psychometric evaluation. The present study evaluates the psychometric properties and validity of an assessment battery for measuring EF in two-year-olds. A sample of 2437 children were administered the assessment battery at a mean age of 2;4 years (SD = 0;3 years) in a large-scale field study. Measures of both hot EF (snack and gift delay tasks) and cool EF (six boxes, memory for location, and visual search task) were included. Confirmatory Factor Analyses showed that a two-factor hot and cool EF model fitted the data better than a one-factor model. Measurement invariance was supported across groups differing in age, gender, socioeconomic status (SES), home language, and test setting. Criterion and convergent validity were evaluated by examining relationships between EF and age, gender, SES, home language, and parent and teacher reports of children's attention and inhibitory control. Predictive validity of the test battery was investigated by regressing children's pre-academic skills and behavioral problems at age three on the latent hot and cool EF factors at age 2 years. The test battery showed satisfactory psychometric quality and criterion, convergent, and predictive validity. Whereas cool EF predicted both pre-academic skills and behavior problems 1 year later, hot EF predicted behavior problems only. These results show that EF can be assessed with psychometrically sound instruments in children as young as 2 years, and that EF tasks can be reliably applied in large scale field research. The current instruments offer new opportunities for investigating EF in early childhood, and for evaluating interventions targeted at improving EF from a young age. PMID

  1. The Role of Executive Functions in Attention Deficit Hyperactivity Disorder: Testing Predictions from Two Models

    ERIC Educational Resources Information Center

    Lee, Donghyung; Riccio, Cynthia A.; Hynd, George W.

    2004-01-01

    The role of executive functions in attention deficit hyperactivity disorder (ADHD) varies considerably depending on the models of ADHD. We examined the interrelationship of two major executive functions (i.e., inhibition and working memory) with behavioral, emotional, and school problems in a group of children who had a comprehensive…

  2. Predicting respiratory morbidity from pulmonary function tests: A reanalysis of ozone chamber studies

    SciTech Connect

    Ostro, B.D.; Lipsett, M.J.; Jewell, N.P.

    1989-10-01

    Some consequences of acute exposure to ozone are best measured in studies of human respiratory responses in controlled exposure chambers. These studies typically examine relationships between exposures to alternative pollutant concentrations and indicators of lung function as measured by spirometry, such as forced expiratory volume in one second, FEV1. However, the association of respiratory morbidity with these changes in lung function is not well established. To gain a better understanding of the relationship between ozone-related changes in pulmonary function and respiratory symptoms, data from several clinical studies have been reanalyzed. Logistic regression models were used to determine the quantitative relationship between changes in FEV1 and the probability of a mild or moderate lower respiratory symptom. Models were developed that corrected for repeated sampling of individuals and both population-averaged and subject-specific effects were determined. The results indicate the existence of a strong and consistent quantitative relationship between changes in lung function and the probability of a respiratory symptom. Specifically, a 10 percent reduction in FEV1 is associated with a 15 percentage point increase in the probability of a mild, moderate or severe lower respiratory symptom and a 6 percentage point increase in the probability of a moderate or severe lower respiratory symptom.

  3. Pretransplant pulmonary function tests predict risk of mortality following fractionated total body irradiation and allogeneic peripheral blood stem cell transplant

    SciTech Connect

    Singh, Anurag K. . E-mail: singan@mail.nih.gov; Karimpour, Shervin E.; Savani, Bipin N.; Guion, Peter M.S.; Hope, Andrew J.; Mansueti, John R.; Ning, Holly; Altemus, Rosemary M. Ph.D.; Wu, Colin O.; Barrett, A. John

    2006-10-01

    Purpose: To determine the value of pulmonary function tests (PFTs) done before peripheral blood stem cell transplant (PBSCT) in predicting mortality after total body irradiation (TBI) performed with or without dose reduction to the lung. Methods and Materials: From 1997 to 2004, 146 consecutive patients with hematologic malignancies received fractionated TBI before PBSCT. With regimen A (n = 85), patients were treated without lung dose reduction to 13.6 gray (Gy). In regimen B (n = 35), total body dose was decreased to 12 Gy (1.5 Gy twice per day for 4 days) and lung dose was limited to 9 Gy by use of lung shielding. In regimen C (n = 26), lung dose was reduced to 6 Gy. All patients received PFTs before treatment, 90 days after treatment, and annually. Results: Median follow-up was 44 months (range, 12-90 months). Sixty-one patients had combined ventilation/diffusion capacity deficits defined as both a forced expiratory volume in the first second (FEV{sub 1}) and a diffusion capacity of carbon dioxide (DLCO) <100% predicted. In this group, there was a 20% improvement in one-year overall survival with lung dose reduction (70 vs. 50%, log-rank test p = 0.042). Conclusion: Among those with combined ventilation/diffusion capacity deficits, lung dose reduction during TBI significantly improved survival.

  4. Performance on the Star Excursion Balance Test predicts functional turnout angle in pre-pubescent female dancers.

    PubMed

    Filipa, Alyson R; Smith, Teresa R; Paterno, Mark V; Ford, Kevin R; Hewett, Timothy E

    2013-12-01

    The purpose of this study was to determine if there was a predictive relationship between performance on the Star Excursion Balance Test (SEBT) and functional turnout angle (FTA) in prepubescent female dancers. Ten dance students, ages 5 to 9 years (mean: 7.3 years), were recruited for this study. The SEBT required the subject to reach in the anterior, posterior-medial, and posteriorlateral directions with her free-limb foot while standing on the reference limb. A composite reach score was determined by calculating the sum of distance reached in the three directions and normalizing to leg length. The FTA was assessed in first position by measuring the angle of bisection between the second and third metatarsals and the midpoint of the calcaneus. Linear regression was used to determine if there was a predictive relationship between performance on the SEBT and FTA in this cohort. The subjects demonstrated a mean FTA of 90.3° ± 17.7°. Composite reach on the dominant limb normalized to leg length (81.4 ± 11.1%) during the SEBT was a significant predictor of FTA (r(2) = 0.49, p = 0.02), while performance on the non-dominant limb (81.9 ± 10.8%) indicated a trend toward a predictive association (r(2) = 0.35, p = 0.07). A decreased composite reach score was predictive of decreased FTA. These measurements may serve as an important screening tool for identifying dancers at risk for lower extremity injury.

  5. Liver Function Tests

    MedlinePlus

    ... herbal supplements you are taking. What are normal ranges for liver function tests? Normal ranges for liver function tests can vary by age, ... other factors. Laboratory test results usually provide normal ranges for each liver function test with your results. ...

  6. Benchmarking density functional theory predictions of framework structures and properties in a chemically diverse test set of metal-organic frameworks

    SciTech Connect

    Nazarian, Dalar; Ganesh, P.; Sholl, David S.

    2015-09-30

    We compiled a test set of chemically and topologically diverse Metal–Organic Frameworks (MOFs) with high accuracy experimentally derived crystallographic structure data. The test set was used to benchmark the performance of Density Functional Theory (DFT) functionals (M06L, PBE, PW91, PBE-D2, PBE-D3, and vdW-DF2) for predicting lattice parameters, unit cell volume, bonded parameters and pore descriptors. On average PBE-D2, PBE-D3, and vdW-DF2 predict more accurate structures, but all functionals predicted pore diameters within 0.5 Å of the experimental diameter for every MOF in the test set. The test set was also used to assess the variance in performance of DFT functionals for elastic properties and atomic partial charges. The DFT predicted elastic properties such as minimum shear modulus and Young's modulus can differ by an average of 3 and 9 GPa for rigid MOFs such as those in the test set. Moreover, we calculated the partial charges by vdW-DF2 deviate the most from other functionals while there is no significant difference between the partial charges calculated by M06L, PBE, PW91, PBE-D2 and PBE-D3 for the MOFs in the test set. We find that while there are differences in the magnitude of the properties predicted by the various functionals, these discrepancies are small compared to the accuracy necessary for most practical applications.

  7. DWI and complex brain network analysis predicts vascular cognitive impairment in spontaneous hypertensive rats undergoing executive function tests

    PubMed Central

    López-Gil, Xavier; Amat-Roldan, Iván; Tudela, Raúl; Castañé, Anna; Prats-Galino, Alberto; Planas, Anna M.; Farr, Tracy D.; Soria, Guadalupe

    2014-01-01

    The identification of biomarkers of vascular cognitive impairment is urgent for its early diagnosis. The aim of this study was to detect and monitor changes in brain structure and connectivity, and to correlate them with the decline in executive function. We examined the feasibility of early diagnostic magnetic resonance imaging (MRI) to predict cognitive impairment before onset in an animal model of chronic hypertension: Spontaneously Hypertensive Rats. Cognitive performance was tested in an operant conditioning paradigm that evaluated learning, memory, and behavioral flexibility skills. Behavioral tests were coupled with longitudinal diffusion weighted imaging acquired with 126 diffusion gradient directions and 0.3 mm3 isometric resolution at 10, 14, 18, 22, 26, and 40 weeks after birth. Diffusion weighted imaging was analyzed in two different ways, by regional characterization of diffusion tensor imaging (DTI) indices, and by assessing changes in structural brain network organization based on Q-Ball tractography. Already at the first evaluated times, DTI scalar maps revealed significant differences in many regions, suggesting loss of integrity in white and gray matter of spontaneously hypertensive rats when compared to normotensive control rats. In addition, graph theory analysis of the structural brain network demonstrated a significant decrease of hierarchical modularity, global and local efficacy, with predictive value as shown by regional three-fold cross validation study. Moreover, these decreases were significantly correlated with the behavioral performance deficits observed at subsequent time points, suggesting that the diffusion weighted imaging and connectivity studies can unravel neuroimaging alterations even overt signs of cognitive impairment become apparent. PMID:25100993

  8. Testing an earthquake prediction algorithm

    USGS Publications Warehouse

    Kossobokov, V.G.; Healy, J.H.; Dewey, J.W.

    1997-01-01

    A test to evaluate earthquake prediction algorithms is being applied to a Russian algorithm known as M8. The M8 algorithm makes intermediate term predictions for earthquakes to occur in a large circle, based on integral counts of transient seismicity in the circle. In a retroactive prediction for the period January 1, 1985 to July 1, 1991 the algorithm as configured for the forward test would have predicted eight of ten strong earthquakes in the test area. A null hypothesis, based on random assignment of predictions, predicts eight earthquakes in 2.87% of the trials. The forward test began July 1, 1991 and will run through December 31, 1997. As of July 1, 1995, the algorithm had forward predicted five out of nine earthquakes in the test area, which success ratio would have been achieved in 53% of random trials with the null hypothesis.

  9. Liver Function Tests

    MedlinePlus

    ... food, store energy, and remove poisons. Liver function tests are blood tests that check to see how well your liver ... hepatitis and cirrhosis. You may have liver function tests as part of a regular checkup. Or you ...

  10. Predicting Changes in Macrophyte Community Structure from Functional Traits in a Freshwater Lake: A Test of Maximum Entropy Model

    PubMed Central

    Fu, Hui; Zhong, Jiayou; Yuan, Guixiang; Guo, Chunjing; Lou, Qian; Zhang, Wei; Xu, Jun; Ni, Leyi; Xie, Ping; Cao, Te

    2015-01-01

    Trait-based approaches have been widely applied to investigate how community dynamics respond to environmental gradients. In this study, we applied a series of maximum entropy (maxent) models incorporating functional traits to unravel the processes governing macrophyte community structure along water depth gradient in a freshwater lake. We sampled 42 plots and 1513 individual plants, and measured 16 functional traits and abundance of 17 macrophyte species. Study results showed that maxent model can be highly robust (99.8%) in predicting the species relative abundance of macrophytes with observed community-weighted mean (CWM) traits as the constraints, while relative low (about 30%) with CWM traits fitted from water depth gradient as the constraints. The measured traits showed notably distinct importance in predicting species abundances, with lowest for perennial growth form and highest for leaf dry mass content. For tuber and leaf nitrogen content, there were significant shifts in their effects on species relative abundance from positive in shallow water to negative in deep water. This result suggests that macrophyte species with tuber organ and greater leaf nitrogen content would become more abundant in shallow water, but would become less abundant in deep water. Our study highlights how functional traits distributed across gradients provide a robust path towards predictive community ecology. PMID:26167856

  11. Predicting Changes in Macrophyte Community Structure from Functional Traits in a Freshwater Lake: A Test of Maximum Entropy Model.

    PubMed

    Fu, Hui; Zhong, Jiayou; Yuan, Guixiang; Guo, Chunjing; Lou, Qian; Zhang, Wei; Xu, Jun; Ni, Leyi; Xie, Ping; Cao, Te

    2015-01-01

    Trait-based approaches have been widely applied to investigate how community dynamics respond to environmental gradients. In this study, we applied a series of maximum entropy (maxent) models incorporating functional traits to unravel the processes governing macrophyte community structure along water depth gradient in a freshwater lake. We sampled 42 plots and 1513 individual plants, and measured 16 functional traits and abundance of 17 macrophyte species. Study results showed that maxent model can be highly robust (99.8%) in predicting the species relative abundance of macrophytes with observed community-weighted mean (CWM) traits as the constraints, while relative low (about 30%) with CWM traits fitted from water depth gradient as the constraints. The measured traits showed notably distinct importance in predicting species abundances, with lowest for perennial growth form and highest for leaf dry mass content. For tuber and leaf nitrogen content, there were significant shifts in their effects on species relative abundance from positive in shallow water to negative in deep water. This result suggests that macrophyte species with tuber organ and greater leaf nitrogen content would become more abundant in shallow water, but would become less abundant in deep water. Our study highlights how functional traits distributed across gradients provide a robust path towards predictive community ecology.

  12. Benchmarking density functional theory predictions of framework structures and properties in a chemically diverse test set of metal-organic frameworks

    DOE PAGESBeta

    Nazarian, Dalar; Ganesh, P.; Sholl, David S.

    2015-09-30

    We compiled a test set of chemically and topologically diverse Metal–Organic Frameworks (MOFs) with high accuracy experimentally derived crystallographic structure data. The test set was used to benchmark the performance of Density Functional Theory (DFT) functionals (M06L, PBE, PW91, PBE-D2, PBE-D3, and vdW-DF2) for predicting lattice parameters, unit cell volume, bonded parameters and pore descriptors. On average PBE-D2, PBE-D3, and vdW-DF2 predict more accurate structures, but all functionals predicted pore diameters within 0.5 Å of the experimental diameter for every MOF in the test set. The test set was also used to assess the variance in performance of DFT functionalsmore » for elastic properties and atomic partial charges. The DFT predicted elastic properties such as minimum shear modulus and Young's modulus can differ by an average of 3 and 9 GPa for rigid MOFs such as those in the test set. Moreover, we calculated the partial charges by vdW-DF2 deviate the most from other functionals while there is no significant difference between the partial charges calculated by M06L, PBE, PW91, PBE-D2 and PBE-D3 for the MOFs in the test set. We find that while there are differences in the magnitude of the properties predicted by the various functionals, these discrepancies are small compared to the accuracy necessary for most practical applications.« less

  13. A prevalidation study on the in vitro skin irritation function test (SIFT) for prediction of acute skin irritation in vivo: results and evaluation of ECVAM Phase III.

    PubMed

    Heylings, J R; Diot, S; Esdaile, D J; Fasano, W J; Manning, L A; Owen, H M

    2003-04-01

    A prevalidation study sponsored by the European Centre for the Validation of Alternative Methods (ECVAM) on in vitro tests for acute skin irritation is aimed at identifying non-animal tests capable of discriminating irritants (I) from non-irritants (NI), as defined according to European Union and OECD. This paper reports on Phase III for one of the methods, the skin integrity function test (SIFT), assessing the protocol performance of the SIFT, in terms of reproducibility and predictive ability, in three laboratories. The barrier function properties of excised mouse skin were determined using a set of 20 coded chemicals (10 I, 10 NI), using the endpoints of trans-epidermal water loss (TEWL) and electrical resistance (ER). The basis of the SIFT prediction model is if the ratios of the pre- and post-application values for either TEWL or ER are greater than five-fold, then the test chemical is deemed irritant (I). If the ratio of both parameters is less than five-fold then the chemical is deemed non-irritant (NI). Analysis of variance (ANOVA) indicated that the intra-lab reproducibility was acceptable but that the inter-lab reproducibility was not. Overall, the SIFT test under-predicted the irritancy of the test chemicals chosen for Phase III with an overall accuracy of only 55%. The sensitivity value (ability to correctly predict I) was only 30%. The specificity (ability to predict NI) of the test was better at 80%. A retrospective examination of the SIFT results was undertaken using Student's t-test and a significance level of P<0.05 to predict an irritant based on changes in the TEWL ratio values. This improved the predictivity of the SIFT test, giving a specificity of 60%, a sensitivity of 80% and an overall accuracy of 70%. Appropriate modifications to the prediction model have now been made and the SIFT will be re-examined in a new validation exercise to investigate the potential of this non-animal method to predict acute skin irritation potential. PMID:12650665

  14. Functional Task Test (FTT)

    NASA Technical Reports Server (NTRS)

    Bloomberg, Jacob J.; Mulavara, Ajitkumar; Peters, Brian T.; Rescheke, Millard F.; Wood, Scott; Lawrence, Emily; Koffman, Igor; Ploutz-Snyder, Lori; Spiering, Barry A.; Feeback, Daniel L.; Platts, Steven H.; Stenger, Michael B.; Lee, Stuart M.C.; Arzeno, Natalia; Feiveson, Alan H.; Ryder, Jeffrey; Garcia, Yamil; Guilliams, Mark E.

    2009-01-01

    This slide presentation reviews the Functional Task Test (FTT), an interdisciplinary testing regimen that has been developed to evaluate astronaut postflight functional performance and related physiological changes. The objectives of the project are: (1) to develop a set of functional tasks that represent critical mission tasks for the Constellation Program, (2) determine the ability to perform these tasks after space flight, (3) Identify the key physiological factors that contribute to functional decrements and (4) Use this information to develop targeted countermeasures.

  15. Pulmonary Function Tests

    PubMed Central

    Ranu, Harpreet; Wilde, Michael; Madden, Brendan

    2011-01-01

    Pulmonary function tests are valuable investigations in the management of patients with suspected or previously diagnosed respiratory disease. They aid diagnosis, help monitor response to treatment and can guide decisions regarding further treatment and intervention. The interpretation of pulmonary functions tests requires knowledge of respiratory physiology. In this review we describe investigations routinely used and discuss their clinical implications. PMID:22347750

  16. Platelet Function Tests

    MedlinePlus

    ... of the clotting process in the body ( in vivo ). A person with normal platelet function test results may still experience excessive bleeding or inappropriate clotting during and after a surgery. Most samples for platelet function testing are only stable for a very short period ...

  17. Predicting communities from functional traits.

    PubMed

    Cadotte, Marc W; Arnillas, Carlos A; Livingstone, Stuart W; Yasui, Simone-Louise E

    2015-09-01

    Species traits influence where species live and how they interact. While there have been many advances in describing the functional composition and diversity of communities, only recently do researchers have the ability to predict community composition and diversity. This predictive ability can offer fundamental insights into ecosystem resilience and restoration. PMID:26190136

  18. Sperm function test

    PubMed Central

    Talwar, Pankaj; Hayatnagarkar, Suryakant

    2015-01-01

    With absolute normal semen analysis parameters it may not be necessary to shift to specialized tests early but in cases with borderline parameters or with history of fertilization failure in past it becomes necessary to do a battery of tests to evaluate different parameters of spermatozoa. Various sperm function tests are proposed and endorsed by different researchers in addition to the routine evaluation of fertility. These tests detect function of a certain part of spermatozoon and give insight on the events in fertilization of the oocyte. The sperms need to get nutrition from the seminal plasma in the form of fructose and citrate (this can be assessed by fructose qualitative and quantitative estimation, citrate estimation). They should be protected from the bad effects of pus cells and reactive oxygen species (ROS) (leukocyte detection test, ROS estimation). Their number should be in sufficient in terms of (count), structure normal to be able to fertilize eggs (semen morphology). Sperms should have intact and functioning membrane to survive harsh environment of vagina and uterine fluids (vitality and hypo-osmotic swelling test), should have good mitochondrial function to be able to provide energy (mitochondrial activity index test). They should also have satisfactory acrosome function to be able to burrow a hole in zona pellucida (acrosome intactness test, zona penetration test). Finally, they should have properly packed DNA in the nucleus to be able to transfer the male genes (nuclear chromatic decondensation test) to the oocyte during fertilization. PMID:26157295

  19. Pulmonary function tests

    MedlinePlus

    ... measured to estimate the lung volume. To measure diffusion capacity , you breathe a harmless gas, called a ... on your report after pulmonary function tests include: Diffusion capacity to carbon monoxide (DLCO) Expiratory reserve volume ( ...

  20. Pulmonary function tests (maximum inspiratory pressure, maximum expiratory pressure, vital capacity, forced vital capacity) predict ventilator use in late-onset Pompe disease.

    PubMed

    Johnson, Erin M; Roberts, Mark; Mozaffar, Tahseen; Young, Peter; Quartel, Adrian; Berger, Kenneth I

    2016-02-01

    In patients with Late-Onset Pompe Disease (LOPD), progressive respiratory muscle involvement leads to reduced pulmonary function, with respiratory failure the most common cause of mortality. Early disease manifestations include sleep-disordered breathing, which can be treated with non-invasive ventilation; however, progressive diurnal deficits can require invasive ventilation. To determine if pulmonary function tests (PFTs) predict the thresholds for ventilation and wheelchair use, a systematic literature review identified cross-sectional clinical patient data (N = 174) that was classified into ventilation and wheelchair cohorts. PFTs included maximum inspiratory pressure (MIP), maximum expiratory pressure (MEP), forced vital capacity (FVC), and vital capacity (VC), with vital capacities measured in the upright (-U) and supine (-S) positions. Receiver operating characteristic (ROC) curves were used to calculate cut-points (CP) and area under the curve (AUC). For all ventilation and mobility thresholds tested, ROC analyses demonstrated AUC values from 86-89% for MIP, 72-96% for MEP, and 74-96% for all vital capacity metrics. Thus, PFTs are useful in predicting the thresholds for nighttime ventilation, daytime ventilation, and wheelchair use, with MIP and VC-U having both high AUC values and consistency. The PFT mobility CPs were low (MIP CP = 0.9 kPa, MEP, CP = 2.6 kPa, VC-U CP = 19% predicted), suggesting an endurance component associated with wheelchair use.

  1. Pulmonary function tests (maximum inspiratory pressure, maximum expiratory pressure, vital capacity, forced vital capacity) predict ventilator use in late-onset Pompe disease.

    PubMed

    Johnson, Erin M; Roberts, Mark; Mozaffar, Tahseen; Young, Peter; Quartel, Adrian; Berger, Kenneth I

    2016-02-01

    In patients with Late-Onset Pompe Disease (LOPD), progressive respiratory muscle involvement leads to reduced pulmonary function, with respiratory failure the most common cause of mortality. Early disease manifestations include sleep-disordered breathing, which can be treated with non-invasive ventilation; however, progressive diurnal deficits can require invasive ventilation. To determine if pulmonary function tests (PFTs) predict the thresholds for ventilation and wheelchair use, a systematic literature review identified cross-sectional clinical patient data (N = 174) that was classified into ventilation and wheelchair cohorts. PFTs included maximum inspiratory pressure (MIP), maximum expiratory pressure (MEP), forced vital capacity (FVC), and vital capacity (VC), with vital capacities measured in the upright (-U) and supine (-S) positions. Receiver operating characteristic (ROC) curves were used to calculate cut-points (CP) and area under the curve (AUC). For all ventilation and mobility thresholds tested, ROC analyses demonstrated AUC values from 86-89% for MIP, 72-96% for MEP, and 74-96% for all vital capacity metrics. Thus, PFTs are useful in predicting the thresholds for nighttime ventilation, daytime ventilation, and wheelchair use, with MIP and VC-U having both high AUC values and consistency. The PFT mobility CPs were low (MIP CP = 0.9 kPa, MEP, CP = 2.6 kPa, VC-U CP = 19% predicted), suggesting an endurance component associated with wheelchair use. PMID:26794303

  2. The role of point-of-care platelet function testing in predicting postoperative bleeding following cardiac surgery: a systematic review and meta-analysis.

    PubMed

    Corredor, C; Wasowicz, M; Karkouti, K; Sharma, V

    2015-06-01

    This systematic review and meta-analysis appraises the utility of point-of-care platelet function tests for predicting blood loss and transfusion requirements in cardiac surgical patients, and analyses whether their use within a transfusion management algorithm is associated with improved patient outcomes. We included 30 observational studies incorporating 3044 patients in the qualitative assessment, and nine randomised controlled trials including 1057 patients in the meta-analysis. Platelet function tests demonstrated significant variability in their ability to predict blood loss and transfusion requirements. Their use within a blood transfusion algorithm demonstrated a reduction in blood loss at longest follow-up (mean difference -102.9 ml (95% CI -149.9 to -56.1 ml), p < 0.001), and transfusion of packed red cells (RR 0.86 (95% CI 0.78-0.94), p = 0.001) and fresh frozen plasma (RR 0.42 (95% CI 0.30-0.59), p < 0.001). Viscoelastic methods used in combination with other platelet function tests achieved greater reduction in blood loss (mean difference -111.8 ml (95% CI -174.9 to -49.1 ml), p = 0.0005) compared with their use alone (mean difference -90.6 ml (95% CI 166.1-15.0 ml), p = 0.02). We conclude that incorporation of point-of-care platelet function tests into transfusion management algorithms is associated with a reduction in blood loss and transfusion requirements in cardiac surgery patients. PMID:25916344

  3. Expansion tube test time predictions

    NASA Technical Reports Server (NTRS)

    Gourlay, Christopher M.

    1988-01-01

    The interaction of an interface between two gases and strong expansion is investigated and the effect on flow in an expansion tube is examined. Two mechanisms for the unsteady Pitot-pressure fluctuations found in the test section of an expansion tube are proposed. The first mechanism depends on the Rayleigh-Taylor instability of the driver-test gas interface in the presence of a strong expansion. The second mechanism depends on the reflection of the strong expansion from the interface. Predictions compare favorably with experimental results. The theory is expected to be independent of the absolute values of the initial expansion tube filling pressures.

  4. Modern vestibular function testing.

    PubMed Central

    Baloh, R W; Furman, J M

    1989-01-01

    Current tests of vestibular function concentrate on the horizontal semicircular canal-ocular reflex because it is the easiest reflex to stimulate (calorically and rotationally) and record (using electro-oculography). Tests of the other vestibulo-ocular reflexes (vertical semicircular canal and otolith) and of the vestibulospinal reflexes have yet to be shown useful in the clinical setting. Digital video recording of eye movements and vestibular-evoked responses are promising new technologies that may affect clinical testing in the near future. PMID:2660408

  5. Predictive testing of environmental carcinogens

    SciTech Connect

    Dickson, J.G.

    1982-01-01

    Two research approaches are presented which address different aspects of predictive testing for environmental carcinogens. In Part I, a well-known microbial assay is used to determine the presence of carcinogens in an environmental sample of suspected hazard. In Part II, a single chemical carcinogen is chosen to demonstrate the utility of three-phase microcosms for prediction of transport and transformations pathways in a reservoir ecosystem. The Ames/Salmonella mutagenicity assay was used to screen processed oil shale extracts for potentially carcinogenic chemicals. Positive mutagenic activity was detected in organic solvent extracts of all four spent shales tested. Problems which might limit application of the Ames assay were explored. The results of assays of one-to-one mixtures of two mutagens which exhibited different dose response curves when assayed separately indicated the response to the mixture was nonadditive. Furthermore, the response to the mixture was determined to be statistically indistinguishable (chi-square analysis) from the dose response curve of one of the mutagens in the majority of cases. This masking effect was found to persist for one strong mutagen (benzo(a)pyrene) even when it composed only 10% of the mixture. The effect of various non-toxic solvents on the mutagenic response of certain mutagens was also determined. Three-phase microcosms were used to study the aquatic fate and effect of a polycyclic aromatic hydrocarbon (PAH), benz(a)antracene.

  6. Predictive Control of Speededness in Adaptive Testing

    ERIC Educational Resources Information Center

    van der Linden, Wim J.

    2009-01-01

    An adaptive testing method is presented that controls the speededness of a test using predictions of the test takers' response times on the candidate items in the pool. Two different types of predictions are investigated: posterior predictions given the actual response times on the items already administered and posterior predictions that use the…

  7. Myeloperoxidase levels predict executive function.

    PubMed

    Haslacher, H; Perkmann, T; Lukas, I; Barth, A; Ponocny-Seliger, E; Michlmayr, M; Scheichenberger, V; Wagner, O; Winker, R

    2012-12-01

    The main purpose of the study was to investigate whether baseline myeloperoxidase (MPO) levels are associated with executive cognitive function in individuals with high physical activity. Baseline serum MPO levels of 56 elderly marathon runners and 58 controls were assessed by ELISA. Standardized tests were applied to survey domain-specific cognitive functions. Changes in brain morphology were visualized by magnetic resonance imaging (MRI). High baseline serum MPO levels correlated with worse outcome in tests assessing executive cognitive function in athletes but not in the control group (NAI maze test p<0.05, Trail Making Test ratio p<0.01). In control participants, subcortical white matter hyperintensities were associated with higher scores on the Geriatric Depression Scale (p<0.05), whereas athletes seem to be protected from this effect. During strenuous exercising, MPO as well as its educts may be elevated due to increased oxygen intake and excretion of pro-inflammatory mediators inducing host tissue damage via oxidative stress. This outweighs the potential benefits of physical activity on cognitive function.

  8. Myeloperoxidase levels predict executive function.

    PubMed

    Haslacher, H; Perkmann, T; Lukas, I; Barth, A; Ponocny-Seliger, E; Michlmayr, M; Scheichenberger, V; Wagner, O; Winker, R

    2012-12-01

    The main purpose of the study was to investigate whether baseline myeloperoxidase (MPO) levels are associated with executive cognitive function in individuals with high physical activity. Baseline serum MPO levels of 56 elderly marathon runners and 58 controls were assessed by ELISA. Standardized tests were applied to survey domain-specific cognitive functions. Changes in brain morphology were visualized by magnetic resonance imaging (MRI). High baseline serum MPO levels correlated with worse outcome in tests assessing executive cognitive function in athletes but not in the control group (NAI maze test p<0.05, Trail Making Test ratio p<0.01). In control participants, subcortical white matter hyperintensities were associated with higher scores on the Geriatric Depression Scale (p<0.05), whereas athletes seem to be protected from this effect. During strenuous exercising, MPO as well as its educts may be elevated due to increased oxygen intake and excretion of pro-inflammatory mediators inducing host tissue damage via oxidative stress. This outweighs the potential benefits of physical activity on cognitive function. PMID:22855218

  9. Pediatric Arm Function Test

    PubMed Central

    Uswatte, Gitendra; Taub, Edward; Griffin, Angi; Rowe, Jan; Vogtle, Laura; Barman, Joydip

    2012-01-01

    Objective Although there are several validated upper-extremity measures in young children with cerebral palsy (CP), none primarily assess capacity to carry out actions and tasks with the more-affected arm. To address this need, we developed the Pediatric Arm Function Test (PAFT), which involves behavioral observation of how children use their more-affected arm during structured play in the laboratory or clinic. This paper evaluates the reliability and validity of the PAFT Functional Ability scale. Design In Study 1, 20 children between 2–8 years with a wide range of upper-extremity hemiparesis due to CP completed the PAFT on two occasions separated by three weeks. In Study 2, 41 children between 2–6 years with similar characteristics completed the PAFT and received a grade reflecting severity of more-affected arm motor impairment. Results In Study 1, the PAFT test-retest reliability correlation coefficient was 0.74. In Study 2, convergent validity was supported by a strong, inverse correlation (r = −0.6, p < .001) between PAFT scores and grade of impairment. Conclusions The PAFT Functional Ability scale is a reliable and valid measure of more-affected arm motor capacity in children with CP between 2–6 years. It can be employed to measure upper-extremity neurorehabilitation outcome. PMID:23103486

  10. A Predictive Analysis Approach to Adaptive Testing.

    ERIC Educational Resources Information Center

    Kirisci, Levent; Hsu, Tse-Chi

    The predictive analysis approach to adaptive testing originated in the idea of statistical predictive analysis suggested by J. Aitchison and I.R. Dunsmore (1975). The adaptive testing model proposed is based on parameter-free predictive distribution. Aitchison and Dunsmore define statistical prediction analysis as the use of data obtained from an…

  11. Quantitative assessment of protein function prediction programs.

    PubMed

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-12-21

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate.

  12. Quantitative assessment of protein function prediction programs.

    PubMed

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-01-01

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate. PMID:26782400

  13. Protein function prediction based on data fusion and functional interrelationship.

    PubMed

    Meng, Jun; Wekesa, Jael-Sanyanda; Shi, Guan-Li; Luan, Yu-Shi

    2016-04-01

    One of the challenging tasks of bioinformatics is to predict more accurate and confident protein functions from genomics and proteomics datasets. Computational approaches use a variety of high throughput experimental data, such as protein-protein interaction (PPI), protein sequences and phylogenetic profiles, to predict protein functions. This paper presents a method that uses transductive multi-label learning algorithm by integrating multiple data sources for classification. Multiple proteomics datasets are integrated to make inferences about functions of unknown proteins and use a directed bi-relational graph to assign labels to unannotated proteins. Our method, bi-relational graph based transductive multi-label function annotation (Bi-TMF) uses functional correlation and topological PPI network properties on both the training and testing datasets to predict protein functions through data fusion of the individual kernel result. The main purpose of our proposed method is to enhance the performance of classifier integration for protein function prediction algorithms. Experimental results demonstrate the effectiveness and efficiency of Bi-TMF on multi-sources datasets in yeast, human and mouse benchmarks. Bi-TMF outperforms other recently proposed methods. PMID:26869536

  14. Enzyme function prediction with interpretable models.

    PubMed

    Syed, Umar; Yona, Golan

    2009-01-01

    Enzymes play central roles in metabolic pathways, and the prediction of metabolic pathways in newly sequenced genomes usually starts with the assignment of genes to enzymatic reactions. However, genes with similar catalytic activity are not necessarily similar in sequence, and therefore the traditional sequence similarity-based approach often fails to identify the relevant enzymes, thus hindering efforts to map the metabolome of an organism.Here we study the direct relationship between basic protein properties and their function. Our goal is to develop a new tool for functional prediction (e.g., prediction of Enzyme Commission number), which can be used to complement and support other techniques based on sequence or structure information. In order to define this mapping we collected a set of 453 features and properties that characterize proteins and are believed to be related to structural and functional aspects of proteins. We introduce a mixture model of stochastic decision trees to learn the set of potentially complex relationships between features and function. To study these correlations, trees are created and tested on the Pfam classification of proteins, which is based on sequence, and the EC classification, which is based on enzymatic function. The model is very effective in learning highly diverged protein families or families that are not defined on the basis of sequence. The resulting tree structures highlight the properties that are strongly correlated with structural and functional aspects of protein families, and can be used to suggest a concise definition of a protein family.

  15. Predicting protein functions from PPI networks using functional aggregation.

    PubMed

    Hou, Jingyu; Chi, Xiaoxiao

    2012-11-01

    Predicting protein functions computationally from massive protein-protein interaction (PPI) data generated by high-throughput technology is one of the challenges and fundamental problems in the post-genomic era. Although there have been many approaches developed for computationally predicting protein functions, the mutual correlations among proteins in terms of protein functions have not been thoroughly investigated and incorporated into existing prediction methods, especially in voting based prediction methods. In this paper, we propose an innovative method to predict protein functions from PPI data by aggregating the functional correlations among relevant proteins using the Choquet-Integral in fuzzy theory. This functional aggregation measures the real impact of each relevant protein function on the final prediction results, and reduces the impact of repeated functional information on the prediction. Accordingly, a new protein similarity and a new iterative prediction algorithm are proposed in this paper. The experimental evaluations on real PPI datasets demonstrate the effectiveness of our method.

  16. Thyroid Function Tests.

    ERIC Educational Resources Information Center

    Glover, Irving T.

    1979-01-01

    Describes two tests, T-4 and T-3, for hypothyroid based on the binding of the hormones by proteins. The tests were performed in courses for physicians, clinical chemists, laboratory technicians, and undergraduate science students by the individuals involved and on their own sera. These tests are commercially available in kit form. (GA)

  17. State Test Results Are Predictable

    ERIC Educational Resources Information Center

    Tienken, Christopher H.

    2014-01-01

    Out-of-school, community demographic and family-level variables have an important influence on student achievement as measured by large-scale standardized tests. Studies described here demonstrated that about half of the test score is accounted for by variables outside the control of teachers and school administrators. The results from these…

  18. Parental Education Predicts Corticostriatal Functionality in Adulthood

    PubMed Central

    Manuck, Stephen B.; Sheu, Lei K.; Kuan, Dora C. H.; Votruba-Drzal, Elizabeth; Craig, Anna E.; Hariri, Ahmad R.

    2011-01-01

    Socioeconomic disadvantage experienced in early development predicts ill health in adulthood. However, the neurobiological pathways linking early disadvantage to adult health remain unclear. Lower parental education—a presumptive indicator of early socioeconomic disadvantage—predicts health-impairing adult behaviors, including tobacco and alcohol dependencies. These behaviors depend, in part, on the functionality of corticostriatal brain systems that 1) show developmental plasticity and early vulnerability, 2) process reward-related information, and 3) regulate impulsive decisions and actions. Hence, corticostriatal functionality in adulthood may covary directly with indicators of early socioeconomic disadvantage, particularly lower parental education. Here, we tested the covariation between parental education and corticostriatal activation and connectivity in 76 adults without confounding clinical syndromes. Corticostriatal activation and connectivity were assessed during the processing of stimuli signaling monetary gains (positive feedback [PF]) and losses (negative feedback). After accounting for participants’ own education and other explanatory factors, lower parental education predicted reduced activation in anterior cingulate and dorsomedial prefrontal cortices during PF, along with reduced connectivity between these cortices and orbitofrontal and striatal areas implicated in reward processing and impulse regulation. In speculation, adult alterations in corticostriatal functionality may represent facets of a neurobiological endophenotype linked to socioeconomic conditions of early development. PMID:20810623

  19. Liver function tests

    MedlinePlus

    ... laboratory results. In: McPherson RA, Pincus MR, eds. Henry's Clinical Diagnosis and Management by Laboratory Methods . 22nd ... liver function. In: McPherson RA, Pincus MR, eds. Henry's Clinical Diagnosis and Management by Laboratory Methods . 22nd ...

  20. Kidney function tests

    MedlinePlus

    Oh MS. Evaluation of renal function, water, electrolytes and acid-base balance. In: McPherson RA, Pincus MR, eds. Henry's Clinical Diagnosis and Management by Laboratory Methods . 22nd ed. Philadelphia, PA: Elsevier Saunders; ...

  1. Pulmonary Function Tests

    MedlinePlus

    ... enters your body. The most common PFT’s are spirometry (spy-RAH-me-tree), diffusion studies and body ... on the day of your test. What is spirometry? Spirometry is one of the most commonly ordered ...

  2. Thyroid function tests

    MedlinePlus

    ... Larsen PR, Kronenberg HM, eds. Williams Textbook of Endocrinology . 13th ed. Philadelphia, PA: Elsevier Saunders; 2016:chap ... testing. In: Jameson JL, De Groot LJ, eds. Endocrinology: Adult and Pediatric . 7th ed. Philadelphia, PA: Elsevier ...

  3. Pulmonary Function Testing in Children

    MedlinePlus

    ... are s pirometry and airway resistance tests . What is spirometry? Spirometry is the most common lung function test done. ... follow very specific instructions. Most children can do spirometry by age 6, though some preschoolers are able ...

  4. PREDICTION OF NONLINEAR SPATIAL FUNCTIONALS. (R827257)

    EPA Science Inventory

    Spatial statistical methodology can be useful in the arena of environmental regulation. Some regulatory questions may be addressed by predicting linear functionals of the underlying signal, but other questions may require the prediction of nonlinear functionals of the signal. ...

  5. Protein Function Prediction: Problems and Pitfalls.

    PubMed

    Pearson, William R

    2015-01-01

    The characterization of new genomes based on their protein sets has been revolutionized by new sequencing technologies, but biologists seeking to exploit new sequence information are often frustrated by the challenges associated with accurately assigning biological functions to newly identified proteins. Here, we highlight some of the challenges in functional inference from sequence similarity. Investigators can improve the accuracy of function prediction by (1) being conservative about the evolutionary distance to a protein of known function; (2) considering the ambiguous meaning of "functional similarity," and (3) being aware of the limitations of annotations in functional databases. Protein function prediction does not offer "one-size-fits-all" solutions. Prediction strategies work better when the idiosyncrasies of function and functional annotation are better understood. PMID:26334923

  6. Protein Function Prediction: Problems and Pitfalls.

    PubMed

    Pearson, William R

    2015-01-01

    The characterization of new genomes based on their protein sets has been revolutionized by new sequencing technologies, but biologists seeking to exploit new sequence information are often frustrated by the challenges associated with accurately assigning biological functions to newly identified proteins. Here, we highlight some of the challenges in functional inference from sequence similarity. Investigators can improve the accuracy of function prediction by (1) being conservative about the evolutionary distance to a protein of known function; (2) considering the ambiguous meaning of "functional similarity," and (3) being aware of the limitations of annotations in functional databases. Protein function prediction does not offer "one-size-fits-all" solutions. Prediction strategies work better when the idiosyncrasies of function and functional annotation are better understood.

  7. Hearing Test May Predict Autism Risk Sooner

    MedlinePlus

    ... news/fullstory_160181.html Hearing Test May Predict Autism Risk Sooner: Study Researchers identify inner-ear problem ... may help identify young children at risk for autism before they're old enough to speak, a ...

  8. Differential Prediction Generalization in College Admissions Testing

    ERIC Educational Resources Information Center

    Aguinis, Herman; Culpepper, Steven A.; Pierce, Charles A.

    2016-01-01

    We introduce the concept of "differential prediction generalization" in the context of college admissions testing. Specifically, we assess the extent to which predicted first-year college grade point average (GPA) based on high-school grade point average (HSGPA) and SAT scores depends on a student's ethnicity and gender and whether this…

  9. Tests of gastric neuromuscular function.

    PubMed

    Parkman, Henry P; Jones, Michael P

    2009-05-01

    Tests of gastric neuromuscular function are used to evaluate patients with symptoms referable to the upper digestive tract. These symptoms can be associated with alterations in the rates of gastric emptying, impaired accommodation, heightened gastric sensation, or alterations in gastric myoelectrical function and contractility. Management of gastric neuromuscular disorders requires an understanding of pathophysiology and treatment options as well as the appropriate use and interpretation of diagnostic tests. These tests include measures of gastric emptying; contractility; electrical activity; regional gastric motility of the fundus, antrum, and pylorus; and tests of sensation and compliance. Tests are also being developed to improve our understanding of the afferent sensory pathways from the stomach to the central nervous system that mediate gastric sensation in health and gastric disorders. This article reviews tests of gastric function and provides a basic description of the tests, the methodologies behind them, descriptions of the physiology that they assess, and their clinical utility. PMID:19293005

  10. Integrating multiple networks for protein function prediction

    PubMed Central

    2015-01-01

    Background High throughput techniques produce multiple functional association networks. Integrating these networks can enhance the accuracy of protein function prediction. Many algorithms have been introduced to generate a composite network, which is obtained as a weighted sum of individual networks. The weight assigned to an individual network reflects its benefit towards the protein functional annotation inference. A classifier is then trained on the composite network for predicting protein functions. However, since these techniques model the optimization of the composite network and the prediction tasks as separate objectives, the resulting composite network is not necessarily optimal for the follow-up protein function prediction. Results We address this issue by modeling the optimization of the composite network and the prediction problems within a unified objective function. In particular, we use a kernel target alignment technique and the loss function of a network based classifier to jointly adjust the weights assigned to the individual networks. We show that the proposed method, called MNet, can achieve a performance that is superior (with respect to different evaluation criteria) to related techniques using the multiple networks of four example species (yeast, human, mouse, and fly) annotated with thousands (or hundreds) of GO terms. Conclusion MNet can effectively integrate multiple networks for protein function prediction and is robust to the input parameters. Supplementary data is available at https://sites.google.com/site/guoxian85/home/mnet. The Matlab code of MNet is available upon request. PMID:25707434

  11. Gesture Performance in Schizophrenia Predicts Functional Outcome After 6 Months

    PubMed Central

    Walther, Sebastian; Eisenhardt, Sarah; Bohlhalter, Stephan; Vanbellingen, Tim; Müri, René; Strik, Werner; Stegmayer, Katharina

    2016-01-01

    The functional outcome of schizophrenia is heterogeneous and markers of the course are missing. Functional outcome is associated with social cognition and negative symptoms. Gesture performance and nonverbal social perception are critically impaired in schizophrenia. Here, we tested whether gesture performance or nonverbal social perception could predict functional outcome and the ability to adequately perform relevant skills of everyday function (functional capacity) after 6 months. In a naturalistic longitudinal study, 28 patients with schizophrenia completed tests of nonverbal communication at baseline and follow-up. In addition, functional outcome, social and occupational functioning, as well as functional capacity at follow-up were assessed. Gesture performance and nonverbal social perception at baseline predicted negative symptoms, functional outcome, and functional capacity at 6-month follow-up. Gesture performance predicted functional outcome beyond the baseline measure of functioning. Patients with gesture deficits at baseline had stable negative symptoms and experienced a decline in social functioning. While in patients without gesture deficits, negative symptom severity decreased and social functioning remained stable. Thus, a simple test of hand gesture performance at baseline may indicate favorable outcomes in short-term follow-up. The results further support the importance of nonverbal communication skills in subjects with schizophrenia. PMID:27566843

  12. Hierarchical Ensemble Methods for Protein Function Prediction

    PubMed Central

    2014-01-01

    Protein function prediction is a complex multiclass multilabel classification problem, characterized by multiple issues such as the incompleteness of the available annotations, the integration of multiple sources of high dimensional biomolecular data, the unbalance of several functional classes, and the difficulty of univocally determining negative examples. Moreover, the hierarchical relationships between functional classes that characterize both the Gene Ontology and FunCat taxonomies motivate the development of hierarchy-aware prediction methods that showed significantly better performances than hierarchical-unaware “flat” prediction methods. In this paper, we provide a comprehensive review of hierarchical methods for protein function prediction based on ensembles of learning machines. According to this general approach, a separate learning machine is trained to learn a specific functional term and then the resulting predictions are assembled in a “consensus” ensemble decision, taking into account the hierarchical relationships between classes. The main hierarchical ensemble methods proposed in the literature are discussed in the context of existing computational methods for protein function prediction, highlighting their characteristics, advantages, and limitations. Open problems of this exciting research area of computational biology are finally considered, outlining novel perspectives for future research. PMID:25937954

  13. Predicting Road Test Performance in Drivers With Stroke

    PubMed Central

    Barco, Peggy P.; Wallendorf, Michael J.; Snellgrove, Carol A.; Ott, Brian R.

    2014-01-01

    OBJECTIVE. The aim of this study was to develop a brief screening battery to predict the on-road performance of drivers who had experienced a stroke. METHOD. We examined 72 people with stroke referred by community physicians to an academic rehabilitation center. The outcome variable was pass or fail on the modified Washington University Road Test. Predictor measures were tests of visual, motor, and cognitive functioning. RESULTS. The best predictive model for failure on the road test included Trail Making Test Part A and the Snellgrove Maze Task®. CONCLUSION. A screening battery that can be performed in less than 5 min was able to assist in the prediction of road test performance in a sample of drivers with stroke. A probability of failure calculator may be useful for clinicians in their decision to refer clients with stroke for a comprehensive driving evaluation. PMID:24581409

  14. Biological cluster evaluation for gene function prediction.

    PubMed

    Klie, Sebastian; Nikoloski, Zoran; Selbig, Joachim

    2014-06-01

    Recent advances in high-throughput omics techniques render it possible to decode the function of genes by using the "guilt-by-association" principle on biologically meaningful clusters of gene expression data. However, the existing frameworks for biological evaluation of gene clusters are hindered by two bottleneck issues: (1) the choice for the number of clusters, and (2) the external measures which do not take in consideration the structure of the analyzed data and the ontology of the existing biological knowledge. Here, we address the identified bottlenecks by developing a novel framework that allows not only for biological evaluation of gene expression clusters based on existing structured knowledge, but also for prediction of putative gene functions. The proposed framework facilitates propagation of statistical significance at each of the following steps: (1) estimating the number of clusters, (2) evaluating the clusters in terms of novel external structural measures, (3) selecting an optimal clustering algorithm, and (4) predicting gene functions. The framework also includes a method for evaluation of gene clusters based on the structure of the employed ontology. Moreover, our method for obtaining a probabilistic range for the number of clusters is demonstrated valid on synthetic data and available gene expression profiles from Saccharomyces cerevisiae. Finally, we propose a network-based approach for gene function prediction which relies on the clustering of optimal score and the employed ontology. Our approach effectively predicts gene function on the Saccharomyces cerevisiae data set and is also employed to obtain putative gene functions for an Arabidopsis thaliana data set.

  15. Year 2 Report: Protein Function Prediction Platform

    SciTech Connect

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  16. Springback Prediction on Slit-Ring Test

    NASA Astrophysics Data System (ADS)

    Chen, Xiao Ming; Shi, Ming F.; Ren, Feng; Xia, Z. Cedric

    2005-08-01

    Advanced high strength steels (AHSS) are increasingly being used in the automotive industry to reduce vehicle weight while improving vehicle crash performance. One of the concerns in manufacturing is springback control after stamping. Although computer simulation technologies have been successfully applied to predict stamping formability, they still face major challenges in springback prediction, particularly for AHSS. Springback analysis is very complicated and involves large deformation problems in the forming stage and mechanical multiplying effect during the elastic recovery after releasing a part from the die. Therefore, the predictions are very sensitive to the simulation parameters used. It is very critical in springback simulation to choose an appropriate material model, element formulation and contact algorithm. In this study, a springback benchmark test, the slit ring cup, is used in the springback simulation with commercially available finite element analysis (FEA) software, LS-DYNA. The sensitivity of seven simulation variables on springback predictions was investigated, and a set of parameters with stable simulation results was identified. Final simulations using the selected set of parameters were conducted on six different materials including two AHSS steels, two conventional high strength steels, one mild steel and an aluminum alloy. The simulation results are compared with experimental measurements for all six materials and a favorable result is achieved. Simulation errors as compared against test results falls within 10%.

  17. Testing a MOND Prediction in NGC3923

    NASA Astrophysics Data System (ADS)

    Miller, Bryan W.; McGaugh, Stacy S.; Mihos, Chris

    2015-01-01

    We report on a test of MOND using the shell system of the elliptical galaxy NGC3923. NGC3923 has 27 known stellar shells due to the disruption of a galaxy that merged with it. Bilek et al. (2014) used MOND to reproduce locations of the existing shells and predicted an additional, lower-surface-brightness shell at a larger projected radius. This is a clean and important test of MOND. We have imaged a field at the predicted edge of the shell as well as a control field at the location of the known Shell 1N/a using the GMOS-S imaging spectrograph at Gemini South. The known Shell 1N/a is clearly detected. No obvious structures are detected at the location of the predicted shell down to a surface brightness of r ~ 28 mag/sq. arc sec. Ongoing work will quantify the detection limits and look for structures at lower surface brightnesses. Implications will be discussed.

  18. GALACSI integration and functional tests

    NASA Astrophysics Data System (ADS)

    La Penna, P.; Ströbele, S.; Aller Carpentier, E.; Argomedo, J.; Arsenault, R.; Conzelmann, R. D.; Delabre, B.; Donaldson, R.; Duchateau, M.; Fedrigo, E.; Gago, F.; Hubin, N.; Quentin, J.; Jolley, P.; Kiekebusch, M.; Kirchbauer, J. P.; Klein, B.; Kolb, J.; Kuntschner, H.; Le Louarn, M.; Lizon, J. L.; Madec, P.-.; Manescau, A.; Mehrgan, L.; Sedghi, B.; Suarez Valles, M.; Soenke, C.; Tordo, S.; Vernet, J.; Zampieri, S.

    2014-07-01

    GALACSI is the Adaptive Optics (AO) modules of the ESO Adaptive Optics Facility (AOF) that will correct the wavefront delivered to the MUSE Integral Field Spectrograph. It will sense with four 40×40 subapertures Shack-Hartmann wavefront sensors the AOF 4 Laser Guide Stars (LGS), acting on the 1170 voice-coils actuators of the Deformable Secondary Mirror (DSM). GALACSI has two operating modes: in Wide Field Mode (WFM), with the four LGS at 64" off axis, the collected energy in a 0.2"×0.2" pixel will be enhanced by a factor 2 at 750 nm over a Field of View (FoV) of 1'×1' using the Ground Layer AO (GLAO) technique. The other mode, the Narrow Field Mode (NFM), provides an enhanced wavefront correction (Strehl Ratio (SR) of 5% (goal 10%) at 650 nm) but in a smaller FoV (7.5"×7.5"), using Laser Tomography AO (LTAO), with the 4 LGS located closer, at 10" off axis. Before being shipped to Paranal, GALACSI will be first integrated and fully tested in stand-alone, and then moved to a dedicated AOF facility to be tested with the DSM in Europe. At present the module is fully assembled, its main functionalities have been implemented and verified, and AO system tests with the DSM are starting. We present here the main system features and the results of the internal functional tests of GALACSI.

  19. Adaptive bandwidth measurements of importance functions for speech intelligibility prediction

    PubMed Central

    Whitmal, Nathaniel A.; DeRoy, Kristina

    2011-01-01

    The Articulation Index (AI) and Speech Intelligibility Index (SII) predict intelligibility scores from measurements of speech and hearing parameters. One component in the prediction is the “importance function,” a weighting function that characterizes contributions of particular spectral regions of speech to speech intelligibility. Previous work with SII predictions for hearing-impaired subjects suggests that prediction accuracy might improve if importance functions for individual subjects were available. Unfortunately, previous importance function measurements have required extensive intelligibility testing with groups of subjects, using speech processed by various fixed-bandwidth low-pass and high-pass filters. A more efficient approach appropriate to individual subjects is desired. The purpose of this study was to evaluate the feasibility of measuring importance functions for individual subjects with adaptive-bandwidth filters. In two experiments, ten subjects with normal-hearing listened to vowel-consonant-vowel (VCV) nonsense words processed by low-pass and high-pass filters whose bandwidths were varied adaptively to produce specified performance levels in accordance with the transformed up-down rules of Levitt [(1971). J. Acoust. Soc. Am. 49, 467–477]. Local linear psychometric functions were fit to resulting data and used to generate an importance function for VCV words. Results indicate that the adaptive method is reliable and efficient, and produces importance function data consistent with that of the corresponding AI/SII importance function. PMID:22225057

  20. Predicting Protein Function Using Multiple Kernels.

    PubMed

    Yu, Guoxian; Rangwala, Huzefa; Domeniconi, Carlotta; Zhang, Guoji; Zhang, Zili

    2015-01-01

    High-throughput experimental techniques provide a wide variety of heterogeneous proteomic data sources. To exploit the information spread across multiple sources for protein function prediction, these data sources are transformed into kernels and then integrated into a composite kernel. Several methods first optimize the weights on these kernels to produce a composite kernel, and then train a classifier on the composite kernel. As such, these approaches result in an optimal composite kernel, but not necessarily in an optimal classifier. On the other hand, some approaches optimize the loss of binary classifiers and learn weights for the different kernels iteratively. For multi-class or multi-label data, these methods have to solve the problem of optimizing weights on these kernels for each of the labels, which are computationally expensive and ignore the correlation among labels. In this paper, we propose a method called Predicting Protein Function using Multiple Kernels (ProMK). ProMK iteratively optimizes the phases of learning optimal weights and reduces the empirical loss of multi-label classifier for each of the labels simultaneously. ProMK can integrate kernels selectively and downgrade the weights on noisy kernels. We investigate the performance of ProMK on several publicly available protein function prediction benchmarks and synthetic datasets. We show that the proposed approach performs better than previously proposed protein function prediction approaches that integrate multiple data sources and multi-label multiple kernel learning methods. The codes of our proposed method are available at https://sites.google.com/site/guoxian85/promk.

  1. Prediction and Testing of Biological Networks Underlying Intestinal Cancer

    PubMed Central

    Mariadason, John M.; Wang, Donghai; Augenlicht, Leonard H.; Chance, Mark R.

    2010-01-01

    Colorectal cancer progresses through an accumulation of somatic mutations, some of which reside in so-called “driver” genes that provide a growth advantage to the tumor. To identify points of intersection between driver gene pathways, we implemented a network analysis framework using protein interactions to predict likely connections – both precedented and novel – between key driver genes in cancer. We applied the framework to find significant connections between two genes, Apc and Cdkn1a (p21), known to be synergistic in tumorigenesis in mouse models. We then assessed the functional coherence of the resulting Apc-Cdkn1a network by engineering in vivo single node perturbations of the network: mouse models mutated individually at Apc (Apc1638N+/−) or Cdkn1a (Cdkn1a−/−), followed by measurements of protein and gene expression changes in intestinal epithelial tissue. We hypothesized that if the predicted network is biologically coherent (functional), then the predicted nodes should associate more specifically with dysregulated genes and proteins than stochastically selected genes and proteins. The predicted Apc-Cdkn1a network was significantly perturbed at the mRNA-level by both single gene knockouts, and the predictions were also strongly supported based on physical proximity and mRNA coexpression of proteomic targets. These results support the functional coherence of the proposed Apc-Cdkn1a network and also demonstrate how network-based predictions can be statistically tested using high-throughput biological data. PMID:20824133

  2. [Exercise test and respiratory muscle function test].

    PubMed

    Akashiba, Tsuneto

    2011-10-01

    Dyspnea on exertion is a chief complaint of patients with COPD, and it has a major effect on the quality of their lives. Dyspnea is, by definition, subjective, but objective approaches are needed for a comprehensive understanding of these patients' conditions. Thus, measuring changes in cardiopulmonary variables during exercise can be very helpful when evaluating patients with COPD. The main purpose of exercise testing is to evaluate exercise tolerance and to identify the factors limiting exercise. Although incremental exercise testing is ideal for these purposes, simple walking tests such as 6-minute walking test, are also useful. PMID:22073578

  3. Blind tests of RNA nearest-neighbor energy prediction.

    PubMed

    Chou, Fang-Chieh; Kladwang, Wipapat; Kappel, Kalli; Das, Rhiju

    2016-07-26

    The predictive modeling and design of biologically active RNA molecules requires understanding the energetic balance among their basic components. Rapid developments in computer simulation promise increasingly accurate recovery of RNA's nearest-neighbor (NN) free-energy parameters, but these methods have not been tested in predictive trials or on nonstandard nucleotides. Here, we present, to our knowledge, the first such tests through a RECCES-Rosetta (reweighting of energy-function collection with conformational ensemble sampling in Rosetta) framework that rigorously models conformational entropy, predicts previously unmeasured NN parameters, and estimates these values' systematic uncertainties. RECCES-Rosetta recovers the 10 NN parameters for Watson-Crick stacked base pairs and 32 single-nucleotide dangling-end parameters with unprecedented accuracies: rmsd of 0.28 kcal/mol and 0.41 kcal/mol, respectively. For set-aside test sets, RECCES-Rosetta gives rmsd values of 0.32 kcal/mol on eight stacked pairs involving G-U wobble pairs and 0.99 kcal/mol on seven stacked pairs involving nonstandard isocytidine-isoguanosine pairs. To more rigorously assess RECCES-Rosetta, we carried out four blind predictions for stacked pairs involving 2,6-diaminopurine-U pairs, which achieved 0.64 kcal/mol rmsd accuracy when tested by subsequent experiments. Overall, these results establish that computational methods can now blindly predict energetics of basic RNA motifs, including chemically modified variants, with consistently better than 1 kcal/mol accuracy. Systematic tests indicate that resolving the remaining discrepancies will require energy function improvements beyond simply reweighting component terms, and we propose further blind trials to test such efforts. PMID:27402765

  4. Blind tests of RNA nearest-neighbor energy prediction.

    PubMed

    Chou, Fang-Chieh; Kladwang, Wipapat; Kappel, Kalli; Das, Rhiju

    2016-07-26

    The predictive modeling and design of biologically active RNA molecules requires understanding the energetic balance among their basic components. Rapid developments in computer simulation promise increasingly accurate recovery of RNA's nearest-neighbor (NN) free-energy parameters, but these methods have not been tested in predictive trials or on nonstandard nucleotides. Here, we present, to our knowledge, the first such tests through a RECCES-Rosetta (reweighting of energy-function collection with conformational ensemble sampling in Rosetta) framework that rigorously models conformational entropy, predicts previously unmeasured NN parameters, and estimates these values' systematic uncertainties. RECCES-Rosetta recovers the 10 NN parameters for Watson-Crick stacked base pairs and 32 single-nucleotide dangling-end parameters with unprecedented accuracies: rmsd of 0.28 kcal/mol and 0.41 kcal/mol, respectively. For set-aside test sets, RECCES-Rosetta gives rmsd values of 0.32 kcal/mol on eight stacked pairs involving G-U wobble pairs and 0.99 kcal/mol on seven stacked pairs involving nonstandard isocytidine-isoguanosine pairs. To more rigorously assess RECCES-Rosetta, we carried out four blind predictions for stacked pairs involving 2,6-diaminopurine-U pairs, which achieved 0.64 kcal/mol rmsd accuracy when tested by subsequent experiments. Overall, these results establish that computational methods can now blindly predict energetics of basic RNA motifs, including chemically modified variants, with consistently better than 1 kcal/mol accuracy. Systematic tests indicate that resolving the remaining discrepancies will require energy function improvements beyond simply reweighting component terms, and we propose further blind trials to test such efforts.

  5. Scoring function to predict solubility mutagenesis

    PubMed Central

    2010-01-01

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

  6. Consistent probabilistic outputs for protein function prediction

    PubMed Central

    Obozinski, Guillaume; Lanckriet, Gert; Grant, Charles; Jordan, Michael I; Noble, William Stafford

    2008-01-01

    In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one another; for example, the predictor may assign a specific GO term to a given protein ('purine nucleotide binding') but not assign the parent term ('nucleotide binding'). Such predictions are difficult to interpret. In this work, we focus on methods for calibrating and combining independent predictions to obtain a set of probabilistic predictions that are consistent with the topology of the ontology. We call this procedure 'reconciliation'. We begin with a baseline method for predicting GO terms from a collection of data types using an ensemble of discriminative classifiers. We apply the method to a previously described benchmark data set, and we demonstrate that the resulting predictions are frequently inconsistent with the topology of the GO. We then consider 11 distinct reconciliation methods: three heuristic methods; four variants of a Bayesian network; an extension of logistic regression to the structured case; and three novel projection methods - isotonic regression and two variants of a Kullback-Leibler projection method. We evaluate each method in three different modes - per term, per protein and joint - corresponding to three types of prediction tasks. Although the principal goal of reconciliation is interpretability, it is important to assess whether interpretability comes at a cost in terms of precision and recall. Indeed, we find that many apparently reasonable reconciliation methods yield reconciled probabilities with significantly lower precision than the original, unreconciled estimates. On the other hand, we find that isotonic regression usually performs better than the underlying, unreconciled method, and almost never performs worse

  7. Testing 40 Predictions from the Transtheoretical Model Again, with Confidence

    ERIC Educational Resources Information Center

    Velicer, Wayne F.; Brick, Leslie Ann D.; Fava, Joseph L.; Prochaska, James O.

    2013-01-01

    Testing Theory-based Quantitative Predictions (TTQP) represents an alternative to traditional Null Hypothesis Significance Testing (NHST) procedures and is more appropriate for theory testing. The theory generates explicit effect size predictions and these effect size estimates, with related confidence intervals, are used to test the predictions.…

  8. Functional Task Test: Data Review

    NASA Technical Reports Server (NTRS)

    Cromwell, Ronita

    2014-01-01

    After space flight there are changes in multiple physiological systems including: Cardiovascular function; Sensorimotor function; and Muscle function. How do changes in these physiological system impact astronaut functional performance?

  9. Testing time-dependent density functional theory with depopulated molecular orbitals for predicting electronic excitation energies of valence, Rydberg, and charge-transfer states and potential energies near a conical intersection

    SciTech Connect

    Li, Shaohong L.; Truhlar, Donald G.

    2014-09-14

    Kohn-Sham (KS) time-dependent density functional theory (TDDFT) with most exchange-correlation functionals is well known to systematically underestimate the excitation energies of Rydberg and charge-transfer excited states of atomic and molecular systems. To improve the description of Rydberg states within the KS TDDFT framework, Gaiduk et al. [Phys. Rev. Lett. 108, 253005 (2012)] proposed a scheme that may be called HOMO depopulation. In this study, we tested this scheme on an extensive dataset of valence and Rydberg excitation energies of various atoms, ions, and molecules. It is also tested on a charge-transfer excitation of NH{sub 3}-F{sub 2} and on the potential energy curves of NH{sub 3} near a conical intersection. We found that the method can indeed significantly improve the accuracy of predicted Rydberg excitation energies while preserving reasonable accuracy for valence excitation energies. However, it does not appear to improve the description of charge-transfer excitations that are severely underestimated by standard KS TDDFT with conventional exchange-correlation functionals, nor does it perform appreciably better than standard TDDFT for the calculation of potential energy surfaces.

  10. Spacecraft contamination prediction and testing techniques

    NASA Technical Reports Server (NTRS)

    Jeffery, J. A.; Maag, C. R.; Morelli, F. A.

    1981-01-01

    Techniques used in the prediction of spacecraft contamination for the Galileo Jupiter Orbiter and in the determination of the effects of such contamination are presented. Following a quick-look assessment of the contributions of ground-based initial contaminant loading, launch vehicle interface effects, vacuum-exposed outgassing deposition and attitude control thruster impingement and venting to the spacecraft contamination burden, the evaluations centered on the effects of the attitude control thruster on the scan platform optics, including calculations of thruster flowfields and a high-fidelity computer simulation of contaminant distribution. The evaluations revealed a considerable problem with thruster contamination, which could be solved by the use of a thrust shield and the avoidance of thruster operation at certain scan platform orientations. The effects of the various possible contaminants on spacecraft thermal and optical system performances were also investigated in studies of the optical transmittance of deposited monomethyl hydrazine nitrate, vacuum optical degradation due to contaminant outgassing and re-emission outgassing, and an operational satellite contaminant monitor on the NOAA-C satellite. It is concluded that with a good evaluation and testing program, contamination control may become a necessary portion of system design procedures, and recommendations for the implementation of various practices and tests to minimize contamination effects are presented.

  11. Benchmark notch test for life prediction

    NASA Technical Reports Server (NTRS)

    Domas, P. A.; Sharpe, W. N.; Ward, M.; Yau, J. F.

    1982-01-01

    The laser Interferometric Strain Displacement Gage (ISDG) was used to measure local strains in notched Inconel 718 test bars subjected to six different load histories at 649 C (1200 F) and including effects of tensile and compressive hold periods. The measurements were compared to simplified Neuber notch analysis predictions of notch root stress and strain. The actual strains incurred at the root of a discontinuity in cyclically loaded test samples subjected to inelastic deformation at high temperature where creep deformations readily occur were determined. The steady state cyclic, stress-strain response at the root of the discontinuity was analyzed. Flat, double notched uniaxially loaded fatigue specimens manufactured from the nickel base, superalloy Inconel 718 were used. The ISDG was used to obtain cycle by cycle recordings of notch root strain during continuous and hold time cycling at 649 C. Comparisons to Neuber and finite element model analyses were made. The results obtained provide a benchmark data set in high technology design where notch fatigue life is the predominant component service life limitation.

  12. 14 CFR 35.40 - Functional test.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Functional test. 35.40 Section 35.40... STANDARDS: PROPELLERS Tests and Inspections § 35.40 Functional test. The variable-pitch propeller system must be subjected to the applicable functional tests of this section. The same propeller system used...

  13. 14 CFR 35.40 - Functional test.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Functional test. 35.40 Section 35.40... STANDARDS: PROPELLERS Tests and Inspections § 35.40 Functional test. The variable-pitch propeller system must be subjected to the applicable functional tests of this section. The same propeller system used...

  14. 14 CFR 35.40 - Functional test.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Functional test. 35.40 Section 35.40... STANDARDS: PROPELLERS Tests and Inspections § 35.40 Functional test. The variable-pitch propeller system must be subjected to the applicable functional tests of this section. The same propeller system used...

  15. Borderline personality traits and disorder: predicting prospective patient functioning

    PubMed Central

    Hopwood, Christopher J.; Zanarini, Mary C.

    2011-01-01

    Objective Decisions about the composition of personality assessment in DSM-V will be heavily influenced by the clinical utility of candidate constructs. This study addressed one aspect of clinical utility by testing the incremental validity of five-factor model personality traits and Borderline Personality Disorder (BPD) symptoms for predicting prospective patient functioning. Method Five-factor personality traits and BPD features were correlated with one another and predicted 2, 4, 6, 8, and 10-year psychosocial functioning scores for 362 personality-disordered patients. Results Traits and symptom domains related significantly and pervasively to one another and to prospective functioning. FFM extraversion and agreeableness tended to be most incrementally predictive of psychosocial functioning across all intervals; cognitive and impulse action features of BPD features incremented FFM traits in some models. Conclusions These data suggest that BPD symptoms and personality traits are important long-term indicators of clinical functioning that both overlap with and increment one another in clinical predictions. Results support the integration of personality traits and disorders in DSM-V. PMID:20658814

  16. 14 CFR 35.40 - Functional test.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... STANDARDS: PROPELLERS Tests and Inspections § 35.40 Functional test. The variable-pitch propeller system must be subjected to the applicable functional tests of this section. The same propeller system used in... representative engine on a test stand or on an airplane. The propeller must complete these tests without...

  17. 14 CFR 35.40 - Functional test.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... STANDARDS: PROPELLERS Tests and Inspections § 35.40 Functional test. The variable-pitch propeller system must be subjected to the applicable functional tests of this section. The same propeller system used in... representative engine on a test stand or on an airplane. The propeller must complete these tests without...

  18. Early executive function predicts reasoning development.

    PubMed

    Richland, Lindsey E; Burchinal, Margaret R

    2013-01-01

    Analogical reasoning is a core cognitive skill that distinguishes humans from all other species and contributes to general fluid intelligence, creativity, and adaptive learning capacities. Yet its origins are not well understood. In the study reported here, we analyzed large-scale longitudinal data from the Study of Early Child Care and Youth Development to test predictors of growth in analogical-reasoning skill from third grade to adolescence. Our results suggest an integrative resolution to the theoretical debate regarding contributory factors arising from smaller-scale, cross-sectional experiments on analogy development. Children with greater executive-function skills (both composite and inhibitory control) and vocabulary knowledge in early elementary school displayed higher scores on a verbal analogies task at age 15 years, even after adjusting for key covariates. We posit that knowledge is a prerequisite to analogy performance, but strong executive-functioning resources during early childhood are related to long-term gains in fundamental reasoning skills.

  19. Experimental testing of quantum mechanical predictions of mutagenicity: aminopyrazoles.

    PubMed

    Leach, Andrew G; McCoull, William; Bailey, Andrew; Barton, Peter; Mee, Christine; Rosevere, Eleanor

    2013-05-20

    A computational method for predicting the likelihood of aromatic amines being active in the Ames test for mutagenicity was trialed on a set of aminopyrazoles. A virtual array of compounds was generated from the available sets of hydrazines and α-cyanoaldehydes (or ketones) and quantum mechanical calculations used to compute a probability of being active in the Ames test. The compounds selected for synthesis and testing were not based on the predictions and so spanned the range of predicted probabilities. The subsequently generated results of the Ames test were in good correspondence with the predictions and confirm this approach as a useful means of predicting likely mutagenic risk. PMID:23541044

  20. Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers.

    PubMed

    Lefcheck, Jonathan S; Duffy, J Emmett

    2015-11-01

    The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context. PMID:27070016

  1. Functional Assays for Neurotoxicity Testing*

    EPA Science Inventory

    Neurobehavioral and pathological evaluations of the nervous system are complementary components of basic research and toxicity testing of pharmaceutical and environmental chemicals. While neuropathological assessments provide insight as to cellular changes in neurons, behavioral ...

  2. Functional Assays for Neurotoxicity Testing

    EPA Science Inventory

    Neurobehavioral and pathological evaluations of the nervous system are complementary components of basic research and toxicity testing of pharmaceutical and environmental chemicals. While neuropathological assessments provide insight as to cellular changes in neurons, behavioral ...

  3. What Are Lung Function Tests?

    MedlinePlus

    ... COPD How the Lungs Work Idiopathic Pulmonary Fibrosis Sarcoidosis Send a link to NHLBI to someone by ... caused by conditions such as pulmonary fibrosis and sarcoidosis (sar-koy-DOE-sis). Also, these tests might ...

  4. Habitual fat intake predicts memory function in younger women.

    PubMed

    Gibson, E Leigh; Barr, Suzanne; Jeanes, Yvonne M

    2013-01-01

    High intakes of fat have been linked to greater cognitive decline in old age, but such associations may already occur in younger adults. We tested memory and learning in 38 women (25 to 45 years old), recruited for a larger observational study in women with polycystic ovary syndrome. These women varied in health status, though not significantly between cases (n = 23) and controls (n = 15). Performance on tests sensitive to medial temporal lobe function (CANTABeclipse, Cambridge Cognition Ltd, Cambridge, UK), i.e., verbal memory, visuo-spatial learning, and delayed pattern matching (DMS), were compared with intakes of macronutrients from 7-day diet diaries and physiological indices of metabolic syndrome. Partial correlations were adjusted for age, activity, and verbal IQ (National Adult Reading Test). Greater intakes of saturated and trans fats, and higher saturated to unsaturated fat ratio (Sat:UFA), were associated with more errors on the visuo-spatial task and with poorer word recall and recognition. Unexpectedly, higher UFA intake predicted poorer performance on the word recall and recognition measures. Fasting insulin was positively correlated with poorer word recognition only, whereas higher blood total cholesterol was associated only with visuo-spatial learning errors. None of these variables predicted performance on a DMS test. The significant nutrient-cognition relationships were tested for mediation by total energy intake: saturated and trans fat intakes, and Sat:UFA, remained significant predictors specifically of visuo-spatial learning errors, whereas total fat and UFA intakes now predicted only poorer word recall. Examination of associations separately for monounsaturated (MUFA) and polyunsaturated fats suggested that only MUFA intake was predictive of poorer word recall. Saturated and trans fats, and fasting insulin, may already be associated with cognitive deficits in younger women. The findings need extending but may have important implications for

  5. Sweat testing to evaluate autonomic function

    PubMed Central

    Illigens, Ben M.W.; Gibbons, Christopher H.

    2011-01-01

    Sudomotor dysfunction is one of the earliest detectable neurophysiologic abnormalities in distal small fiber neuropathy. Traditional neurophysiologic measurements of sudomotor function include thermoregulatory sweat testing (TST), quantitative sudomotor axon reflex testing (QSART), silicone impressions, the sympathetic skin response (SSR), and the recent addition of quantitative direct and indirect axon reflex testing (QDIRT). These testing techniques, when used in combination, can detect and localized pre- and postganglionic lesions, can provide early diagnosis of sudomotor dysfunction and can monitor disease progression or disease recovery. In this article, we review the common tests available for assessment of sudomotor function, detail the testing methodology, review the limitations and provide examples of test results. PMID:18989618

  6. Integrative fascial release and functional testing.

    PubMed

    Hammer, W

    2000-03-01

    Soft tissue techniques, including Integrative Myofascial Release (IFR) can be more effective if the area of treatment can be determined by functional testing. The patient's source of pain may not necessarily be located at the area of complaint and functional testing helps in pinpointing the source. Post-treatment functional testing will provide feedback to both the patient and the doctor as to whether the technique was effective. This paper will describe some typical functional tests and treatment using IFR of the posterior cervical/thoracolumbar fascia. PMID:17987166

  7. Predicted and tested performance of durable TPS

    NASA Technical Reports Server (NTRS)

    Shideler, John L.

    1992-01-01

    The development of thermal protection systems (TPS) for aerospace vehicles involves combining material selection, concept design, and verification tests to evaluate the effectiveness of the system. The present paper reviews verification tests of two metallic and one carbon-carbon thermal protection system. The test conditions are, in general, representative of Space Shuttle design flight conditions which may be more or less severe than conditions required for future space transportation systems. The results of this study are intended to help establish a preliminary data base from which the designers of future entry vehicles can evaluate the applicability of future concepts to their vehicles.

  8. A Prediction Model of the Capillary Pressure J-Function

    PubMed Central

    Xu, W. S.; Luo, P. Y.; Sun, L.; Lin, N.

    2016-01-01

    The capillary pressure J-function is a dimensionless measure of the capillary pressure of a fluid in a porous medium. The function was derived based on a capillary bundle model. However, the dependence of the J-function on the saturation Sw is not well understood. A prediction model for it is presented based on capillary pressure model, and the J-function prediction model is a power function instead of an exponential or polynomial function. Relative permeability is calculated with the J-function prediction model, resulting in an easier calculation and results that are more representative. PMID:27603701

  9. A Prediction Model of the Capillary Pressure J-Function.

    PubMed

    Xu, W S; Luo, P Y; Sun, L; Lin, N

    2016-01-01

    The capillary pressure J-function is a dimensionless measure of the capillary pressure of a fluid in a porous medium. The function was derived based on a capillary bundle model. However, the dependence of the J-function on the saturation Sw is not well understood. A prediction model for it is presented based on capillary pressure model, and the J-function prediction model is a power function instead of an exponential or polynomial function. Relative permeability is calculated with the J-function prediction model, resulting in an easier calculation and results that are more representative. PMID:27603701

  10. Researchers Get Closer to Test Predicting Colon Cancer's Return

    MedlinePlus

    ... Get Closer to Test Predicting Colon Cancer's Return DNA-based screen would aid treatment decisions for people ... News) -- A blood test that detects bits of DNA shed from colon cancers may someday help doctors ...

  11. Revolutionizing Toxicity Testing For Predicting Developmental Outcomes (DNT4)

    EPA Science Inventory

    Characterizing risk from environmental chemical exposure currently requires extensive animal testing; however, alternative approaches are being researched to increase throughput of chemicals screened, decrease reliance on animal testing, and improve accuracy in predicting adverse...

  12. Protein-Based Urine Test Predicts Kidney Transplant Outcomes

    MedlinePlus

    ... News Releases News Release Thursday, August 22, 2013 Protein-based urine test predicts kidney transplant outcomes NIH- ... supporting development of noninvasive tests. Levels of a protein in the urine of kidney transplant recipients can ...

  13. Construct and Predictive Validities of the Perceptual Ability Test.

    ERIC Educational Resources Information Center

    Kramer, Gene A.; And Others

    1989-01-01

    The construct and predictive validities of the Perceptual Ability Test (PAT) were examined. The results indicate that each of the subtests exhibits different predictive validity. A linear combination of PAT subtest scores was found to be more predictive of first-year dental school technique performance than the total PAT score. (Author/MLW)

  14. The use of serum glial fibrillary acidic protein test as a promising tool for intracerebral hemorrhage diagnosis in Chinese patients and prediction of the short-term functional outcomes.

    PubMed

    Xiong, Lijun; Yang, Yan; Zhang, Mei; Xu, Wuping

    2015-11-01

    The objective of this study was to explore the efficacy of glial fibrillary acidic protein (GFAP) in differentiating intracerebral hemorrhage (ICH) from ischemic stroke (IS). Suspicious patients of acute stroke were screened and finally diagnosed by computed tomography and magnetic resonance imaging. Blood samples were collected within 2-6 h after onset of symptoms, and serum GFAP level was determined by ELISA assay. The functional outcome for the patients was determined by modified Rankin Scale (mRS) 90 days after onset of symptoms. 43 ICH patients and 65 IS patients were enrolled. GFAP concentration in ICH group was significantly higher than in IS group (p < 0.001). Significant correlation was found when comparing GFAP with National Institutes of Health Stroke Scale (NIHSS) (r = 0.418, p = 0.005) and hemorrhage volume (r = 0.840, p < 0.001) in ICH group, while such correlation was not observed in IS group. ROC analysis indicated that GFAP level at the cut-point of 0.7 ng/ml yielded an AUC of 0.901 (95 % CI 0.828-0.950) with high sensitivity (86.0 %) and specificity (76.9 %) to differentiate ICH from IS. Patients with higher serum GFAP concentration in ICH group experienced poorer functional disability (r = 0.755, p < 0.001), while this phenomenon was not observed in IS group (r = -0.114, p = 0.368). ROC curve analysis found that GFAP level at the cut-point of 1.04 ng/ml yielded an AUC of 0.936 (95 % CI 0.817-0.988) in identifying patients with poor functional outcome, at the sensitivity and specificity of 95.7 and 80.0 %, respectively. GFAP test is a promising technique for diagnosis of ICH from IS and prediction of short-term functional outcomes.

  15. Predictive Validity of the Gesell School Readiness Tests.

    ERIC Educational Resources Information Center

    Graue, M. Elizabeth; Shepard, Lorrie A.

    1989-01-01

    Examined the predictive validity of the Gesell School Readiness Tests by correlating measured developmental age and performance in 151 first-grade students. Results show a positive relationship between developmental age and report card grades, modest predictive validity for standardized tests, and low validity for teacher judgment of first-grade…

  16. The Predictive Validity of the Stanford Early School Achievement Test

    ERIC Educational Resources Information Center

    Ames, Steven G.; And Others

    1977-01-01

    A sample of first grade children were pretested with the Stanford Early School Achievement Test and posttested with the Stanford Achievement Test. Results demonstrated moderate validity of theformer for predicting first grade achievement. Prediction was better in verbal achievement than in mathematics achievement. (Author/JKS)

  17. Statistical tests for prediction of lignite quality

    SciTech Connect

    C.J. Kolovos

    2007-06-15

    Domestic lignite from large, bucket wheel excavators based open pit mines is the main fuel for electricity generation in Greece. Lignite from one or more mines may arrive at any power plant stockyard. The mixture obtained constitutes the lignite fuel fed to the power plant. The fuel is sampled in regular time intervals. These samples are considered as results of observations of values of spatial random variables. The aim was to form and statistically test many small sample populations. Statistical tests on the values of the humidity content, the ash-water free content, and the lower heating value of the lignite fuel indicated that the sample values form a normal population. The Kolmogorov-Smirnov test was applied for testing goodness-of-fit of sample distribution for a three year period and different power plants of the Kozani-Ptolemais area, western Macedonia, Greece. The normal distribution hypothesis can be widely accepted for forecasting the distribution of values of the basic quality characteristics even for a small number of samples.

  18. Predictivity, genetic tests and insurance law.

    PubMed

    Romeo Casabona, Carlos Maria

    2009-01-01

    An increasing discussion today consists of whether emerging genetic tests will provide a powerful tool for individual risk assessments for the life, health, disability and accident policies underwritten by private insurance companies and what could be the consequences of this for the insurance contract system built throughout the last decades. Thus, access to such risk information will facilitate more precise actuarial premium assessments.

  19. Predicting functional decline in behavioural variant frontotemporal dementia.

    PubMed

    Josephs, Keith A; Whitwell, Jennifer L; Weigand, Stephen D; Senjem, Matthew L; Boeve, Bradley F; Knopman, David S; Smith, Glenn E; Ivnik, Robert J; Jack, Clifford R; Petersen, Ronald C

    2011-02-01

    Behavioural variant frontotemporal dementia is characterized by a change in comportment. It is associated with considerable functional decline over the course of the illness albeit with sometimes dramatic variability among patients. It is unknown whether any baseline features, or combination of features, could predict rate of functional decline in behavioural variant frontotemporal dementia. The aim of this study was to investigate the effects of different baseline clinical, neuropsychological, neuropsychiatric, genetic and anatomic predictors on the rate of functional decline as measured by the Clinical Dementia Rating Sum of Boxes scale. We identified 86 subjects with behavioural variant frontotemporal dementia that had multiple serial Clinical Dementia Rating Sum of Boxes assessments (mean 4, range 2-18). Atlas-based parcellation was used to generate volumes for specific regions of interest at baseline. Volumes were utilized to classify subjects into different anatomical subtypes using the advanced statistical technique of cluster analysis and were assessed as predictor variables. Composite scores were generated for the neuropsychological domains of executive, language, memory and visuospatial function. Behaviours from the brief questionnaire form of the Neuropsychiatric Inventory were assessed. Linear mixed-effects regression modelling was used to determine which baseline features predict rate of future functional decline. Rates of functional decline differed across the anatomical subtypes of behavioural variant frontotemporal dementia, with faster rates observed in the frontal dominant and frontotemporal subtypes. In addition, subjects with poorer performance on neuropsychological tests of executive, language and visuospatial function, less disinhibition, agitation/aggression and night-time behaviours at presentation, and smaller medial, lateral and orbital frontal lobe volumes showed faster rates of decline. In many instances, the effect of the predictor

  20. Solvent retention capacity (SRC) testing of wheat flour: Principles and value in predicting flour functionality in different wheat-based food processes and in wheat breeding—a review

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solvent retention capacity (SRC) technology, its history, principles, and applications are reviewed. Originally, SRC testing was created and developed for evaluating soft wheat flour functionality, but it has also been shown to be applicable to evaluating flour functionality for hard wheat products....

  1. Platelet Serotonin Transporter Function Predicts Default-Mode Network Activity

    PubMed Central

    Kasess, Christian H.; Meyer, Bernhard M.; Hofmaier, Tina; Diers, Kersten; Bartova, Lucie; Pail, Gerald; Huf, Wolfgang; Uzelac, Zeljko; Hartinger, Beate; Kalcher, Klaudius; Perkmann, Thomas; Haslacher, Helmuth; Meyer-Lindenberg, Andreas; Kasper, Siegfried; Freissmuth, Michael; Windischberger, Christian; Willeit, Matthäus; Lanzenberger, Rupert; Esterbauer, Harald; Brocke, Burkhard; Moser, Ewald; Sitte, Harald H.; Pezawas, Lukas

    2014-01-01

    Background The serotonin transporter (5-HTT) is abundantly expressed in humans by the serotonin transporter gene SLC6A4 and removes serotonin (5-HT) from extracellular space. A blood-brain relationship between platelet and synaptosomal 5-HT reuptake has been suggested, but it is unknown today, if platelet 5-HT uptake can predict neural activation of human brain networks that are known to be under serotonergic influence. Methods A functional magnetic resonance study was performed in 48 healthy subjects and maximal 5-HT uptake velocity (Vmax) was assessed in blood platelets. We used a mixed-effects multilevel analysis technique (MEMA) to test for linear relationships between whole-brain, blood-oxygen-level dependent (BOLD) activity and platelet Vmax. Results The present study demonstrates that increases in platelet Vmax significantly predict default-mode network (DMN) suppression in healthy subjects independent of genetic variation within SLC6A4. Furthermore, functional connectivity analyses indicate that platelet Vmax is related to global DMN activation and not intrinsic DMN connectivity. Conclusion This study provides evidence that platelet Vmax predicts global DMN activation changes in healthy subjects. Given previous reports on platelet-synaptosomal Vmax coupling, results further suggest an important role of neuronal 5-HT reuptake in DMN regulation. PMID:24667541

  2. Arc Jet Facility Test Condition Predictions Using the ADSI Code

    NASA Technical Reports Server (NTRS)

    Palmer, Grant; Prabhu, Dinesh; Terrazas-Salinas, Imelda

    2015-01-01

    The Aerothermal Design Space Interpolation (ADSI) tool is used to interpolate databases of previously computed computational fluid dynamic solutions for test articles in a NASA Ames arc jet facility. The arc jet databases are generated using an Navier-Stokes flow solver using previously determined best practices. The arc jet mass flow rates and arc currents used to discretize the database are chosen to span the operating conditions possible in the arc jet, and are based on previous arc jet experimental conditions where possible. The ADSI code is a database interpolation, manipulation, and examination tool that can be used to estimate the stagnation point pressure and heating rate for user-specified values of arc jet mass flow rate and arc current. The interpolation is performed in the other direction (predicting mass flow and current to achieve a desired stagnation point pressure and heating rate). ADSI is also used to generate 2-D response surfaces of stagnation point pressure and heating rate as a function of mass flow rate and arc current (or vice versa). Arc jet test data is used to assess the predictive capability of the ADSI code.

  3. Template-based prediction of protein function.

    PubMed

    Petrey, Donald; Chen, T Scott; Deng, Lei; Garzon, Jose Ignacio; Hwang, Howook; Lasso, Gorka; Lee, Hunjoong; Silkov, Antonina; Honig, Barry

    2015-06-01

    We discuss recent approaches for structure-based protein function annotation. We focus on template-based methods where the function of a query protein is deduced from that of a template for which both the structure and function are known. We describe the different ways of identifying a template. These are typically based on sequence analysis but new methods based on purely structural similarity are also being developed that allow function annotation based on structural relationships that cannot be recognized by sequence. The growing number of available structures of known function, improved homology modeling techniques and new developments in the use of structure allow template-based methods to be applied on a proteome-wide scale and in many different biological contexts. This progress significantly expands the range of applicability of structural information in function annotation to a level that previously was only achievable by sequence comparison.

  4. Which Working Memory Functions Predict Intelligence?

    ERIC Educational Resources Information Center

    Oberauer, Klaus; Sub, Heinz-Martin; Wilhelm, Oliver; Wittmann, Werner W.

    2008-01-01

    Investigates the relationship between three factors of working memory (storage and processing, relational integration, and supervision) and four factors of intelligence (reasoning, speed, memory, and creativity) using structural equation models. Relational integration predicted reasoning ability at least as well as the storage-and-processing…

  5. PSCL: predicting protein subcellular localization based on optimal functional domains.

    PubMed

    Wang, Kai; Hu, Le-Le; Shi, Xiao-He; Dong, Ying-Song; Li, Hai-Peng; Wen, Tie-Qiao

    2012-01-01

    It is well known that protein subcellular localizations are closely related to their functions. Although many computational methods and tools are available from Internet, it is still necessary to develop new algorithms in this filed to gain a better understanding of the complex mechanism of plant subcellular localization. Here, we provide a new web server named PSCL for plant protein subcellular localization prediction by employing optimized functional domains. After feature optimization, 848 optimal functional domains from InterPro were obtained to represent each protein. By calculating the distances to each of the seven categories, PSCL showing the possibilities of a protein located into each of those categories in ascending order. Toward our dataset, PSCL achieved a first-order predicted accuracy of 75.7% by jackknife test. Gene Ontology enrichment analysis showing that catalytic activity, cellular process and metabolic process are strongly correlated with the localization of plant proteins. Finally, PSCL, a Linux Operate System based web interface for the predictor was designed and is accessible for public use at http://pscl.biosino.org/.

  6. Prediction of functional phosphorylation sites by incorporating evolutionary information.

    PubMed

    Niu, Shen; Wang, Zhen; Ge, Dongya; Zhang, Guoqing; Li, Yixue

    2012-09-01

    Protein phosphorylation is a ubiquitous protein post-translational modification, which plays an important role in cellular signaling systems underlying various physiological and pathological processes. Current in silico methods mainly focused on the prediction of phosphorylation sites, but rare methods considered whether a phosphorylation site is functional or not. Since functional phosphorylation sites are more valuable for further experimental research and a proportion of phosphorylation sites have no direct functional effects, the prediction of functional phosphorylation sites is quite necessary for this research area. Previous studies have shown that functional phosphorylation sites are more conserved than non-functional phosphorylation sites in evolution. Thus, in our method, we developed a web server by integrating existing phosphorylation site prediction methods, as well as both absolute and relative evolutionary conservation scores to predict the most likely functional phosphorylation sites. Using our method, we predicted the most likely functional sites of the human, rat and mouse proteomes and built a database for the predicted sites. By the analysis of overall prediction results, we demonstrated that protein phosphorylation plays an important role in all the enriched KEGG pathways. By the analysis of protein-specific prediction results, we demonstrated the usefulness of our method for individual protein studies. Our method would help to characterize the most likely functional phosphorylation sites for further studies in this research area.

  7. Laboratory testing for platelet function disorders.

    PubMed

    Israels, S J

    2015-05-01

    Platelet function testing is both complex and labor intensive. A stepwise approach to the evaluation of patients with suspected platelet disorders will optimize the use of laboratory resources, beginning with an appropriate clinical evaluation to determine whether the bleeding is consistent with a defect of primary hemostasis. Bleeding assessment tools, evaluation of platelet counts, and review of peripheral blood cell morphology can aid the initial assessment. For patients requiring further laboratory testing, platelet aggregometry, secretion assays, and von Willebrand factor assays are the most useful next steps and will direct further specialized testing including flow cytometry, electron microscopy, and molecular diagnostics. Guidelines and recommendations for standardizing platelet function testing, with a particular focus on light transmission aggregometry, are available and can provide a template for clinical laboratories in establishing procedures that will optimize diagnosis and assure quality results. This review outlines an approach to platelet function testing and reviews testing methods available to clinical laboratories.

  8. Binomial test statistics using Psi functions

    SciTech Connect

    Bowman, Kimiko o

    2007-01-01

    For the negative binomial model (probability generating function (p + 1 - pt){sup -k}) a logarithmic derivative is the Psi function difference {psi}(k + x) - {psi}(k); this and its derivatives lead to a test statistic to decide on the validity of a specified model. The test statistic uses a data base so there exists a comparison available between theory and application. Note that the test function is not dominated by outliers. Applications to (i) Fisher's tick data, (ii) accidents data, (iii) Weldon's dice data are included.

  9. Predicting FCI gain with a nonverbal intelligence test

    NASA Astrophysics Data System (ADS)

    Semak, M. R.; Dietz, R. D.; Pearson, R. H.; Willis, C. W.

    2013-01-01

    We have administered both a commercial, nonverbal intelligence test (the GAMA) and Lawson's Classroom Test of Scientific Reasoning to students in two introductory physics classes to determine if either test can successfully predict normalized gains on the Force Concept Inventory. Since gain on the FCI is known to be related to gender, we adopted a linear model with gain on the FCI as the dependent variable and gender and a test score as the independent variables. We found that the GAMA score did not predict a significant amount of variation beyond gender. Lawson's test, however, did predict a small but significant variation beyond gender. When simple linear regressions were run separately for males and females with the Lawson score as a predictor, we found that the Lawson score did not significantly predict gains for females but was a marginally significant predictor for males.

  10. The Evolutionary Legacy of Diversification Predicts Ecosystem Function.

    PubMed

    Yguel, Benjamin; Jactel, Hervé; Pearse, Ian S; Moen, Daniel; Winter, Marten; Hortal, Joaquin; Helmus, Matthew R; Kühn, Ingolf; Pavoine, Sandrine; Purschke, Oliver; Weiher, Evan; Violle, Cyrille; Ozinga, Wim; Brändle, Martin; Bartish, Igor; Prinzing, Andreas

    2016-10-01

    Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.

  11. The Evolutionary Legacy of Diversification Predicts Ecosystem Function.

    PubMed

    Yguel, Benjamin; Jactel, Hervé; Pearse, Ian S; Moen, Daniel; Winter, Marten; Hortal, Joaquin; Helmus, Matthew R; Kühn, Ingolf; Pavoine, Sandrine; Purschke, Oliver; Weiher, Evan; Violle, Cyrille; Ozinga, Wim; Brändle, Martin; Bartish, Igor; Prinzing, Andreas

    2016-10-01

    Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning. PMID:27622874

  12. Confronting species distribution model predictions with species functional traits.

    PubMed

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  13. γ-Glutamyl Transpeptidase in Men and Alanine Aminotransferase in Women are the Most Suitable Parameters Among Liver Function Tests for the Prediction of Metabolic Syndrome in Nonviral Hepatitis and Nonfatty Liver in the Elderly

    PubMed Central

    Pei, Dee; Hsia, Te-Lin; Chao, Ting-Ting; Lin, Jiunn-Diann; Hsu, Chun-Hsien; Wu, Chung-Ze; Hsieh, Chang-Hsun; Liang, Yao-Jen; Chen, Yen-Lin

    2015-01-01

    Background/Aims: Nonalchoholic fatty liver disease (NAFLD) has been reported as a hepatic manifestation of metabolic syndrome (MetS); it is common and accounts for 80% of the cases with abnormal liver function tests (LFTs). In addition, several studies have proved that there is a correlation between abnormal LFTs and MetS. Therefore, LFTs may represent the abnormal metabolic status of livers in the patients with MetS. To identify the early state of metabolic dysfunction, we investigate the value of LFTs for the future MetS development in the relatively healthy (non-NAFLD) elderly. Patients and Methods: A total of 16,912 subjects met the criteria for analysis. In the first stage of this study, subjects were enrolled in the cross-sectional study in order to find out the optimal cutoff value in different LFTs with higher chances to have MetS. In the second stage of the present study, subjects with MetS at baseline were excluded from the same study group, and a median 5.6-year longitudinal study was conducted on the rest of the group. Results: Among all LFTs, only aspartate aminotransferase in both genders and the α-fetal protein in women failed to show the significance in distinguishing subjects with MetS by the receiver operating characteristic curve. In the Kaplan–Meier plot, only γ-glutamyl transpeptidase (γ-GT) in men and the alanine aminotransferase (ALT) in women could be used to successfully separate subjects with higher risk of developing the MetS from those with lower risk. Finally, in the multivariant Cox regression model, similar results were identified. Still, the hazard ratio (HR) to have future MetS, γ-GT in men, and ALT in women showed significance (HR = 1.511 in men and 1.504 in women). Conclusion: Among all the different LFTs, γ-GT (>16 U/L) in male and ALT (>21 U/L) in female were the best predictors for the development of MetS in healthy elderly. These two liver markers could be an ancillary test in predicting future MetS development

  14. Predictive Validity of the Gesell School Readiness Tests.

    ERIC Educational Resources Information Center

    Graue, M. Elizabeth; Shepard, Lorrie A.

    In response to the fact that technical standards for screening and placement tests must be more rigorous than those for readiness tests, the predictive validity of the Gesell School Readiness Tests (GSRT) was examined. The purpose of the GSRT, a commonly used screening instrument, is the assessment of children's developmental behaviors to aid in…

  15. MASS FUNCTION PREDICTIONS BEYOND {Lambda}CDM

    SciTech Connect

    Bhattacharya, Suman; Lukic, Zarija; Habib, Salman; Heitmann, Katrin; White, Martin; Wagner, Christian

    2011-05-10

    The statistics of dark matter halos is an essential component of precision cosmology. The mass distribution of halos, as specified by the halo mass function, is a key input for several cosmological probes. The sizes of N-body simulations are now such that, for the most part, results need no longer be statistics-limited, but are still subject to various systematic uncertainties. Discrepancies in the results of simulation campaigns for the halo mass function remain in excess of statistical uncertainties and of roughly the same size as the error limits set by near-future observations; we investigate and discuss some of the reasons for these differences. Quantifying error sources and compensating for them as appropriate, we carry out a high-statistics study of dark matter halos from 67 N-body simulations to investigate the mass function and its evolution for a reference {Lambda}CDM cosmology and for a set of wCDM cosmologies. For the reference {Lambda}CDM cosmology (close to WMAP5), we quantify the breaking of universality in the form of the mass function as a function of redshift, finding an evolution of as much as 10% away from the universal form between redshifts z = 0 and z = 2. For cosmologies very close to this reference we provide a fitting formula to our results for the (evolving) {Lambda}CDM mass function over a mass range of 6 x 10{sup 11}-3 x 10{sup 15} M{sub sun} to an estimated accuracy of about 2%. The set of wCDM cosmologies is taken from the Coyote Universe simulation suite. The mass functions from this suite (which includes a {Lambda}CDM cosmology and others with w {approx_equal} -1) are described by the fitting formula for the reference {Lambda}CDM case at an accuracy level of 10%, but with clear systematic deviations. We argue that, as a consequence, fitting formulae based on a universal form for the mass function may have limited utility in high-precision cosmological applications.

  16. Mass Function Predictions Beyond ΛCDM

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Suman; Heitmann, Katrin; White, Martin; Lukić, Zarija; Wagner, Christian; Habib, Salman

    2011-05-01

    The statistics of dark matter halos is an essential component of precision cosmology. The mass distribution of halos, as specified by the halo mass function, is a key input for several cosmological probes. The sizes of N-body simulations are now such that, for the most part, results need no longer be statistics-limited, but are still subject to various systematic uncertainties. Discrepancies in the results of simulation campaigns for the halo mass function remain in excess of statistical uncertainties and of roughly the same size as the error limits set by near-future observations; we investigate and discuss some of the reasons for these differences. Quantifying error sources and compensating for them as appropriate, we carry out a high-statistics study of dark matter halos from 67 N-body simulations to investigate the mass function and its evolution for a reference ΛCDM cosmology and for a set of wCDM cosmologies. For the reference ΛCDM cosmology (close to WMAP5), we quantify the breaking of universality in the form of the mass function as a function of redshift, finding an evolution of as much as 10% away from the universal form between redshifts z = 0 and z = 2. For cosmologies very close to this reference we provide a fitting formula to our results for the (evolving) ΛCDM mass function over a mass range of 6 × 1011-3 × 1015 M sun to an estimated accuracy of about 2%. The set of wCDM cosmologies is taken from the Coyote Universe simulation suite. The mass functions from this suite (which includes a ΛCDM cosmology and others with w ~= -1) are described by the fitting formula for the reference ΛCDM case at an accuracy level of 10%, but with clear systematic deviations. We argue that, as a consequence, fitting formulae based on a universal form for the mass function may have limited utility in high-precision cosmological applications.

  17. Utility functions predict variance and skewness risk preferences in monkeys.

    PubMed

    Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

    2016-07-26

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals' preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals' preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys' choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences. PMID:27402743

  18. Utility functions predict variance and skewness risk preferences in monkeys

    PubMed Central

    Genest, Wilfried; Stauffer, William R.; Schultz, Wolfram

    2016-01-01

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals’ preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals’ preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys’ choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences. PMID:27402743

  19. Utility functions predict variance and skewness risk preferences in monkeys.

    PubMed

    Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

    2016-07-26

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals' preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals' preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys' choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences.

  20. Artificial neural network to predict degradation of non-metallic lining materials from laboratory tests

    SciTech Connect

    Silverman, D.C.

    1994-12-31

    Artificial neural networks are computer simulations that have the potential of ``finding`` the same patterns that corrosion practitioners recognize to relate experimental test results to lifetime predictions. This potential ability was utilized to construct an artificial neural network to recognize the pattern between results from a sequential immersion test for organic non-metallic lining materials and their ability to function as linings in actual applications. The network so constructed has been shown to predict field performance from this test. The network was incorporated within an Expert System to simplify data input and output, allow for simple consistency checks, and to make the final prediction.

  1. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  2. State of the Art in Platelet Function Testing

    PubMed Central

    E. Kehrel, Beate; F. Brodde, Martin

    2013-01-01

    Summary Platelets perform many functions in hemostasis but also in other areas of physiology and pathology. Therefore, it is obvious that many different function tests have been developed, each one conceived and standardized for a special purpose. This review will summarize the different fields in which platelet function testing is currently in use; diagnostics of patients with bleeding disorders, monitoring patients’ response to anti-platelet therapy, monitoring in transfusion medicine (blood donors, platelet concentrates, and after transfusion), and monitoring in perioperative medicine to predict bleeding tendency. The second part of the review outlines different methods for platelet function testing, spanning bleeding time, and platelet counting as well as determining platelet adhesion, platelet secretion, platelet aggregation, platelet morphology, platelet signal transduction, platelet procoagulant activity, platelet apoptosis, platelet proteomics, and molecular biology. PMID:23653569

  3. Functional prediction of hypothetical proteins in human adenoviruses.

    PubMed

    Dorden, Shane; Mahadevan, Padmanabhan

    2015-01-01

    Assigning functional information to hypothetical proteins in virus genomes is crucial for gaining insight into their proteomes. Human adenoviruses are medium sized viruses that cause a range of diseases. Their genomes possess proteins with uncharacterized function known as hypothetical proteins. Using a wide range of protein function prediction servers, functional information was obtained about these hypothetical proteins. A comparison of functional information obtained from these servers revealed that some of them produced functional information, while others provided little functional information about these human adenovirus hypothetical proteins. The PFP, ESG, PSIPRED, 3d2GO, and ProtFun servers produced the most functional information regarding these hypothetical proteins. PMID:26664031

  4. CIT photoheliograph functional verification unit test program

    NASA Technical Reports Server (NTRS)

    1973-01-01

    Tests of the 2/3-meter photoheliograph functional verification unit FVU were performed with the FVU installed in its Big Bear Solar Observatory vacuum chamber. Interferometric tests were run both in Newtonian (f/3.85) and Gregorian (f/50) configurations. Tests were run in both configurations with optical axis horizontal, vertical, and at 45 deg to attempt to determine any gravity effects on the system. Gravity effects, if present, were masked by scatter in the data associated with the system wavefront error of 0.16 lambda rms ( = 6328A) apparently due to problems in the primary mirror. Tests showed that the redesigned secondary mirror assembly works well.

  5. Predictive Accuracy of Exercise Stress Testing the Healthy Adult.

    ERIC Educational Resources Information Center

    Lamont, Linda S.

    1981-01-01

    Exercise stress testing provides information on the aerobic capacity, heart rate, and blood pressure responses to graded exercises of a healthy adult. The reliability of exercise tests as a diagnostic procedure is discussed in relation to sensitivity and specificity and predictive accuracy. (JN)

  6. Predicting Work Activities with Divergent Thinking Tests: A Longitudinal Study

    ERIC Educational Resources Information Center

    Clapham, Maria M.; Cowdery, Edwina M.; King, Kelly E.; Montang, Melissa A.

    2005-01-01

    This study examined whether divergent thinking test scores obtained from engineering students during college predicted creative work activities fifteen years later. Results showed that a subscore of the "Owens Creativity Test", which assesses divergent thinking about mechanical objects, correlated significantly with self-ratings of creative work…

  7. Dopamine neurons share common response function for reward prediction error

    PubMed Central

    Eshel, Neir; Tian, Ju; Bukwich, Michael; Uchida, Naoshige

    2016-01-01

    Dopamine neurons are thought to signal reward prediction error, or the difference between actual and predicted reward. How dopamine neurons jointly encode this information, however, remains unclear. One possibility is that different neurons specialize in different aspects of prediction error; another is that each neuron calculates prediction error in the same way. We recorded from optogenetically-identified dopamine neurons in the lateral ventral tegmental area (VTA) while mice performed classical conditioning tasks. Our tasks allowed us to determine the full prediction error functions of dopamine neurons and compare them to each other. We found striking homogeneity among individual dopamine neurons: their responses to both unexpected and expected rewards followed the same function, just scaled up or down. As a result, we could describe both individual and population responses using just two parameters. Such uniformity ensures robust information coding, allowing each dopamine neuron to contribute fully to the prediction error signal. PMID:26854803

  8. Dopamine neurons share common response function for reward prediction error.

    PubMed

    Eshel, Neir; Tian, Ju; Bukwich, Michael; Uchida, Naoshige

    2016-03-01

    Dopamine neurons are thought to signal reward prediction error, or the difference between actual and predicted reward. How dopamine neurons jointly encode this information, however, remains unclear. One possibility is that different neurons specialize in different aspects of prediction error; another is that each neuron calculates prediction error in the same way. We recorded from optogenetically identified dopamine neurons in the lateral ventral tegmental area (VTA) while mice performed classical conditioning tasks. Our tasks allowed us to determine the full prediction error functions of dopamine neurons and compare them to each other. We found marked homogeneity among individual dopamine neurons: their responses to both unexpected and expected rewards followed the same function, just scaled up or down. As a result, we were able to describe both individual and population responses using just two parameters. Such uniformity ensures robust information coding, allowing each dopamine neuron to contribute fully to the prediction error signal. PMID:26854803

  9. Dopamine neurons share common response function for reward prediction error.

    PubMed

    Eshel, Neir; Tian, Ju; Bukwich, Michael; Uchida, Naoshige

    2016-03-01

    Dopamine neurons are thought to signal reward prediction error, or the difference between actual and predicted reward. How dopamine neurons jointly encode this information, however, remains unclear. One possibility is that different neurons specialize in different aspects of prediction error; another is that each neuron calculates prediction error in the same way. We recorded from optogenetically identified dopamine neurons in the lateral ventral tegmental area (VTA) while mice performed classical conditioning tasks. Our tasks allowed us to determine the full prediction error functions of dopamine neurons and compare them to each other. We found marked homogeneity among individual dopamine neurons: their responses to both unexpected and expected rewards followed the same function, just scaled up or down. As a result, we were able to describe both individual and population responses using just two parameters. Such uniformity ensures robust information coding, allowing each dopamine neuron to contribute fully to the prediction error signal.

  10. Predicting Item Difficulty in a Reading Comprehension Test with an Artificial Neural Network.

    ERIC Educational Resources Information Center

    Perkins, Kyle; And Others

    This paper reports the results of using a three-layer backpropagation artificial neural network to predict item difficulty in a reading comprehension test. Two network structures were developed, one with and one without a sigmoid function in the output processing unit. The data set, which consisted of a table of coded test items and corresponding…

  11. AGR-1 Safety Test Predictions using the PARFUME code

    SciTech Connect

    Blaise Collin

    2012-05-01

    The PARFUME modeling code was used to predict failure probability of TRISO-coated fuel particles and diffusion of fission products through these particles during safety tests following the first irradiation test of the Advanced Gas Reactor program (AGR-1). These calculations support the AGR-1 Safety Testing Experiment, which is part of the PIE effort on AGR-1. Modeling of the AGR-1 Safety Test Predictions includes a 620-day irradiation followed by a 300-hour heat-up phase of selected AGR-1 compacts. Results include fuel failure probability, palladium penetration, and fractional release of fission products. Results show that no particle failure is predicted during irradiation or heat-up, and that fractional release of fission products is limited during irradiation but that it significantly increases during heat-up.

  12. Postgenomic medicine. Presymptomatic testing for prediction and prevention.

    PubMed

    McCabe, L L; McCabe, E R

    2001-06-01

    Significant changes are occurring in genetic screening paradigms. Genetic screening is moving from traditional analytes, such as small molecules and proteins, to molecular genetic testing involving DNA and RNA. There are significant consequences to these changes, involving issues for the family unit, such as misattribution of parentage, and concerns regarding discrimination, confidentiality, and privacy. Although these latter issues have broader concerns for medicine and medical information, in the context of genetic testing, information derived from one individual can have a significant impact on others within their family. Screening is also changing from mendelian disease ascertainment to predictive testing. Issues that arise involve appropriate age at testing for adult-onset disorders, the clinical validity and clinical use of genetic testing for complex diseases, and the efficacy of interventions following genetic testing. We are also learning that the phenotypes of even simple mendelian disorders are influenced by complex genetic and environmental factors. The observations that genotypes rarely predict phenotypes absolutely have significant ramifications for counseling based on mutation analysis, for example in neonates who have not yet manifested symptoms and in older children and in adults undergoing predictive testing. Molecular genetic testing often proceeds rapidly from the research laboratory to the clinical setting. We must recognize that for single-gene disorders with high penetrance, the information derived from such testing may be relatively easy to interpret and apply. For complex diseases, however, the populations studied and their demographic characteristics are extremely important for extrapolation to counseling of individual patients. The value of population-based predictive testing is exemplified by newborn screening. It is clear that the Human Genome Project, and the information and technologies from it, will have a much broader impact on

  13. Functional testing: Approaches and injury management integration.

    PubMed

    Johnson, Laurie J.; Miller, Margot

    2001-01-01

    Functional Capacity Evaluations (FCEs) have become the standard for identifying an individual's physical abilities and/or limitations following injury or illness. While philosophies and approaches differ, the focus of most FCE systems is to identify the individual's maximum capabilities. This article will discuss the usefulness of the FCE information and how FCEs are impacted by multiple factors including APTA guidelines, machine based testing, therapist expertise, medical legal credibility and court testimony, IMEs and FCE, and return to work/return to function.

  14. An automated system for pulmonary function testing

    NASA Technical Reports Server (NTRS)

    Mauldin, D. G.

    1974-01-01

    An experiment to quantitate pulmonary function was accepted for the space shuttle concept verification test. The single breath maneuver and the nitrogen washout are combined to reduce the test time. Parameters are defined from the forced vital capacity maneuvers. A spirometer measures the breath volume and a magnetic section mass spectrometer provides definition of gas composition. Mass spectrometer and spirometer data are analyzed by a PDP-81 digital computer.

  15. Testing the link between functional diversity and ecosystem functioning in a Minnesota grassland experiment.

    PubMed

    Clark, Christopher M; Flynn, Dan F B; Butterfield, Bradley J; Reich, Peter B

    2012-01-01

    The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the association between eight leading functional diversity metrics (Rao's Q, FD, FDis, FEve, FDiv, convex hull volume, and species and functional group richness) that emphasize different attributes of functional diversity, plus 11 extensions of these existing metrics that incorporate heterogeneous species abundances and trait variation. We assess the relationships among these metrics and compare their performances for predicting three key ecosystem functions (above- and belowground biomass and light capture) within a long-term grassland biodiversity experiment. Many metrics were highly correlated, although unique information was captured in FEve, FDiv, and dendrogram-based measures (FD) that were adjusted by abundance. FD adjusted by abundance outperformed all other metrics in predicting both above- and belowground biomass, although several others also performed well (e.g. Rao's Q, FDis, FDiv). More generally, trait-based richness metrics and hybrid metrics incorporating multiple diversity attributes outperformed evenness metrics and single-attribute metrics, results that were not changed when combinations of metrics were explored. For light capture, species richness alone was the best predictor, suggesting that traits for canopy architecture would be necessary to improve predictions. Our study provides a comprehensive test linking different attributes of functional diversity with ecosystem function for a grassland system.

  16. A new protein structure representation for efficient protein function prediction.

    PubMed

    Maghawry, Huda A; Mostafa, Mostafa G M; Gharib, Tarek F

    2014-12-01

    One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average.

  17. Functional identity and diversity of animals predict ecosystem functioning better than species-based indices.

    PubMed

    Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

    2015-02-22

    Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.

  18. Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

    PubMed Central

    Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M.; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G.; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo

    2015-01-01

    Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. PMID:25567651

  19. Anonymous predictive testing for Huntington's disease in the United States.

    PubMed

    Visintainer, C L; Matthias-Hagen, V; Nance, M A

    2001-01-01

    The widespread use of a predictive genetic test for Huntington's disease (HD) since 1993 has brought to the forefront issues regarding genetic privacy. Although the possibility of anonymous genetic testing has been discussed, its use in the United States has not been described previously. We review the experiences of 11 genetics specialists with anonymous predictive testing for HD. We found that more men than women requested anonymous testing, for reasons that more often related to personal privacy than to insurance or discrimination concerns. A number of approaches to anonymity were used, and genetics specialists varied in the degree to which they were comfortable with the process. A number of legal, medical, and practical questions are raised, which will require resolution if anonymous testing is to be performed with a greater frequency in the future.

  20. Phytoplankton traits predict ecosystem function in a global set of lakes.

    PubMed

    Zwart, Jacob A; Solomon, Christopher T; Jones, Stuart E

    2015-08-01

    Predicting ecosystem function from environmental conditions is a central goal of ecosystem ecology. However, many traditional ecosystem models are tailored for specific regions or ecosystem types, requiring several regional models to predict the same function. Alternatively, trait-based approaches have been effectively used to predict community structure in both terrestrial and aquatic environments and ecosystem function in a limited number of terrestrial examples. Here, we test the efficacy of a trait-based model in predicting gross primary production (GPP) in lake ecosystems. We incorporated data from >1000 United States lakes along with laboratory-generated phytoplankton trait data to build a trait-based model of GPP and then validated the model with GPP observations from a separate set of globally distributed lakes. The trait-based model performed as well as or outperformed two ecosystem models both spatially and temporally, demonstrating the efficacy of trait-based models for predicting ecosystem function over a range of environmental conditions.

  1. Sexual abuse predicts functional somatic symptoms: an adolescent population study.

    PubMed

    Bonvanie, Irma J; van Gils, Anne; Janssens, Karin A M; Rosmalen, Judith G M

    2015-08-01

    The main aim of this study was to investigate the effect of childhood sexual abuse on medically not well explained or functional somatic symptoms (FSSs) in adolescents. We hypothesized that sexual abuse predicts higher levels of FSSs and that anxiety and depression contribute to this relationship. In addition, we hypothesized that more severe abuse is associated with higher levels of FSSs and that sexual abuse is related to gastrointestinal FSSs in particular. This study was part of the Tracking Adolescents' Individual Lives Survey (TRAILS): a general population cohort which started in 2001 (N=2,230; 50.8% girls, mean age 11.1 years). The current study uses data of 1,680 participants over four assessment waves (75% of baseline, mean duration of follow-up: 8 years). FSSs were measured by the Somatic Complaints subscale of the Youth Self-Report at all waves. Sexual abuse before the age of sixteen was assessed retrospectively with a questionnaire at T4. To test the hypotheses linear mixed models were used adjusted for age, sex, socioeconomic status, anxiety and depression. Sexual abuse predicted higher levels of FSSs after adjustment for age sex and socioeconomic status (B=.06) and after additional adjustment for anxiety and depression (B=.03). While sexual abuse involving physical contact significantly predicted the level of FSSs (assault; B=.08, rape; B=.05), non-contact sexual abuse was not significantly associated with FSSs (B=.04). Sexual abuse was not a stronger predictor of gastrointestinal FSSs (B=.06) than of all FSSs. Further research is needed to clarify possible mechanisms underlying relationship between sexual abuse and FSSs. PMID:26142915

  2. Does obesity predict functional outcome in the dysvascular amputee?

    PubMed

    Kalbaugh, Corey A; Taylor, Spence M; Kalbaugh, Brooke A; Halliday, Matthew; Daniel, Grace; Cass, Anna L; Blackhurst, Dawn W; Cull, David L; Langan, Eugene M; Carsten, Christopher G; York, John W; Snyder, Bruce A; Youkey, Jerry R

    2006-08-01

    Limited information is available concerning the effects of obesity on the functional outcomes of patients requiring major lower limb amputation because of peripheral arterial disease (PAD). The purpose of this study was to examine the predictive ability of body mass index (BMI) to determine functional outcome in the dysvascular amputee. To do this, 434 consecutive patients (mean age, 65.8 +/- 13.3, 59% male, 71.4% diabetic) undergoing major limb amputation (225 below-knee amputation, 27 through-knee amputation, 132 above-knee amputation, and 50 bilateral) as a complication of PAD from January 1998 through May 2004 were analyzed according to preoperative BMI. BMI was classified according to the four-group Center for Disease Control system: underweight, 0 to 18.4 kg/m2; normal, 18.5 to 24.9 kg/m2; overweight, 25 to 29.9 kg/m2; and obese, > or = 30 kg/m2. Outcome parameters measured included prosthetic usage, maintenance of ambulation, survival, and maintenance of independent living status. The chi2 test for association was used to examine prosthesis wear. Kaplan-Meier curves were constructed to assess maintenance of ambulation, survival, and maintenance of independent living status. Multivariate analysis using the multiple logistic regression model and a Cox proportional hazards model were used to predict variables independently associated with prosthetic use and ambulation, survival, and independence, respectively. Overall prosthetic usage and 36-month ambulation, survival, and independent living status for the entire cohort was 48.6 per cent, 42.8 per cent, 48.1 per cent, 72.3 per cent, and for patients with normal BMI was 41.5 per cent, 37.4 per cent, 45.6 per cent, and 69.5 per cent, respectively. There was no statistically significant difference in outcomes for overweight patients (59.2%, 50.7%, 52.5%, and 75%) or obese patients (51.8%, 46.2%, 49.7%, and 75%) when compared with normal patients. Although there were significantly poorer outcomes for underweight

  3. Gas Test Loop Functional and Technical Requirements

    SciTech Connect

    Glen R. Longhurst; Soli T. Khericha; James L. Jones

    2004-09-01

    This document defines the technical and functional requirements for a gas test loop (GTL) to be constructed for the purpose of providing a high intensity fast-flux irradiation environment for developers of advanced concept nuclear reactors. This capability is needed to meet fuels and materials testing requirements of the designers of Generation IV (GEN IV) reactors and other programs within the purview of the Advanced Fuel Cycle Initiative (AFCI). Space nuclear power development programs may also benefit by the services the GTL will offer. The overall GTL technical objective is to provide developers with the means for investigating and qualifying fuels and materials needed for advanced reactor concepts. The testing environment includes a fast-flux neutron spectrum of sufficient intensity to perform accelerated irradiation testing. Appropriate irradiation temperature, gaseous environment, test volume, diagnostics, and access and handling features are also needed. This document serves to identify those requirements as well as generic requirements applicable to any system of this kind.

  4. A Survey of Computational Intelligence Techniques in Protein Function Prediction

    PubMed Central

    Tiwari, Arvind Kumar; Srivastava, Rajeev

    2014-01-01

    During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Therefore, to alleviate the problems associated with homology based traditional approaches, numerous computational intelligence techniques have been proposed in the recent past. This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network, and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein coupled receptors, membrane proteins, and pathway analysis from gene expression datasets. This paper also summarizes the result obtained by many researchers to solve these problems by using computational intelligence techniques with appropriate datasets to improve the prediction performance. The summary shows that ensemble classifiers and integration of multiple heterogeneous data are useful for protein function prediction. PMID:25574395

  5. Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

    PubMed Central

    Nilmeier, Jerome P.; Kirshner, Daniel A.; Wong, Sergio E.; Lightstone, Felice C.

    2013-01-01

    We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues – The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches. PMID:23675414

  6. Rapid catalytic template searching as an enzyme function prediction procedure.

    PubMed

    Nilmeier, Jerome P; Kirshner, Daniel A; Wong, Sergio E; Lightstone, Felice C

    2013-01-01

    We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues--The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches.

  7. A Unitary Executive Function Predicts Intelligence in Children

    ERIC Educational Resources Information Center

    Brydges, Christopher R.; Reid, Corinne L.; Fox, Allison M.; Anderson, Mike

    2012-01-01

    Executive functions (EF) and intelligence are of critical importance to success in many everyday tasks. Working memory, or updating, which is one latent variable identified in confirmatory factor analytic models of executive functions, predicts intelligence (both fluid and crystallised) in adults, but inhibition and shifting do not (Friedman et…

  8. Protein Structure and Function Prediction Using I-TASSER.

    PubMed

    Yang, Jianyi; Zhang, Yang

    2015-01-01

    I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets.

  9. Predictive testing for Huntington's disease with linked DNA markers.

    PubMed

    Brock, D J; Mennie, M; Curtis, A; Millan, F A; Barron, L; Raeburn, J A; Dinwoodie, D; Holloway, S; Crosbie, A; Wright, A

    1989-08-26

    Availability of new DNA markers, more tightly linked to the Huntington's disease (HD) locus than the original G8 (D4S10) probes, has improved predictive accuracy for both presymptomatic and prenatal exclusion testing. 50 predictive tests were carried out on high-risk individuals. 6 of these were on first-trimester chorionic villus biopsy specimens; in 2 cases the HD gene was not transmitted to the fetus while in 4 cases no exclusion could be made. The remaining 44 tests were on adults with either 25 or 50% risk of manifesting the disease; 19 had a greatly increased risk and 25 a substantially decreased risk of HD. Family structures in Scotland are suitable for testing about 75% of potentially affected individuals, and the new generation of DNA markers makes virtually all families fully informative.

  10. Prospective prediction of functional difficulties among recently separated veterans.

    PubMed

    Larson, Gerald E; Norman, Sonya B

    2014-01-01

    Reports of functional problems are common among Veterans who served post-9/11 (more than 25% report functional difficulties in at least one domain). However, little prospective work has examined the risk and protective factors for functional difficulties among Veterans. In a sample of recently separated Marines, we used stepwise logistic and multiple regressions to identify predictors of functional impairment, including work-related problems, financial problems, unlawful behavior, activity limitations due to mental health symptoms, and perceived difficulty reintegrating into civilian life. Posttraumatic stress disorder symptoms assessed both before and after military separation significantly predicted functional difficulties across all domains except unlawful behavior. Certain outcomes, such as unlawful behavior and activity limitations due to mental health symptoms, were predicted by other or additional predictors. Although several forms of functioning were examined, the list was not exhaustive. The results highlight a number of areas where targeted interventions may facilitate the reintegration of military servicemembers into civilian life.

  11. Platelet function tests: a comparative review

    PubMed Central

    Paniccia, Rita; Priora, Raffaella; Alessandrello Liotta, Agatina; Abbate, Rosanna

    2015-01-01

    In physiological hemostasis a prompt recruitment of platelets on the vessel damage prevents the bleeding by the rapid formation of a platelet plug. Qualitative and/or quantitative platelet defects promote bleeding, whereas the high residual reactivity of platelets in patients on antiplatelet therapies moves forward thromboembolic complications. The biochemical mechanisms of the different phases of platelet activation – adhesion, shape change, release reaction, and aggregation – have been well delineated, whereas their complete translation into laboratory assays has not been so fulfilled. Laboratory tests of platelet function, such as bleeding time, light transmission platelet aggregation, lumiaggregometry, impedance aggregometry on whole blood, and platelet activation investigated by flow cytometry, are traditionally utilized for diagnosing hemostatic disorders and managing patients with platelet and hemostatic defects, but their use is still limited to specialized laboratories. To date, a point-of-care testing (POCT) dedicated to platelet function, using pertinent devices much simpler to use, has now become available (ie, PFA-100, VerifyNow System, Multiplate Electrode Aggregometry [MEA]). POCT includes new methodologies which may be used in critical clinical settings and also in general laboratories because they are rapid and easy to use, employing whole blood without the necessity of sample processing. Actually, these different platelet methodologies for the evaluation of inherited and acquired bleeding disorders and/or for monitoring antiplatelet therapies are spreading and the study of platelet function is strengthening. In this review, well-tried and innovative platelet function tests and their methodological features and clinical applications are considered. PMID:25733843

  12. A new scintigraphic test of neorectal function

    SciTech Connect

    O'Connell, P.R.; Omdahl, A.L.; Brown, M.L.; Kelly, K.A.

    1985-05-01

    Current tests of neorectal function after colectomy, mucosal rectectomy and ileal pouch-anal anastomosis are inadequate. The authors developed a new scintigraphic test that uses an artificial stool made of aluminium magnesium silicate gel (Veegum). Solutions of the gel were labeled with 1 mCi Tc-99m by stirring Veegum powder into water containing the isotope at 37/sup 0/C. Excellent binding was obtained with the sulfur colloid form of the isotope compared with the pertechnetate or ovalbumin forms (Table). The sulfur colloid isotope in 7.5% gel was used in subsequent tests. The volume given to the patients corresponded to the maximum capacity of the ileal pouch as measured manometrically; it averaged 300 ml. Ten patients have been studied to date with minimal patient discomfort. The gel was introduced over a 2 minute period via a 16Fr. transanal tube with the patient in the left lateral position. After 5 minutes AP standing and R lateral scans were taken. Then a dynamic scan was taken while the patient evacuated the gel into a commode. After evacuation AP and R lateral scans were repeated. Computer analysis was used to determine both the functional pouch capacity and the rates of emptying of the pouch and the more proximal ileum. The test has proven useful in the assessment of neorectal anatomy and function after ileal pouch-anal anastomosis.

  13. Prediction of R-curves from small coupon tests

    NASA Technical Reports Server (NTRS)

    Yeh, J. R.; Bray, G. H.; Bucci, R. J.; Macheret, Y.

    1994-01-01

    R-curves were predicted for Alclad 2024-T3 and C188-T3 sheet using the results of small-coupon Kahn tear tests in combination with two-dimensional elastic-plastic finite element stress analyses. The predictions were compared to experimental R-curves from 6.3, 16 and 60-inch wide M(T) specimens and good agreement was obtained. The method is an inexpensive alternative to wide panel testing for characterizing the fracture toughness of damage-tolerant sheet alloys. The usefulness of this approach was demonstrated by performing residual strength calculations for a two-bay crack in a representative fuselage structure. C188-T3 was predicted to have a 24 percent higher load carrying capability than 2024-T3 in this application as a result of its superior fracture toughness.

  14. For Tests That Are Predictively Powerful and without Social Prejudice

    ERIC Educational Resources Information Center

    Soares, Joseph A.

    2012-01-01

    In Philip Pullman's dark matter sci-fi trilogy, there is a golden compass that in the hands of the right person is predictively powerful; the same was supposed to be true of the SAT/ACT--the statistically indistinguishable standardized tests for college admissions. They were intended to be reliable mechanisms for identifying future trajectories,…

  15. Volunteering for Job Enrichment: A Test of Expectancy Theory Predictions

    ERIC Educational Resources Information Center

    Giles, William F.

    1977-01-01

    In order to test predictions derived from an expectancy theory model developed by E. E. Lawler, measures of higher-order need satisfaction, locus of control, and intrinsic motivation were obtained from 252 female assembly line workers. Implications of the results for placement of individuals in enriched jobs are discussed. (Editor/RK)

  16. The Second Century of Ability Testing: Some Predictions and Speculations

    ERIC Educational Resources Information Center

    Embretson, Susan E.

    2004-01-01

    The last century was marked by dazzling changes in many areas, such as technology and communications. Predictions into the second century of testing are seemingly difficult in such a context. Yet, looking back to the turn of the last century, Kirkpatrick (1900), in his American Psychological Association presidential address, presented fundamental…

  17. Cut-off point for the trail making test to predict unsafe driving after stroke

    PubMed Central

    Choi, Seong Youl; Lee, Jae Shin; Oh, Young Ju

    2016-01-01

    [Purpose] This study examined the cut-off point of the Trail Making Test in predicting the risk of unsafe driving in stroke patients. [Subjects and Methods] A total of 81 stroke patients with a driver’s license participated in this study. The DriveABLE Cognitive Assessment Tool, Trail Making Test-A, and Trail Making Test-B evaluations were conducted in all participants. All participants were classified into the safety or risk groups based on the DriveABLE Cognitive Assessment Tool evaluation results. The Trail Making Test results underwent a receiver operating characteristic analysis in each group. [Results] The results of the receiver operating characteristic curve analysis showed that the cut-off point for Trail Making Test-A was 32 seconds and the cut-off point for Trail Making Test-B was 79 seconds. The positive predictive values of the Trail Making Test-A and Trail Making Test-B were 98.3% and 98.3%, respectively, and the negative predictive values of the Trail Making Test-A and Trail Making Test-B were 81.0% and 73.9%, respectively. [Conclusion] The Trail Making Test is a useful tool for predicting the risk of unsafe driving in stroke patients. This tool is expected to be used more actively for screening stroke drivers with respect to their cognitive function. PMID:27512277

  18. Cut-off point for the trail making test to predict unsafe driving after stroke.

    PubMed

    Choi, Seong Youl; Lee, Jae Shin; Oh, Young Ju

    2016-07-01

    [Purpose] This study examined the cut-off point of the Trail Making Test in predicting the risk of unsafe driving in stroke patients. [Subjects and Methods] A total of 81 stroke patients with a driver's license participated in this study. The DriveABLE Cognitive Assessment Tool, Trail Making Test-A, and Trail Making Test-B evaluations were conducted in all participants. All participants were classified into the safety or risk groups based on the DriveABLE Cognitive Assessment Tool evaluation results. The Trail Making Test results underwent a receiver operating characteristic analysis in each group. [Results] The results of the receiver operating characteristic curve analysis showed that the cut-off point for Trail Making Test-A was 32 seconds and the cut-off point for Trail Making Test-B was 79 seconds. The positive predictive values of the Trail Making Test-A and Trail Making Test-B were 98.3% and 98.3%, respectively, and the negative predictive values of the Trail Making Test-A and Trail Making Test-B were 81.0% and 73.9%, respectively. [Conclusion] The Trail Making Test is a useful tool for predicting the risk of unsafe driving in stroke patients. This tool is expected to be used more actively for screening stroke drivers with respect to their cognitive function.

  19. Gamow states as continuous linear functionals over analytical test functions

    SciTech Connect

    Bollini, C.G.; Civitarese, O.; De Paoli, A.L.; Rocca, M.C. |

    1996-09-01

    The space of analytical test functions {xi}, rapidly decreasing on the real axis (i.e., Schwartz test functions of the type S on the real axis), is used to construct the rigged Hilbert space (RHS) ({xi},H,{xi}{prime}). Gamow states (GS) can be defined in RHS starting from Dirac{close_quote}s formula. It is shown that the expectation value of a self-adjoint operator acting on a GS is real. We have computed exactly the probability of finding a system in a GS and found that it is finite. The validity of recently proposed approximations to calculate the expectation value of self-adjoint operators in a GS is discussed. {copyright} {ital 1996 American Institute of Physics.}

  20. Prediction of Erectile Function Following Treatment for Prostate Cancer

    PubMed Central

    Alemozaffar, Mehrdad; Regan, Meredith M.; Cooperberg, Matthew R.; Wei, John T.; Michalski, Jeff M.; Sandler, Howard M.; Hembroff, Larry; Sadetsky, Natalia; Saigal, Christopher S.; Litwin, Mark S.; Klein, Eric; Kibel, Adam S.; Hamstra, Daniel A.; Pisters, Louis L.; Kuban, Deborah A.; Kaplan, Irving D.; Wood, David P.; Ciezki, Jay; Dunn, Rodney L.; Carroll, Peter R.; Sanda, Martin G.

    2013-01-01

    Context Sexual function is the health-related quality of life (HRQOL) domain most commonly impaired after prostate cancer treatment; however, validated tools to enable personalized prediction of erectile dysfunction after prostate cancer treatment are lacking. Objective To predict long-term erectile function following prostate cancer treatment based on individual patient and treatment characteristics. Design Pretreatment patient characteristics, sexual HRQOL, and treatment details measured in a longitudinal academic multicenter cohort (Prostate Cancer Outcomes and Satisfaction With Treatment Quality Assessment; enrolled from 2003 through 2006), were used to develop models predicting erectile function 2 years after treatment. A community-based cohort (community-based Cancer of the Prostate Strategic Urologic Research Endeavor [CaPSURE]; enrolled 1995 through 2007) externally validated model performance. Patients in US academic and community-based practices whose HRQOL was measured pretreatment (N = 1201) underwent follow-up after prostatectomy, external radiotherapy, or brachytherapy for prostate cancer. Sexual outcomes among men completing 2 years’ follow-up (n = 1027) were used to develop models predicting erectile function that were externally validated among 1913 patients in a community-based cohort. Main Outcome Measures Patient-reported functional erections suitable for intercourse 2 years following prostate cancer treatment. Results Two years after prostate cancer treatment, 368 (37% [95% CI, 34%–40%]) of all patients and 335 (48% [95% CI, 45%–52%]) of those with functional erections prior to treatment reported functional erections; 531 (53% [95% CI, 50%–56%]) of patients without penile prostheses reported use of medications or other devices for erectile dysfunction. Pretreatment sexual HRQOL score, age, serum prostate-specific antigen level, race/ethnicity, body mass index, and intended treatment details were associated with functional erections 2

  1. Predictive genetic testing in urology: ethical and social issues.

    PubMed

    Mehlman, Maxwell J

    2004-02-01

    In order to maximize the benefits of predictive genetic testing in urology, the potential ethical and social risks must be identified and minimized. Necessary steps include providing adequate information for patients and families; preparing them to receive test results; maintaining confidentiality to avoid social stigma and discrimination; preserving the principal of solidarity to provide assurances of medical care and social support for persons at risk of genetic illness; and avoiding inappropriate social pressure to prevent the birth of at-risk individuals. Health professionals must play a significant role in helping individuals, families, and society in general to make sound testing decisions and policy. PMID:14691643

  2. Non-animal test methods for predicting skin sensitization potentials.

    PubMed

    Mehling, Annette; Eriksson, Tove; Eltze, Tobias; Kolle, Susanne; Ramirez, Tzutzuy; Teubner, Wera; van Ravenzwaay, Bennard; Landsiedel, Robert

    2012-08-01

    Contact allergies are complex diseases, and it is estimated that 15-20 % of the general population suffers from contact allergy, with increasing prevalence. Evaluation of the sensitization potential of a substance is usually carried out in animal models. Nowadays, there is much interest in reducing and ultimately replacing current animal tests. Furthermore, as of 2013, the EU has posed a ban on animal testing of cosmetic ingredients that includes skin sensitization. Therefore, predictive and robust in vitro tests are urgently needed. In order to establish alternatives to animal testing, the in vitro tests must mimic the very complex interactions between the sensitizing chemical and the different parts of the immune system. This review article summarizes recent efforts to develop in vitro tests for predicting skin sensitizers. Cell-based assays, in chemico methods and, to a lesser extent, in silico methods are presented together with a discussion of their current status. With considerable progress having been achieved during the last years, the rationale today is that data from different non-animal test methods will have to be combined in order to obtain reliable hazard and potency information on potential skin sensitizers. PMID:22707154

  3. Simple exercise test for the prediction of relative heat tolerance

    SciTech Connect

    Kenney, W.L.; Lewis, D.A.; Anderson, R.K.; Kamon, E.

    1986-04-01

    A medical screening exercise test is presented which accurately predicts relative heat tolerance during work in very hot environments. The test consisted of 15-20 min of exercise at a standard absolute intensity of about 600 kcal/hr (140W) with the subject wearing a vapor-barrier suit. Five minutes after the subject exercised, recovery heart rate was measured. When this heart rate is used, a physiological limit (+/- approximately 5 min) can be predicted with 95% confidence for the most intense work-heat conditions found in nuclear power stations. In addition, site health and safety personnel can establish qualification criteria for work on hot jobs, based on the test results. The test as developed can be performed in an office environment with the use of a minimum of equipment by personnel with minimal expertise and training. Total maximal test duration is about 20-25 min per person and only heart rate need be monitored (simple pulse palpation will suffice). Test modality is adaptable to any ergometer, the most readily available and least expensive of which is bench-stepping. It is recommended that this test be available for use for those persons who, based upon routine medical examination or past history, are suspected of being relatively heat intolerant.

  4. Platelet Function Tests in Bleeding Disorders.

    PubMed

    Lassila, Riitta

    2016-04-01

    Functional disorders of platelets can involve any aspect of platelet physiology, with many different effects or outcomes. These include platelet numbers (thrombocytosis or thrombocytopenia); changes in platelet production or destruction, or capture to the liver (Ashwell receptor); altered adhesion to vascular injury sites and/or influence on hemostasis and wound healing; and altered activation or receptor functions, shape change, spreading and release reactions, procoagulant and antifibrinolytic activity. Procoagulant membrane alterations, and generation of thrombin and fibrin, also affect platelet aggregation. The above parameters can all be studied, but standardization and quality control of assay methods have been limited despite several efforts. Only after a comprehensive clinical bleeding assessment, including family history, information on drug use affecting platelets, and exclusion of coagulation factor, and tissue deficits, should platelet function testing be undertaken to confirm an abnormality. Current diagnostic tools include blood cell counts, platelet characteristics according to the cell counter parameters, peripheral blood smear, exclusion of pseudothrombocytopenia, whole blood aggregometry (WBA) or light transmission aggregometry (LTA) in platelet-rich plasma, luminescence, platelet function analysis (PFA-100) for platelet adhesion and deposition to collagen cartridges under blood flow, and finally transmission electron microscopy to exclude rare structural defects leading to functional deficits. The most validated test panels are included in WBA, LTA, and PFA. Because platelets are isolated from their natural environment, many simplifications occur, as circulating blood and interaction with vascular wall are omitted in these assays. The target to reach a highly specific platelet disorder diagnosis in routine clinical management can be exhaustive, unless needed for genetic counseling. The elective overall assessment of platelet function disorder

  5. Further development of forensic eye color predictive tests.

    PubMed

    Ruiz, Y; Phillips, C; Gomez-Tato, A; Alvarez-Dios, J; Casares de Cal, M; Cruz, R; Maroñas, O; Söchtig, J; Fondevila, M; Rodriguez-Cid, M J; Carracedo, A; Lareu, M V

    2013-01-01

    In forensic analysis predictive tests for external visible characteristics (or EVCs), including inference of iris color, represent a potentially useful tool to guide criminal investigations. Two recent studies, both focused on forensic testing, have analyzed single nucleotide polymorphism (SNP) genotypes underlying common eye color variation (Mengel-From et al., Forensic Sci. Int. Genet. 4:323 and Walsh et al., Forensic Sci. Int. Genet. 5:170). Each study arrived at different recommendations for eye color predictive tests aiming to type the most closely associated SNPs, although both confirmed rs12913832 in HERC2 as the key predictor, widely recognized as the most strongly associated marker with blue and brown iris colors. Differences between these two studies in identification of other eye color predictors may partly arise from varying approaches to assigning phenotypes, notably those not unequivocally blue or dark brown and therefore occupying an intermediate iris color continuum. We have developed two single base extension assays typing 37 SNPs in pigmentation-associated genes to study SNP-genotype based prediction of eye, skin, and hair color variation. These assays were used to test the performance of different sets of eye color predictors in 416 subjects from six populations of north and south Europe. The presence of a complex and continuous range of intermediate phenotypes distinct from blue and brown eye colors was confirmed by establishing eye color populations compared to genetic clusters defined using Structure software. Our study explored the effect of an expanded SNP combination beyond six markers has on the ability to predict eye color in a forensic test without extending the SNP assay excessively - thus maintaining a balance between the test's predictive value and an ability to reliably type challenging DNA with a multiplex of manageable size. Our evaluation used AUC analysis (area under the receiver operating characteristic curves) and na

  6. Artificial neural network predictions of degradation of nonmetallic lining materials from laboratory tests

    SciTech Connect

    Silverman, D.C. )

    1994-06-01

    Such organic materials of construction as plastics (thermoplastics and thermosets) and elastomers play an increasingly important role in the containment of corrosive fluids. One major impediment to their routine use is the inability to predict their performance from laboratory tests rapidly and reliably. Artificial neural networks are computer simulations that have the potential to find the same patterns that corrosion practitioners recognize to relate experimental test results to lifetime predictions. This potential was used to construct an artificial neural network to recognize the pattern between results from a sequential immersion test for organic nonmetallic lining materials and their ability to function as linings in actual applications. The network was shown to predict field performance. The network was incorporated within an expert system to simplify data input and output, to allow for simple consistency checks between sample appearance and network output, and to make the final prediction.

  7. Testing galaxy formation models with galaxy stellar mass functions

    NASA Astrophysics Data System (ADS)

    Lim, S. H.; Mo, H. J.; Lan, Ting-Wen; Ménard, Brice

    2016-10-01

    We compare predictions of a number of empirical models and numerical simulations of galaxy formation to the conditional stellar mass functions (CSMF) of galaxies in groups of different masses obtained recently by Lan et al. to test how well different models accommodate the data. The observational data clearly prefer a model in which star formation in low-mass halos changes behavior at a characteristic redshift zc ˜ 2. There is also tentative evidence that this characteristic redshift depends on environment, becoming zc ˜ 4 in regions that eventually evolve into rich clusters of galaxies. The constrained model is used to understand how galaxies form and evolve in dark matter halos, and to make predictions for other statistical properties of the galaxy population, such as the stellar mass functions of galaxies at high z, the star formation and stellar mass assembly histories in dark matter halos. A comparison of our model predictions with those of other empirical models shows that different models can make vastly different predictions, even though all of them are tuned to match the observed stellar mass functions of galaxies.

  8. PredictProtein—an open resource for online prediction of protein structural and functional features

    PubMed Central

    Yachdav, Guy; Kloppmann, Edda; Kajan, Laszlo; Hecht, Maximilian; Goldberg, Tatyana; Hamp, Tobias; Hönigschmid, Peter; Schafferhans, Andrea; Roos, Manfred; Bernhofer, Michael; Richter, Lothar; Ashkenazy, Haim; Punta, Marco; Schlessinger, Avner; Bromberg, Yana; Schneider, Reinhard; Vriend, Gerrit; Sander, Chris; Ben-Tal, Nir; Rost, Burkhard

    2014-01-01

    PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org. PMID:24799431

  9. Predicting neuropsychological test performance on the basis of temporal orientation.

    PubMed

    Ryan, Joseph J; Glass, Laura A; Bartels, Jared M; Bergner, CariAnn M; Paolo, Anthony M

    2009-05-01

    Temporal orientation is often disrupted in the context of psychiatric or neurological disease; tests assessing this function are included in most mental status examinations. The present study examined the relationship between scores on the Temporal Orientation Scale (TOS) and performance on a battery of tests that assess memory, language, and cognitive functioning in a sample of patients with Alzheimer's disease (N = 55). Pearson-product moment correlations showed that, in all but two instances, the TOS was significantly correlated with each neuropsychological measure, p values < or = .05. Also, severely disoriented (i.e., TOS score < or = -8) patients were consistently 'impaired' on memory tests but not on tests of language and general cognitive functioning.

  10. Predicted Turbine Heat Transfer for a Range of Test Conditions

    NASA Technical Reports Server (NTRS)

    Boyle, R. J.; Lucci, B. L.

    1996-01-01

    Comparisons are shown between predictions and experimental data for blade and endwall heat transfer. The comparisons of computational domain parisons are given for both vane and rotor geometries over an extensive range of Reynolds and Mach numbers. Comparisons are made with experimental data from a variety of sources. A number of turbulence models are available for predicting blade surface heat transfer, as well as aerodynamic performance. The results of an investigation to determine the turbulence model which gives the best agreement with experimental data over a wide range of test conditions are presented.

  11. ANDROMEDA DWARFS IN LIGHT OF MOND. II. TESTING PRIOR PREDICTIONS

    SciTech Connect

    McGaugh, Stacy; Milgrom, Mordehai

    2013-10-01

    We employ recently published measurements of the velocity dispersions in the newly discovered dwarf satellite galaxies of Andromeda to test our previously published predictions of this quantity. The data are in good agreement with our specific predictions for each dwarf made a priori with modified Newtonian dynamics (MOND), with reasonable stellar mass-to-light ratios, and no dark matter, while Newtonian dynamics point to quite large mass discrepancies in these systems. MOND distinguishes between regimes where the internal field of the dwarf, or the external field of the host, dominates. The data appear to recognize this distinction, which is a unique feature of MOND not explicable in ΛCDM.

  12. Predicting First-Quarter Test Scores from the New Medical College Admission Test.

    ERIC Educational Resources Information Center

    Cullen, Thomas J.; And Others

    1980-01-01

    The predictive validity of the new Medical College Admission Test as it relates to end-of-quarter examinations in anatomy, histology, physiology, biochemistry, and "ages of man" is presented. Results indicate that the Science Knowledge assessment areas of chemistry and physics and the Science Problems subtest were most useful in predicting student…

  13. Prediction of Postchemotherapy Ovarian Function Using Markers of Ovarian Reserve

    PubMed Central

    Xia, Rong; Schott, Anne F.; McConnell, Daniel; Banerjee, Mousumi; Hayes, Daniel F.

    2014-01-01

    Background. Reproductive-aged women frequently receive both chemotherapy and endocrine therapy as part of their treatment regimen for early stage hormone receptor-positive breast cancer. Chemotherapy results in transient or permanent ovarian failure in the majority of women. The difficulty in determining which patients will recover ovarian function has implications for adjuvant endocrine therapy decision making. We hypothesized that pretreatment serum anti-Müllerian hormone (AMH) and inhibin B concentrations would predict for ovarian function following chemotherapy. Methods. Pre- and perimenopausal women aged 25–50 years with newly diagnosed breast cancer were enrolled. Subjects underwent phlebotomy for assessment of serum AMH, inhibin B, follicle-stimulating hormone, and estradiol prior to chemotherapy and 1 month and 1 year following completion of treatment. Associations among hormone concentrations, clinical factors, and biochemically assessed ovarian function were assessed. Results. Twenty-seven subjects were evaluable for the primary endpoint. Median age was 41. Twenty subjects (74.1%) experienced recovery of ovarian function within 18 months. Of the 26 evaluable subjects assessed prior to chemotherapy, 19 (73.1%) had detectable serum concentrations of AMH. The positive predictive value of a detectable baseline serum AMH concentration for recovery of ovarian function was 94.7%, and the negative predictive value was 85.7%. On univariate analysis, younger age and detectable serum AMH concentration at chemotherapy initiation were predictive of increased likelihood of recovery of ovarian function. Conclusion. Prechemotherapy assessment of serum AMH may be useful for predicting postchemotherapy ovarian function. This finding has implications for decision making about adjuvant endocrine therapy in premenopausal women treated with chemotherapy. PMID:24319018

  14. 33 CFR 157.12f - Workshop functional test requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Workshop functional test... CARRYING OIL IN BULK Design, Equipment, and Installation § 157.12f Workshop functional test requirements... functional test on a suitable test bench prior to delivery. The detailed program for a functional test...

  15. 33 CFR 157.12f - Workshop functional test requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Workshop functional test... CARRYING OIL IN BULK Design, Equipment, and Installation § 157.12f Workshop functional test requirements... functional test on a suitable test bench prior to delivery. The detailed program for a functional test...

  16. 33 CFR 157.12f - Workshop functional test requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Workshop functional test... CARRYING OIL IN BULK Design, Equipment, and Installation § 157.12f Workshop functional test requirements... functional test on a suitable test bench prior to delivery. The detailed program for a functional test...

  17. Evolutionary Ensemble for In Silico Prediction of Ames Test Mutagenicity

    NASA Astrophysics Data System (ADS)

    Chen, Huanhuan; Yao, Xin

    Driven by new regulations and animal welfare, the need to develop in silico models has increased recently as alternative approaches to safety assessment of chemicals without animal testing. This paper describes a novel machine learning ensemble approach to building an in silico model for the prediction of the Ames test mutagenicity, one of a battery of the most commonly used experimental in vitro and in vivo genotoxicity tests for safety evaluation of chemicals. Evolutionary random neural ensemble with negative correlation learning (ERNE) [1] was developed based on neural networks and evolutionary algorithms. ERNE combines the method of bootstrap sampling on training data with the method of random subspace feature selection to ensure diversity in creating individuals within an initial ensemble. Furthermore, while evolving individuals within the ensemble, it makes use of the negative correlation learning, enabling individual NNs to be trained as accurate as possible while still manage to maintain them as diverse as possible. Therefore, the resulting individuals in the final ensemble are capable of cooperating collectively to achieve better generalization of prediction. The empirical experiment suggest that ERNE is an effective ensemble approach for predicting the Ames test mutagenicity of chemicals.

  18. Executive function does not predict coping with symptoms in stable patients with a diagnosis of schizophrenia

    PubMed Central

    Bak, Maarten; Krabbendam, Lydia; Delespaul, Philippe; Huistra, Karola; Walraven, Wil; van Os, Jim

    2008-01-01

    Background Associations between coping with and control over psychotic symptoms were examined using the Maastricht Assessment of Coping Strategies-24, testing the hypothesis that the cognitive domain of executive functioning predicted quality and quantity of coping. Methods MACS-24 was administered to 32 individuals with a diagnosis of schizophrenia. For each of 24 symptoms, experience of distress, type of coping and the resulting degree of perceived control were assessed. Coping types were reduced to two contrasting coping categories: symptomatic coping (SC) and non-symptomatic coping (NSC; combining active problem solving, passive illness behaviour, active problem avoiding, and passive problem avoiding). Cognitive functioning was assessed using the GIT (Groninger Intelligence Test), the Zoo map (BADS: Behavioural Assessment of Dysexecutive function), Stroop-test and Trail making. Results Cognitive function was not associated with frequency of coping, nor did cognitive function differentially predict SC or NSC. Cognitive function similarly was not associated with symptom distress or level of perceived control over the symptom. Conclusion There was no evidence that cognitive function predicts quantity or quality of coping with symptoms in people with a diagnosis of schizophrenia. Variation in the realm of emotion regulation and social cognition may be more predictive of coping with psychotic symptoms. PMID:18510757

  19. Predicting real-world functional milestones in schizophrenia.

    PubMed

    Olsson, Anna-Karin; Hjärthag, Fredrik; Helldin, Lars

    2016-08-30

    Schizophrenia is a severe disorder that often causes impairments in major areas of functioning, and most patients do not achieve expected real-world functional milestones. The aim of this study was to identify which variables of demography, illness activity, and functional capacity predict patients' ability to attain real-world functional milestones. Participants were 235 outpatients, 149 men and 86 women, diagnosed with schizophrenia spectrum disorder. Our results showed that younger patients managed to achieve a higher level of functioning in educational level, marital status, and social contacts. Patients' functional capacity was primarily associated with educational level and housing situation. We also found that women needed less support regarding housing and obtained a higher level of marital status as compared with men. Our findings demonstrate the importance of considering current symptoms, especially negative symptoms, and remission stability over time, together with age, duration of illness, gender, educational level, and current functional capacity, when predicting patients' future real-world functioning. We also conclude that there is an advantage in exploring symptoms divided into positive, negative, and general domains considering their probable impact on functional achievements.

  20. Functional structure of biological communities predicts ecosystem multifunctionality.

    PubMed

    Mouillot, David; Villéger, Sébastien; Scherer-Lorenzen, Michael; Mason, Norman W H

    2011-01-01

    The accelerating rate of change in biodiversity patterns, mediated by ever increasing human pressures and global warming, demands a better understanding of the relationship between the structure of biological communities and ecosystem functioning (BEF). Recent investigations suggest that the functional structure of communities, i.e. the composition and diversity of functional traits, is the main driver of ecological processes. However, the predictive power of BEF research is still low, the integration of all components of functional community structure as predictors is still lacking, and the multifunctionality of ecosystems (i.e. rates of multiple processes) must be considered. Here, using a multiple-processes framework from grassland biodiversity experiments, we show that functional identity of species and functional divergence among species, rather than species diversity per se, together promote the level of ecosystem multifunctionality with a predictive power of 80%. Our results suggest that primary productivity and decomposition rates, two key ecosystem processes upon which the global carbon cycle depends, are primarily sustained by specialist species, i.e. those that hold specialized combinations of traits and perform particular functions. Contrary to studies focusing on single ecosystem functions and considering species richness as the sole measure of biodiversity, we found a linear and non-saturating effect of the functional structure of communities on ecosystem multifunctionality. Thus, sustaining multiple ecological processes would require focusing on trait dominance and on the degree of community specialization, even in species-rich assemblages.

  1. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  2. Prediction of functional sites in proteins using conserved functional group analysis.

    PubMed

    Innis, C Axel; Anand, A Prem; Sowdhamini, R

    2004-04-01

    A detailed knowledge of a protein's functional site is an absolute prerequisite for understanding its mode of action at the molecular level. However, the rapid pace at which sequence and structural information is being accumulated for proteins greatly exceeds our ability to determine their biochemical roles experimentally. As a result, computational methods are required which allow for the efficient processing of the evolutionary information contained in this wealth of data, in particular that related to the nature and location of functionally important sites and residues. The method presented here, referred to as conserved functional group (CFG) analysis, relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologues. We show that CFG analysis can fully or partially predict the location of functional sites in approximately 96% of the 470 cases tested and that, unlike other methods available, it is able to tolerate wide variations in sequence identity. In addition, we discuss its potential in a structural genomics context, where automation, scalability and efficiency are critical, and an increasing number of protein structures are determined with no prior knowledge of function. This is exemplified by our analysis of the hypothetical protein Ydde_Ecoli, whose structure was recently solved by members of the North East Structural Genomics consortium. Although the proposed active site for this protein needs to be validated experimentally, this example illustrates the scope of CFG analysis as a general tool for the identification of residues likely to play an important role in a protein's biochemical function. Thus, our method offers a convenient solution to rapidly and automatically process the vast amounts of data that are beginning to emerge from structural genomics projects. PMID:15033369

  3. Testing the reward prediction error hypothesis with an axiomatic model.

    PubMed

    Rutledge, Robb B; Dean, Mark; Caplin, Andrew; Glimcher, Paul W

    2010-10-01

    Neuroimaging studies typically identify neural activity correlated with the predictions of highly parameterized models, like the many reward prediction error (RPE) models used to study reinforcement learning. Identified brain areas might encode RPEs or, alternatively, only have activity correlated with RPE model predictions. Here, we use an alternate axiomatic approach rooted in economic theory to formally test the entire class of RPE models on neural data. We show that measurements of human neural activity from the striatum, medial prefrontal cortex, amygdala, and posterior cingulate cortex satisfy necessary and sufficient conditions for the entire class of RPE models. However, activity measured from the anterior insula falsifies the axiomatic model, and therefore no RPE model can account for measured activity. Further analysis suggests the anterior insula might instead encode something related to the salience of an outcome. As cognitive neuroscience matures and models proliferate, formal approaches of this kind that assess entire model classes rather than specific model exemplars may take on increased significance.

  4. Psychodynamic theory and counseling in predictive testing for Huntington's disease.

    PubMed

    Tassicker, Roslyn J

    2005-04-01

    This paper revisits psychodynamic theory, which can be applied in predictive testing counseling for Huntington's Disease (HD). Psychodynamic theory has developed from the work of Freud and places importance on early parent-child experiences. The nature of these relationships, or attachments are reflected in adult expectations and relationships. Two significant concepts, identification and fear of abandonment, have been developed and expounded by the psychodynamic theorist, Melanie Klein. The processes of identification and fear of abandonment can become evident in predictive testing counseling and are colored by the client's experience of growing up with a parent affected by Huntington's Disease. In reflecting on family-of-origin experiences, clients can also express implied expectations of the future, and future relationships. Case examples are given to illustrate the dynamic processes of identification and fear of abandonment which may present in the clinical setting. Counselor recognition of these processes can illuminate and inform counseling practice.

  5. Psychodynamic theory and counseling in predictive testing for Huntington's disease.

    PubMed

    Tassicker, Roslyn J

    2005-04-01

    This paper revisits psychodynamic theory, which can be applied in predictive testing counseling for Huntington's Disease (HD). Psychodynamic theory has developed from the work of Freud and places importance on early parent-child experiences. The nature of these relationships, or attachments are reflected in adult expectations and relationships. Two significant concepts, identification and fear of abandonment, have been developed and expounded by the psychodynamic theorist, Melanie Klein. The processes of identification and fear of abandonment can become evident in predictive testing counseling and are colored by the client's experience of growing up with a parent affected by Huntington's Disease. In reflecting on family-of-origin experiences, clients can also express implied expectations of the future, and future relationships. Case examples are given to illustrate the dynamic processes of identification and fear of abandonment which may present in the clinical setting. Counselor recognition of these processes can illuminate and inform counseling practice. PMID:15959641

  6. Testing and Life Prediction for Composite Rotor Hub Flexbeams

    NASA Technical Reports Server (NTRS)

    Murri, Gretchen B.

    2004-01-01

    A summary of several studies of delamination in tapered composite laminates with internal ply-drops is presented. Initial studies used 2D FE models to calculate interlaminar stresses at the ply-ending locations in linear tapered laminates under tension loading. Strain energy release rates for delamination in these laminates indicated that delamination would likely start at the juncture of the tapered and thin regions and grow unstably in both directions. Tests of glass/epoxy and graphite/epoxy linear tapered laminates under axial tension delaminated as predicted. Nonlinear tapered specimens were cut from a full-size helicopter rotor hub and were tested under combined constant axial tension and cyclic transverse bending loading to simulate the loading experienced by a rotorhub flexbeam in flight. For all the tested specimens, delamination began at the tip of the outermost dropped ply group and grew first toward the tapered region. A 2D FE model was created that duplicated the test flexbeam layup, geometry, and loading. Surface strains calculated by the model agreed very closely with the measured surface strains in the specimens. The delamination patterns observed in the tests were simulated in the model by releasing pairs of MPCs along those interfaces. Strain energy release rates associated with the delamination growth were calculated for several configurations and using two different FE analysis codes. Calculations from the codes agreed very closely. The strain energy release rate results were used with material characterization data to predict fatigue delamination onset lives for nonlinear tapered flexbeams with two different ply-dropping schemes. The predicted curves agreed well with the test data for each case studied.

  7. Protein side chain conformation predictions with an MMGBSA energy function.

    PubMed

    Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas

    2016-06-01

    The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc.

  8. Predicting the biomechanical strength of proximal femur specimens with Minkowski functionals and support vector regression

    NASA Astrophysics Data System (ADS)

    Yang, Chien-Chun; Nagarajan, Mahesh B.; Huber, Markus B.; Carballido-Gamio, Julio; Bauer, Jan S.; Baum, Thomas; Eckstein, Felix; Lochmüller, Eva-Maria; Link, Thomas M.; Wismüller, Axel

    2014-03-01

    Regional trabecular bone quality estimation for purposes of femoral bone strength prediction is important for improving the clinical assessment of osteoporotic fracture risk. In this study, we explore the ability of 3D Minkowski Functionals derived from multi-detector computed tomography (MDCT) images of proximal femur specimens in predicting their corresponding biomechanical strength. MDCT scans were acquired for 50 proximal femur specimens harvested from human cadavers. An automated volume of interest (VOI)-fitting algorithm was used to define a consistent volume in the femoral head of each specimen. In these VOIs, the trabecular bone micro-architecture was characterized by statistical moments of its BMD distribution and by topological features derived from Minkowski Functionals. A linear multiregression analysis and a support vector regression (SVR) algorithm with a linear kernel were used to predict the failure load (FL) from the feature sets; the predicted FL was compared to the true FL determined through biomechanical testing. The prediction performance was measured by the root mean square error (RMSE) for each feature set. The best prediction result was obtained from the Minkowski Functional surface used in combination with SVR, which had the lowest prediction error (RMSE = 0.939 ± 0.345) and which was significantly lower than mean BMD (RMSE = 1.075 ± 0.279, p<0.005). Our results indicate that the biomechanical strength prediction can be significantly improved in proximal femur specimens with Minkowski Functionals extracted from on MDCT images used in conjunction with support vector regression.

  9. Uses of esophageal function testing: dysphagia.

    PubMed

    Yazaki, Etsuro; Woodland, Philip; Sifrim, Daniel

    2014-10-01

    Esophageal function testing should be used for differential diagnosis of dysphagia. Dysphagia can be the consequence of hypermotility or hypomotility of the muscles of the esophagus. Decreased esophageal or esophagogastric junction distensibility can provoke dysphagia. The most well established esophageal dysmotility is achalasia. Other motility disorders can also cause dysphagia. High-resolution manometry (HRM) is the gold standard investigation for esophageal motility disorders. Simultaneous measurement of HRM and intraluminal impedance can be useful to assess motility and bolus transit. Impedance planimetry measures distensibility of the esophageal body and gastroesophageal junction in patients with achalasia and eosinophilic esophagitis. PMID:25216909

  10. Functional Performance Testing After Anterior Cruciate Ligament Reconstruction

    PubMed Central

    Abrams, Geoffrey D.; Harris, Joshua D.; Gupta, Anil K.; McCormick, Frank M.; Bush-Joseph, Charles A.; Verma, Nikhil N.; Cole, Brian J.; Bach, Bernard R.

    2014-01-01

    testing was the most commonly reported functional test following ACL reconstruction. Increases in performance on functional tests were predictably seen as time increased following surgery. Those with hamstring autografts may experience increased strength deficits with knee flexion versus those having BPTB autograft. These data provide information that may assist providers in determining timing of return to unrestricted sporting activity. PMID:26535266

  11. Predicting early clinical function after hip or knee arthroplasty

    PubMed Central

    Poitras, S.; Wood, K. S.; Savard, J.; Dervin, G. F.; Beaule, P. E.

    2015-01-01

    Objectives Patient function after arthroplasty should ideally quickly improve. It is not known which peri-operative function assessments predict length of stay (LOS) and short-term functional recovery. The objective of this study was to identify peri-operative functions assessments predictive of hospital LOS and short-term function after hospital discharge in hip or knee arthroplasty patients. Methods In total, 108 patients were assessed peri-operatively with the timed-up-and-go (TUG), Iowa level of assistance scale, post-operative quality of recovery scale, readiness for hospital discharge scale, and the Western Ontario and McMaster Osteoarthritis Index (WOMAC). The older Americans resources and services activities of daily living (ADL) questionnaire (OARS) was used to assess function two weeks after discharge. Results Following multiple regressions, the pre- and post-operative day two TUG was significantly associated with LOS and OARS score, while the pre-operative WOMAC function subscale was associated with the OARS score. Pre-operatively, a cut-off TUG time of 11.7 seconds for LOS and 10.3 seconds for short-term recovery yielded the highest sensitivity and specificity, while a cut-off WOMAC function score of 48.5/100 yielded the highest sensitivity and specificity. Post-operatively, a cut-off day two TUG time of 31.5 seconds for LOS and 30.9 seconds for short-term function yielded the highest sensitivity and specificity. Conclusions The pre- and post-operative day two TUG can indicate hospital LOS and short-term functional capacities, while the pre-operative WOMAC function subscale can indicate short-term functional capacities. Cite this article: Bone Joint Res 2015;4:145–151. PMID:26336897

  12. Protein function prediction using guilty by association from interaction networks.

    PubMed

    Piovesan, Damiano; Giollo, Manuel; Ferrari, Carlo; Tosatto, Silvio C E

    2015-12-01

    Protein function prediction from sequence using the Gene Ontology (GO) classification is useful in many biological problems. It has recently attracted increasing interest, thanks in part to the Critical Assessment of Function Annotation (CAFA) challenge. In this paper, we introduce Guilty by Association on STRING (GAS), a tool to predict protein function exploiting protein-protein interaction networks without sequence similarity. The assumption is that whenever a protein interacts with other proteins, it is part of the same biological process and located in the same cellular compartment. GAS retrieves interaction partners of a query protein from the STRING database and measures enrichment of the associated functional annotations to generate a sorted list of putative functions. A performance evaluation based on CAFA metrics and a fair comparison with optimized BLAST similarity searches is provided. The consensus of GAS and BLAST is shown to improve overall performance. The PPI approach is shown to outperform similarity searches for biological process and cellular compartment GO predictions. Moreover, an analysis of the best practices to exploit protein-protein interaction networks is also provided.

  13. Disorganized symptoms and executive functioning predict impaired social functioning in subjects at risk for psychosis.

    PubMed

    Eslami, Ali; Jahshan, Carol; Cadenhead, Kristin S

    2011-01-01

    Predictors of social functioning deficits were assessed in 22 individuals "at risk" for psychosis. Disorganized symptoms and executive functioning predicted social functioning at follow-up. Early intervention efforts that focus on social and cognitive skills are indicated in this vulnerable population.

  14. Functional Task Test: 2. Spaceflight-Induced Cardiovascular Change and Recovery During NASA's Functional Task Test

    NASA Technical Reports Server (NTRS)

    Phillips, Tiffany; Arzeno, Natalia M.; Stenger, Michael; Lee, Stuart M. C.; Bloomberg, Jacob J.; Platts, Steven H.

    2011-01-01

    The overall objective of the functional task test (FTT) is to correlate spaceflight-induced physiological adaptations with changes in performance of high priority exploration mission-critical tasks. This presentation will focus on the recovery from fall/stand test (RFST), which measures the cardiovascular response to the transition from the prone posture (simulated fall) to standing in normal gravity, as well as heart rate (HR) during 11 functional tasks. As such, this test describes some aspects of spaceflight-induced cardiovascular deconditioning and the course of recovery in Space Shuttle and International Space Station (ISS) astronauts. The sensorimotor and neuromuscular components of the FTT are described in two separate abstracts: Functional Task Test 1 and 3.

  15. Pattern recognition methods for protein functional site prediction.

    PubMed

    Yang, Zheng Rong; Wang, Lipo; Young, Natasha; Trudgian, Dave; Chou, Kuo-Chen

    2005-10-01

    Protein functional site prediction is closely related to drug design, hence to public health. In order to save the cost and the time spent on identifying the functional sites in sequenced proteins in biology laboratory, computer programs have been widely used for decades. Many of them are implemented using the state-of-the-art pattern recognition algorithms, including decision trees, neural networks and support vector machines. Although the success of this effort has been obvious, advanced and new algorithms are still under development for addressing some difficult issues. This review will go through the major stages in developing pattern recognition algorithms for protein functional site prediction and outline the future research directions in this important area. PMID:16248799

  16. Predicting plants -modeling traits as a function of environment

    NASA Astrophysics Data System (ADS)

    Franklin, Oskar

    2016-04-01

    A central problem in understanding and modeling vegetation dynamics is how to represent the variation in plant properties and function across different environments. Addressing this problem there is a strong trend towards trait-based approaches, where vegetation properties are functions of the distributions of functional traits rather than of species. Recently there has been enormous progress in in quantifying trait variability and its drivers and effects (Van Bodegom et al. 2012; Adier et al. 2014; Kunstler et al. 2015) based on wide ranging datasets on a small number of easily measured traits, such as specific leaf area (SLA), wood density and maximum plant height. However, plant function depends on many other traits and while the commonly measured trait data are valuable, they are not sufficient for driving predictive and mechanistic models of vegetation dynamics -especially under novel climate or management conditions. For this purpose we need a model to predict functional traits, also those not easily measured, and how they depend on the plants' environment. Here I present such a mechanistic model based on fitness concepts and focused on traits related to water and light limitation of trees, including: wood density, drought response, allocation to defense, and leaf traits. The model is able to predict observed patterns of variability in these traits in relation to growth and mortality, and their responses to a gradient of water limitation. The results demonstrate that it is possible to mechanistically predict plant traits as a function of the environment based on an eco-physiological model of plant fitness. References Adier, P.B., Salguero-Gómez, R., Compagnoni, A., Hsu, J.S., Ray-Mukherjee, J., Mbeau-Ache, C. et al. (2014). Functional traits explain variation in plant lifehistory strategies. Proc. Natl. Acad. Sci. U. S. A., 111, 740-745. Kunstler, G., Falster, D., Coomes, D.A., Hui, F., Kooyman, R.M., Laughlin, D.C. et al. (2015). Plant functional traits

  17. Integrated Locomotor Function Tests for Countermeasure Evaluation

    NASA Technical Reports Server (NTRS)

    Bloomberg, J. J.; Mulavara, A. P.; Peters, B. T.; Cohen, H. S.; Landsness, E. C.; Black, F. O.

    2005-01-01

    Following spaceflight crewmembers experience locomotor dysfunction due to inflight adaptive alterations in sensorimotor function. Countermeasures designed to mitigate these postflight gait alterations need to be assessed with a new generation of tests that evaluate the interaction of various sensorimotor sub-systems central to locomotor control. The goal of the present study was to develop new functional tests of locomotor control that could be used to test the efficacy of countermeasures. These tests were designed to simultaneously examine the function of multiple sensorimotor systems underlying the control of locomotion and be operationally relevant to the astronaut population. Traditionally, gaze stabilization has been studied almost exclusively in seated subjects performing target acquisition tasks requiring only the involvement of coordinated eye-head movements. However, activities like walking involve full-body movement and require coordination between lower limbs and the eye-head-trunk complex to achieve stabilized gaze during locomotion. Therefore the first goal of this study was to determine how the multiple, interdependent, full-body sensorimotor gaze stabilization subsystems are functionally coordinated during locomotion. In an earlier study we investigated how alteration in gaze tasking changes full-body locomotor control strategies. Subjects walked on a treadmill and either focused on a central point target or read numeral characters. We measured: temporal parameters of gait, full body sagittal plane segmental kinematics of the head, trunk, thigh, shank and foot, accelerations along the vertical axis at the head and the shank, and the vertical forces acting on the support surface. In comparison to the point target fixation condition, the results of the number reading task showed that compensatory head pitch movements increased, peak head acceleration was reduced and knee flexion at heel-strike was increased. In a more recent study we investigated the

  18. Andean microrefugia: testing the Holocene to predict the Anthropocene.

    PubMed

    Valencia, Bryan G; Matthews-Bird, Frazer; Urrego, Dunia H; Williams, Joseph J; Gosling, William D; Bush, Mark

    2016-10-01

    Microrefugia are important for supporting populations during periods of unfavourable climate change and in facilitating rapid migration as conditions ameliorate. With ongoing anthropogenic climate change, microrefugia could have an important conservation value; however, a simple tool has not been developed and tested to predict which settings are microrefugial. We provide a tool based on terrain ruggedness modelling of individual catchments to predict Andean microrefugia. We tested the predictions using nine Holocene Polylepis pollen records. We used the mid-Holocene dry event, a period of peak aridity for the last 100 000 yr, as an analogue climate scenario for the near future. The results suggest that sites with high terrain rugosity have the greatest chance of sustaining mesic conditions under drier-than-modern climates. Fire is a feature of all catchments; however, an increase in fire is only recorded in settings with low rugosity. Owing to rising temperatures and greater precipitation variability, Andean ecosystems are threatened by increasing moisture stress. Our results suggest that high terrain rugosity helps to create more resilient catchments by trapping moisture through orographic rainfall and providing firebreaks that shelter forest from fire. On this basis, conservation policy should target protection and management of catchments with high terrain rugosity.

  19. Development of a forensic skin colour predictive test.

    PubMed

    Maroñas, Olalla; Phillips, Chris; Söchtig, Jens; Gomez-Tato, Antonio; Cruz, Raquel; Alvarez-Dios, José; de Cal, María Casares; Ruiz, Yarimar; Fondevila, Manuel; Carracedo, Ángel; Lareu, María V

    2014-11-01

    There is growing interest in skin colour prediction in the forensic field. However, a lack of consensus approaches for recording skin colour phenotype plus the complicating factors of epistatic effects, environmental influences such as exposure to the sun and unidentified genetic variants, present difficulties for the development of a forensic skin colour predictive test centred on the most strongly associated SNPs. Previous studies have analysed skin colour variation in single unadmixed population groups, including South Asians (Stokowski et al., 2007, Am. J. Hum. Genet, 81: 1119-32) and Europeans (Jacobs et al., 2013, Hum Genet. 132: 147-58). Nevertheless, a major challenge lies in the analysis of skin colour in admixed individuals, where co-ancestry proportions do not necessarily dictate any one person's skin colour. Our study sought to analyse genetic differences between African, European and admixed African-European subjects where direct spectrometric measurements and photographs of skin colour were made in parallel. We identified strong associations to skin colour variation in the subjects studied from a pigmentation SNP discovery panel of 59 markers and developed a forensic online classifier based on naïve Bayes analysis of the SNP profiles made. A skin colour predictive test is described using the ten most strongly associated SNPs in 8 genes linked to skin pigmentation variation. PMID:25082135

  20. Andean microrefugia: testing the Holocene to predict the Anthropocene.

    PubMed

    Valencia, Bryan G; Matthews-Bird, Frazer; Urrego, Dunia H; Williams, Joseph J; Gosling, William D; Bush, Mark

    2016-10-01

    Microrefugia are important for supporting populations during periods of unfavourable climate change and in facilitating rapid migration as conditions ameliorate. With ongoing anthropogenic climate change, microrefugia could have an important conservation value; however, a simple tool has not been developed and tested to predict which settings are microrefugial. We provide a tool based on terrain ruggedness modelling of individual catchments to predict Andean microrefugia. We tested the predictions using nine Holocene Polylepis pollen records. We used the mid-Holocene dry event, a period of peak aridity for the last 100 000 yr, as an analogue climate scenario for the near future. The results suggest that sites with high terrain rugosity have the greatest chance of sustaining mesic conditions under drier-than-modern climates. Fire is a feature of all catchments; however, an increase in fire is only recorded in settings with low rugosity. Owing to rising temperatures and greater precipitation variability, Andean ecosystems are threatened by increasing moisture stress. Our results suggest that high terrain rugosity helps to create more resilient catchments by trapping moisture through orographic rainfall and providing firebreaks that shelter forest from fire. On this basis, conservation policy should target protection and management of catchments with high terrain rugosity. PMID:27374975

  1. Phagonaute: A web-based interface for phage synteny browsing and protein function prediction.

    PubMed

    Delattre, Hadrien; Souiai, Oussema; Fagoonee, Khema; Guerois, Raphaël; Petit, Marie-Agnès

    2016-09-01

    Distant homology search tools are of great help to predict viral protein functions. However, due to the lack of profile databases dedicated to viruses, they can lack sensitivity. We constructed HMM profiles for more than 80,000 proteins from both phages and archaeal viruses, and performed all pairwise comparisons with HHsearch program. The whole resulting database can be explored through a user-friendly "Phagonaute" interface to help predict functions. Results are displayed together with their genetic context, to strengthen inferences based on remote homology. Beyond function prediction, this tool permits detections of co-occurrences, often indicative of proteins completing a task together, and observation of conserved patterns across large evolutionary distances. As a test, Herpes simplex virus I was added to Phagonaute, and 25% of its proteome matched to bacterial or archaeal viral protein counterparts. Phagonaute should therefore help virologists in their quest for protein functions and evolutionary relationships. PMID:27254594

  2. Phagonaute: A web-based interface for phage synteny browsing and protein function prediction.

    PubMed

    Delattre, Hadrien; Souiai, Oussema; Fagoonee, Khema; Guerois, Raphaël; Petit, Marie-Agnès

    2016-09-01

    Distant homology search tools are of great help to predict viral protein functions. However, due to the lack of profile databases dedicated to viruses, they can lack sensitivity. We constructed HMM profiles for more than 80,000 proteins from both phages and archaeal viruses, and performed all pairwise comparisons with HHsearch program. The whole resulting database can be explored through a user-friendly "Phagonaute" interface to help predict functions. Results are displayed together with their genetic context, to strengthen inferences based on remote homology. Beyond function prediction, this tool permits detections of co-occurrences, often indicative of proteins completing a task together, and observation of conserved patterns across large evolutionary distances. As a test, Herpes simplex virus I was added to Phagonaute, and 25% of its proteome matched to bacterial or archaeal viral protein counterparts. Phagonaute should therefore help virologists in their quest for protein functions and evolutionary relationships.

  3. Towards computational prediction of microRNA function and activity

    PubMed Central

    Ulitsky, Igor; Laurent, Louise C.; Shamir, Ron

    2010-01-01

    While it has been established that microRNAs (miRNAs) play key roles throughout development and are dysregulated in many human pathologies, the specific processes and pathways regulated by individual miRNAs are mostly unknown. Here, we use computational target predictions in order to automatically infer the processes affected by human miRNAs. Our approach improves upon standard statistical tools by addressing specific characteristics of miRNA regulation. Our analysis is based on a novel compendium of experimentally verified miRNA-pathway and miRNA-process associations that we constructed, which can be a useful resource by itself. Our method also predicts novel miRNA-regulated pathways, refines the annotation of miRNAs for which only crude functions are known, and assigns differential functions to miRNAs with closely related sequences. Applying our approach to groups of co-expressed genes allows us to identify miRNAs and genomic miRNA clusters with functional importance in specific stages of early human development. A full list of the predicted mRNA functions is available at http://acgt.cs.tau.ac.il/fame/. PMID:20576699

  4. Drug-target interaction prediction by integrating chemical, genomic, functional and pharmacological data.

    PubMed

    Yang, Fan; Xu, Jinbo; Zeng, Jianyang

    2014-01-01

    In silico prediction of unknown drug-target interactions (DTIs) has become a popular tool for drug repositioning and drug development. A key challenge in DTI prediction lies in integrating multiple types of data for accurate DTI prediction. Although recent studies have demonstrated that genomic, chemical and pharmacological data can provide reliable information for DTI prediction, it remains unclear whether functional information on proteins can also contribute to this task. Little work has been developed to combine such information with other data to identify new interactions between drugs and targets. In this paper, we introduce functional data into DTI prediction and construct biological space for targets using the functional similarity measure. We present a probabilistic graphical model, called conditional random field (CRF), to systematically integrate genomic, chemical, functional and pharmacological data plus the topology of DTI networks into a unified framework to predict missing DTIs. Tests on two benchmark datasets show that our method can achieve excellent prediction performance with the area under the precision-recall curve (AUPR) up to 94.9. These results demonstrate that our CRF model can successfully exploit heterogeneous data to capture the latent correlations of DTIs, and thus will be practically useful for drug repositioning. Supplementary Material is available at http://iiis.tsinghua.edu.cn/~compbio/papers/psb2014/psb2014_sm.pdf. PMID:24297542

  5. A simple osmotic stress test to predict boar sperm cryosurvival.

    PubMed

    Garzon-Perez, Cesar; Flores, Hector F; Medrano, Alfredo

    2010-01-01

    This work was carried out to test whether viability of pig spermatozoa subjected to an osmotic test is correlated to sperm cryosurvival. Spermatozoa were cooled from 22 degrees C to -5 degrees C, aliquots were exposed to a series of hyperosmotic solutions (300-2100 mOsm/kg) for 15 min, immediately spermatozoa were re-warmed to 37 degrees C and isosmolarity was restored. Spermatozoa were cooled from 22 degrees C to -5 degrees C and one aliquot was exposed to the osmotic test while diluted spermatozoa were frozen-thawed. Plasma membrane-intact spermatozoa decreased as osmolarity increased (P < 0.0001), a further decreased (P < 0.0001) was observed when isotonicity was restored. Proportions of plasma membrane-intact and acrosome-intact cells from the osmotic test were no different from those after freeze-thawing: 36% vs. 35%, 80% vs. 80%, respectively. A significant correlation was found between the proportion of acrosome-intact cells after freeze-thawing and that from the osmotic test (r = 0.81, P <0.01). This test provides a useful and economical mean to predict in vitro boar sperm cryosurvival.

  6. Bayesian Markov Random Field analysis for protein function prediction based on network data.

    PubMed

    Kourmpetis, Yiannis A I; van Dijk, Aalt D J; Bink, Marco C A M; van Ham, Roeland C H J; ter Braak, Cajo J F

    2010-02-24

    Inference of protein functions is one of the most important aims of modern biology. To fully exploit the large volumes of genomic data typically produced in modern-day genomic experiments, automated computational methods for protein function prediction are urgently needed. Established methods use sequence or structure similarity to infer functions but those types of data do not suffice to determine the biological context in which proteins act. Current high-throughput biological experiments produce large amounts of data on the interactions between proteins. Such data can be used to infer interaction networks and to predict the biological process that the protein is involved in. Here, we develop a probabilistic approach for protein function prediction using network data, such as protein-protein interaction measurements. We take a Bayesian approach to an existing Markov Random Field method by performing simultaneous estimation of the model parameters and prediction of protein functions. We use an adaptive Markov Chain Monte Carlo algorithm that leads to more accurate parameter estimates and consequently to improved prediction performance compared to the standard Markov Random Fields method. We tested our method using a high quality S. cereviciae validation network with 1622 proteins against 90 Gene Ontology terms of different levels of abstraction. Compared to three other protein function prediction methods, our approach shows very good prediction performance. Our method can be directly applied to protein-protein interaction or coexpression networks, but also can be extended to use multiple data sources. We apply our method to physical protein interaction data from S. cerevisiae and provide novel predictions, using 340 Gene Ontology terms, for 1170 unannotated proteins and we evaluate the predictions using the available literature.

  7. THERMAL PREDICTIONS OF NEW COMPOSITE MATERIAL DURING INPILE TESTING

    SciTech Connect

    Donna Post Guillen; W. David Swank; Heng Ban; Kurt Harris; Adam Zabriskie

    2011-09-01

    An inpile experiment is currently underway wherein specimens comprised of a newly developed material are being irradiated at Idaho National Laboratory's Advanced Test Reactor (ATR) in conjunction with Utah State University under the auspices of the ATR National Scientific User Facility. This paper provides the thermophysical properties of this new material measured prior to irradiation. After the irradiation campaign is complete, the thermophysical properties of the specimens will be measured and compared to the preirradiation values. A finite-element model was constructed to predict bounding specimen temperatures during irradiation. Results from the thermal hydraulic modeling, including the steady-state temperatures of the specimens within sealed capsules, are presented. After the irradiation campaign is completed, best-estimate thermal predictions will be performed for the individual specimens using the actual as-run irradiation power levels.

  8. Two-Speed Gearbox Dynamic Simulation Predictions and Test Validation

    NASA Technical Reports Server (NTRS)

    Lewicki, David G.; DeSmidt, Hans; Smith, Edward C.; Bauman, Steven W.

    2010-01-01

    Dynamic simulations and experimental validation tests were performed on a two-stage, two-speed gearbox as part of the drive system research activities of the NASA Fundamental Aeronautics Subsonics Rotary Wing Project. The gearbox was driven by two electromagnetic motors and had two electromagnetic, multi-disk clutches to control output speed. A dynamic model of the system was created which included a direct current electric motor with proportional-integral-derivative (PID) speed control, a two-speed gearbox with dual electromagnetically actuated clutches, and an eddy current dynamometer. A six degree-of-freedom model of the gearbox accounted for the system torsional dynamics and included gear, clutch, shaft, and load inertias as well as shaft flexibilities and a dry clutch stick-slip friction model. Experimental validation tests were performed on the gearbox in the NASA Glenn gear noise test facility. Gearbox output speed and torque as well as drive motor speed and current were compared to those from the analytical predictions. The experiments correlate very well with the predictions, thus validating the dynamic simulation methodologies.

  9. Identifying functional sites based on prediction of charged group behavior.

    PubMed

    Ondrechen, Mary Jo

    2004-09-01

    This protocol describes the implementation and interpretation of THEMATICS, a simple computational predictor of functional information for proteins from the three-dimensional structure. This method is based on the computation of the electrical potential function for the protein and the calculation of the predicted titration curves for each of the titratable groups in the protein. While most of the titratable residues in a protein have predicted titration behavior that fits the Henderson-Hasselbalch equation, the ionizable residues in the active site generally deviate dramatically from the typical behavior. From the calculated titration curves, one identifies those residues that deviate significantly from Henderson-Hasselbalch behavior. A cluster of two or more of such deviant titratable residues in physical proximity is a reliable predictor of active-site location.

  10. Plant functional traits predict green roof ecosystem services.

    PubMed

    Lundholm, Jeremy; Tran, Stephanie; Gebert, Luke

    2015-02-17

    Plants make important contributions to the services provided by engineered ecosystems such as green roofs. Ecologists use plant species traits as generic predictors of geographical distribution, interactions with other species, and ecosystem functioning, but this approach has been little used to optimize engineered ecosystems. Four plant species traits (height, individual leaf area, specific leaf area, and leaf dry matter content) were evaluated as predictors of ecosystem properties and services in a modular green roof system planted with 21 species. Six indicators of ecosystem services, incorporating thermal, hydrological, water quality, and carbon sequestration functions, were predicted by the four plant traits directly or indirectly via their effects on aggregate ecosystem properties, including canopy density and albedo. Species average height and specific leaf area were the most useful traits, predicting several services via effects on canopy density or growth rate. This study demonstrates that easily measured plant traits can be used to select species to optimize green roof performance across multiple key services.

  11. Plant functional traits predict green roof ecosystem services.

    PubMed

    Lundholm, Jeremy; Tran, Stephanie; Gebert, Luke

    2015-02-17

    Plants make important contributions to the services provided by engineered ecosystems such as green roofs. Ecologists use plant species traits as generic predictors of geographical distribution, interactions with other species, and ecosystem functioning, but this approach has been little used to optimize engineered ecosystems. Four plant species traits (height, individual leaf area, specific leaf area, and leaf dry matter content) were evaluated as predictors of ecosystem properties and services in a modular green roof system planted with 21 species. Six indicators of ecosystem services, incorporating thermal, hydrological, water quality, and carbon sequestration functions, were predicted by the four plant traits directly or indirectly via their effects on aggregate ecosystem properties, including canopy density and albedo. Species average height and specific leaf area were the most useful traits, predicting several services via effects on canopy density or growth rate. This study demonstrates that easily measured plant traits can be used to select species to optimize green roof performance across multiple key services. PMID:25599106

  12. Prediction of protein complexes using empirical free energy functions.

    PubMed Central

    Weng, Z.; Vajda, S.; Delisi, C.

    1996-01-01

    A long sought goal in the physical chemistry of macromolecular structure, and one directly relevant to understanding the molecular basis of biological recognition, is predicting the geometry of bimolecular complexes from the geometries of their free monomers. Even when the monomers remain relatively unchanged by complex formation, prediction has been difficult because the free energies of alternative conformations of the complex have been difficult to evaluate quickly and accurately. This has forced the use of incomplete target functions, which typically do no better than to provide tens of possible complexes with no way of choosing between them. Here we present a general framework for empirical free energy evaluation and report calculations, based on a relatively complete and easily executable free energy function, that indicate that the structures of complexes can be predicted accurately from the structures of monomers, including close sequence homologues. The calculations also suggest that the binding free energies themselves may be predicted with reasonable accuracy. The method is compared to an alternative formulation that has also been applied recently to the same data set. Both approaches promise to open new opportunities in macromolecular design and specificity modification. PMID:8845751

  13. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

    PubMed

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

    2016-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue.

  14. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

    PubMed

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

    2016-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. PMID:26635392

  15. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

    PubMed Central

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P.; Kasif, Simon; Roberts, Richard J.; Steffen, Martin

    2016-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. PMID:26635392

  16. High Precision Prediction of Functional Sites in Protein Structures

    PubMed Central

    Buturovic, Ljubomir; Wong, Mike; Tang, Grace W.; Altman, Russ B.; Petkovic, Dragutin

    2014-01-01

    We address the problem of assigning biological function to solved protein structures. Computational tools play a critical role in identifying potential active sites and informing screening decisions for further lab analysis. A critical parameter in the practical application of computational methods is the precision, or positive predictive value. Precision measures the level of confidence the user should have in a particular computed functional assignment. Low precision annotations lead to futile laboratory investigations and waste scarce research resources. In this paper we describe an advanced version of the protein function annotation system FEATURE, which achieved 99% precision and average recall of 95% across 20 representative functional sites. The system uses a Support Vector Machine classifier operating on the microenvironment of physicochemical features around an amino acid. We also compared performance of our method with state-of-the-art sequence-level annotator Pfam in terms of precision, recall and localization. To our knowledge, no other functional site annotator has been rigorously evaluated against these key criteria. The software and predictive models are incorporated into the WebFEATURE service at http://feature.stanford.edu/wf4.0-beta. PMID:24632601

  17. Tests of Substorm Models' Predictions Using ISTP Observations

    NASA Technical Reports Server (NTRS)

    Sanchez, Ennio R.

    1998-01-01

    This report provides progress to test the predictions of substorm models using ISTP observations. During the first year, two investigations were initiated in collaboration with a number of ISTP researchers. Both investigations use a combination of simultaneous measurements from high-, low-, and ground-altitude instruments to: (1) explore the role of MHD resonances in the onset and evolution of substorms, and (2) establish the timing of events in the magnetosphere and ionosphere during the substorm evolution beginning with the growth phase and ending with the recovery phase.

  18. Platelet Function Testing-Guided Antiplatelet Therapy

    PubMed Central

    Spannagl, Michael

    2013-01-01

    Cardiovascular diseases are the leading cause of death in the Western world. Several factors have led to the increase in vascular disorders, including the aging population, unhealthy lifestyles, increasing rates of diabetes and raised lipids, and further risk factors resulting in inflammation and calcification of the vascular endothelium. Activated platelets in damaged blood vessels can trigger arterial thrombus formation, leading to vascular occlusion with subsequent organ hypoperfusion and clinical manifestation of myocardial infarction, stroke, or peripheral artery disease. Platelet inhibitors such as aspirin and clopidogrel (Plavix® and generics) are prescribed as primary or secondary prevention to attenuate chronic platelet activation. However, a significant proportion of patients do not respond adequately to uniform antiplatelet treatment. These ‘non-responders’ have an increased risk for stent thrombosis, stroke, and other ischemic complications. Platelet function (PF) tests can identify these patients thus enabling physicians to offer personalized and alternative treatment strategies. Recent alternatives to clopidogrel include prasugrel (Efient®) and ticagrelor (Brilique®) – that are both more potent than clopidogrel but also more expensive and associated with a higher risk of bleeding complications. Given these drawbacks, PF testing might help clinicians to prescribe optimal antiplatelet agent to maximize patient safety and efficacy while minimizing costs. While randomized studies using different test systems have left clinicians puzzled about the medical value of tailored antiplatelet therapy, accumulated evidence from recent studies on tailored antiplatelet therapies and the association with improved outcomes have now resulted in a consensus expert opinion for the specific adoption of PF diagnostics into clinical practice.

  19. Predictions of Geospace Drivers By the Probability Distribution Function Model

    NASA Astrophysics Data System (ADS)

    Bussy-Virat, C.; Ridley, A. J.

    2014-12-01

    Geospace drivers like the solar wind speed, interplanetary magnetic field (IMF), and solar irradiance have a strong influence on the density of the thermosphere and the near-Earth space environment. This has important consequences on the drag on satellites that are in low orbit and therefore on their position. One of the basic problems with space weather prediction is that these drivers can only be measured about one hour before they affect the environment. In order to allow for adequate planning for some members of the commercial, military, or civilian communities, reliable long-term space weather forecasts are needed. The study presents a model for predicting geospace drivers up to five days in advance. This model uses the same general technique to predict the solar wind speed, the three components of the IMF, and the solar irradiance F10.7. For instance, it uses Probability distribution functions (PDFs) to relate the current solar wind speed and slope to the future solar wind speed, as well as the solar wind speed to the solar wind speed one solar rotation in the future. The PDF Model has been compared to other models for predictions of the speed. It has been found that it is better than using the current solar wind speed (i.e., persistence), and better than the Wang-Sheeley-Arge Model for prediction horizons of 24 hours. Once the drivers are predicted, and the uncertainty on the drivers are specified, the density in the thermosphere can be derived using various models of the thermosphere, such as the Global Ionosphere Thermosphere Model. In addition, uncertainties on the densities can be estimated, based on ensembles of simulations. From the density and uncertainty predictions, satellite positions, as well as the uncertainty in those positions can be estimated. These can assist operators in determining the probability of collisions between objects in low Earth orbit.

  20. Density functional theory predictions of isotropic hyperfine coupling constants.

    PubMed

    Hermosilla, L; Calle, P; García de la Vega, J M; Sieiro, C

    2005-02-17

    The reliability of density functional theory (DFT) in the determination of the isotropic hyperfine coupling constants (hfccs) of the ground electronic states of organic and inorganic radicals is examined. Predictions using several DFT methods and 6-31G, TZVP, EPR-III and cc-pVQZ basis sets are made and compared to experimental values. The set of 75 radicals here studied was selected using a wide range of criteria. The systems studied are neutral, cationic, anionic; doublet, triplet, quartet; localized, and conjugated radicals, containing 1H, 9Be, 11B, 13C, 14N, 17O, 19F, 23Na, 25Mg, 27Al, 29Si, 31P, 33S, and 35Cl nuclei. The considered radicals provide 241 theoretical hfcc values, which are compared with 174 available experimental ones. The geometries of the studied systems are obtained by theoretical optimization using the same functional and basis set with which the hfccs were calculated. Regression analysis is used as a basic and appropriate methodology for this kind of comparative study. From this analysis, we conclude that DFT predictions of the hfccs are reliable for B3LYP/TZVP and B3LYP/EPR-III combinations. Both functional/basis set scheme are the more useful theoretical tools for predicting hfccs if compared to other much more expensive methods.

  1. Functional brain imaging predicts public health campaign success.

    PubMed

    Falk, Emily B; O'Donnell, Matthew Brook; Tompson, Steven; Gonzalez, Richard; Dal Cin, Sonya; Strecher, Victor; Cummings, Kenneth Michael; An, Lawrence

    2016-02-01

    Mass media can powerfully affect health decision-making. Pre-testing through focus groups or surveys is a standard, though inconsistent, predictor of effectiveness. Converging evidence demonstrates that activity within brain systems associated with self-related processing can predict individual behavior in response to health messages. Preliminary evidence also suggests that neural activity in small groups can forecast population-level campaign outcomes. Less is known about the psychological processes that link neural activity and population-level outcomes, or how these predictions are affected by message content. We exposed 50 smokers to antismoking messages and used their aggregated neural activity within a 'self-localizer' defined region of medial prefrontal cortex to predict the success of the same campaign messages at the population level (n = 400,000 emails). Results demonstrate that: (i) independently localized neural activity during health message exposure complements existing self-report data in predicting population-level campaign responses (model combined R(2) up to 0.65) and (ii) this relationship depends on message content-self-related neural processing predicts outcomes in response to strong negative arguments against smoking and not in response to compositionally similar neutral images. These data advance understanding of the psychological link between brain and large-scale behavior and may aid the construction of more effective media health campaigns.

  2. AGR-2 safety test predictions using the PARFUME code

    SciTech Connect

    Collin, Blaise P.

    2014-09-01

    This report documents calculations performed to predict failure probability of TRISO-coated fuel particles and diffusion of fission products through these particles during safety tests following the second irradiation test of the Advanced Gas Reactor program (AGR-2). The calculations include the modeling of the AGR-2 irradiation that occurred from June 2010 to October 2013 in the Advanced Test Reactor (ATR) and the modeling of a safety testing phase to support safety tests planned at Oak Ridge National Laboratory and at Idaho National Laboratory (INL) for a selection of AGR-2 compacts. The heat-up of AGR-2 compacts is a critical component of the AGR-2 fuel performance evaluation, and its objectives are to identify the effect of accident test temperature, burnup, and irradiation temperature on the performance of the fuel at elevated temperature. Safety testing of compacts will be followed by detailed examinations of the fuel particles to further evaluate fission product retention and behavior of the kernel and coatings. The modeling was performed using the particle fuel model computer code PARFUME developed at INL. PARFUME is an advanced gas-cooled reactor fuel performance modeling and analysis code (Miller 2009). It has been developed as an integrated mechanistic code that evaluates the thermal, mechanical, and physico-chemical behavior of fuel particles during irradiation to determine the failure probability of a population of fuel particles given the particle-to-particle statistical variations in physical dimensions and material properties that arise from the fuel fabrication process, accounting for all viable mechanisms that can lead to particle failure. The code also determines the diffusion of fission products from the fuel through the particle coating layers, and through the fuel matrix to the coolant boundary. The subsequent release of fission products is calculated at the compact level (release of fission products from the compact). PARFUME calculates the

  3. Reported differences between tested and predicted steam turbine vaccuum corrections

    SciTech Connect

    Silvestri, G.J. Jr.; Collins, D.M.; Price, M.R.

    1995-06-01

    Turbine performance results which have been reported at an engineering conference indicate significant differences between the turbine vacuum corrections obtained from plant tests and those supplied by the turbine vendor. In the vicinity of the design vacuum considerably lower or higher than the design levels the differences are significant. Anomalies were observed (by one of the authors) in vacuum corrections during cycle studies conducted in 1970 and 1975. Subsequent analysis of the data revealed that the assumptions used in determining the boiler feed pump/boiler feed pump turbine, BP/BFPT, performance were responsible for the anomalies. If the field data are not corrected for deviations from the heat balance BFP/BFPT and feedwater heater operating assumptions, it will result in deviations between the tested and predicted vacuum corrections.

  4. Use of clinical movement screening tests to predict injury in sport.

    PubMed

    Chimera, Nicole J; Warren, Meghan

    2016-04-18

    Clinical movement screening tests are gaining popularity as a means to determine injury risk and to implement training programs to prevent sport injury. While these screens are being used readily in the clinical field, it is only recently that some of these have started to gain attention from a research perspective. This limits applicability and poses questions to the validity, and in some cases the reliability, of the clinical movement tests as they relate to injury prediction, intervention, and prevention. This editorial will review the following clinical movement screening tests: Functional Movement Screen™, Star Excursion Balance Test, Y Balance Test, Drop Jump Screening Test, Landing Error Scoring System, and the Tuck Jump Analysis in regards to test administration, reliability, validity, factors that affect test performance, intervention programs, and usefulness for injury prediction. It is important to review the aforementioned factors for each of these clinical screening tests as this may help clinicians interpret the current body of literature. While each of these screening tests were developed by clinicians based on what appears to be clinical practice, this paper brings to light that this is a need for collaboration between clinicians and researchers to ensure validity of clinically meaningful tests so that they are used appropriately in future clinical practice. Further, this editorial may help to identify where the research is lacking and, thus, drive future research questions in regards to applicability and appropriateness of clinical movement screening tools. PMID:27114928

  5. Use of clinical movement screening tests to predict injury in sport

    PubMed Central

    Chimera, Nicole J; Warren, Meghan

    2016-01-01

    Clinical movement screening tests are gaining popularity as a means to determine injury risk and to implement training programs to prevent sport injury. While these screens are being used readily in the clinical field, it is only recently that some of these have started to gain attention from a research perspective. This limits applicability and poses questions to the validity, and in some cases the reliability, of the clinical movement tests as they relate to injury prediction, intervention, and prevention. This editorial will review the following clinical movement screening tests: Functional Movement Screen™, Star Excursion Balance Test, Y Balance Test, Drop Jump Screening Test, Landing Error Scoring System, and the Tuck Jump Analysis in regards to test administration, reliability, validity, factors that affect test performance, intervention programs, and usefulness for injury prediction. It is important to review the aforementioned factors for each of these clinical screening tests as this may help clinicians interpret the current body of literature. While each of these screening tests were developed by clinicians based on what appears to be clinical practice, this paper brings to light that this is a need for collaboration between clinicians and researchers to ensure validity of clinically meaningful tests so that they are used appropriately in future clinical practice. Further, this editorial may help to identify where the research is lacking and, thus, drive future research questions in regards to applicability and appropriateness of clinical movement screening tools. PMID:27114928

  6. Origin and Functional Prediction of Pollen Allergens in Plants.

    PubMed

    Chen, Miaolin; Xu, Jie; Devis, Deborah; Shi, Jianxin; Ren, Kang; Searle, Iain; Zhang, Dabing

    2016-09-01

    Pollen allergies have long been a major pandemic health problem for human. However, the evolutionary events and biological function of pollen allergens in plants remain largely unknown. Here, we report the genome-wide prediction of pollen allergens and their biological function in the dicotyledonous model plant Arabidopsis (Arabidopsis thaliana) and the monocotyledonous model plant rice (Oryza sativa). In total, 145 and 107 pollen allergens were predicted from rice and Arabidopsis, respectively. These pollen allergens are putatively involved in stress responses and metabolic processes such as cell wall metabolism during pollen development. Interestingly, these putative pollen allergen genes were derived from large gene families and became diversified during evolution. Sequence analysis across 25 plant species from green alga to angiosperms suggest that about 40% of putative pollen allergenic proteins existed in both lower and higher plants, while other allergens emerged during evolution. Although a high proportion of gene duplication has been observed among allergen-coding genes, our data show that these genes might have undergone purifying selection during evolution. We also observed that epitopes of an allergen might have a biological function, as revealed by comprehensive analysis of two known allergens, expansin and profilin. This implies a crucial role of conserved amino acid residues in both in planta biological function and allergenicity. Finally, a model explaining how pollen allergens were generated and maintained in plants is proposed. Prediction and systematic analysis of pollen allergens in model plants suggest that pollen allergens were evolved by gene duplication and then functional specification. This study provides insight into the phylogenetic and evolutionary scenario of pollen allergens that will be helpful to future characterization and epitope screening of pollen allergens. PMID:27436829

  7. Formal functional test designs with a test representation language

    NASA Technical Reports Server (NTRS)

    Hops, J. M.

    1993-01-01

    The application of the category-partition method to the test design phase of hardware, software, or system test development is discussed. The method provides a formal framework for reducing the total number of possible test cases to a minimum logical subset for effective testing. An automatic tool and a formal language were developed to implement the method and produce the specification of test cases.

  8. Hanford tanks initiative test facility functions and requirements

    SciTech Connect

    Krieg, S.A., Fluor Daniel Hanford

    1997-03-01

    This document presents the functions and requirements for a test facility for testing single-shell tank waste retrieval equipment and systems for the Hanford Tanks Initiative (HTI) project. This effort includes review of previous test facility functions and requirements and conducting a workshop to develop specific functions and requirements for HTI testing needs. Functions and requirements for testing future retrieval systems that follow HTI are also identified.

  9. Assessment of simulation predictions of hydrocarbon pool fire tests.

    SciTech Connect

    Luketa-Hanlin, Anay Josephine

    2010-04-01

    An uncertainty quantification (UQ) analysis is performed on the fuel regression rate model within SIERRA/Fuego by comparing to a series of hydrocarbon tests performed in the Thermal Test Complex. The fuels used for comparison for the fuel regression rate model include methanol, ethanol, JP8, and heptane. The recently implemented flamelet combustion model is also assessed with a limited comparison to data involving measurements of temperature and relative mole fractions within a 2-m diameter methanol pool fire. The comparison of the current fuel regression rate model to data without UQ indicates that the model over predicts the fuel regression rate by 65% for methanol, 63% for ethanol, 95% for JP8, and 15% for heptane. If a UQ analysis is performed incorporating a range of values for transmittance, reflectance, and heat flux at the surface the current model predicts fuel regression rates within 50% of measured values. An alternative model which uses specific heats at inlet and boiling temperatures respectively and does not approximate the sensible heat is also compared to data. The alternative model with UQ significantly improves the comparison to within 25% for all fuels except heptane. Even though the proposed alternative model provides better agreement to data, particularly for JP8 and ethanol (within 15%), there are still outstanding issues regarding significant uncertainties which include heat flux gauge measurement and placement, boiling at the fuel surface, large scale convective motion within the liquid, and semi-transparent behavior.

  10. Remote sensing of vegetation ecophysiological function for improved hydrologic prediction

    NASA Astrophysics Data System (ADS)

    Drewry, D.; Ruddell, B. L.

    2014-12-01

    Land surface hydrology in vegetated landscapes is strongly controlled by ecophysiological function. The coupling between photosynthesis, stomatal dynamics and leaf energy balance fundamentally links the hydrologic and carbon cycles, and provides a basis for examining the utility of observations of functional plant traits for hydrologic prediction. Here we explore the potential of solar induced fluorescence (SIF) and thermal infrared (TIR) remote sensing observations to improve the accuracy and reduce the uncertainty in hydrologic prediction. While SIF represents an emission of radiation associated with photosynthesis, TIR provides information on foliage temperature and is related to stomatal function and water stress. A set of remote observing system simulation experiments are conducted to quantify the value of remotely sensed observations of SIF and TIR when assimilated into a detailed vegetation biophysical model. The MLCan model discretizes a dense plant canopy to resolve vertical variation in photosynthesis, water vapor and energy exchange. Here we present extensions to MLCan that allow for direct computation of the canopy emission of both SIF and TIR. The detailed representation of the physical environment and biological functioning of structurally complex canopies makes MLCan an ideal simulation tool for exploring the impact of these two unique, and potentially synergistic observables. This work specifically addresses remote sensing capabilities on both recently launched (OCO-2) and near-term (ECOSTRESS) satellite platforms. We contrast the information gained through the assimilation of SIF and TIR observations to that of the assimilation of data related to physical states such as soil moisture and leaf area index.

  11. Spinal meningiomas: clinicoradiological factors predicting recurrence and functional outcome.

    PubMed

    Maiti, Tanmoy K; Bir, Shyamal C; Patra, Devi Prasad; Kalakoti, Piyush; Guthikonda, Bharat; Nanda, Anil

    2016-08-01

    OBJECTIVE Spinal meningiomas are benign tumors with a wide spectrum of clinical and radiological features at presentation. The authors analyzed multiple clinicoradiological factors to predict recurrence and functional outcome in a cohort with a mean follow-up of more than 4 years. The authors also discuss the results of clinical studies regarding spinal meningiomas in the last 15 years. METHODS The authors retrospectively reviewed the clinical and radiological details of patients who underwent surgery for spinal tumors between 2001 and 2015 that were histopathologically confirmed as meningiomas. Demographic parameters, such as age, sex, race, and association with neurofibromatosis Type 2, were considered. Radiological parameters, such as tumor size, signal changes of spinal cord, spinal level, number of levels, location of tumor attachment, shape of tumor, and presence of dural tail/calcification, were noted. These factors were analyzed to predict recurrence and functional outcome. Furthermore, a pooled analysis was performed from 13 reports of spinal meningiomas in the last 15 years. RESULTS A total of 38 patients were included in this study. Male sex and tumors with radiological evidence of a dural tail were associated with an increased risk of recurrence at a mean follow-up of 51.2 months. Ventral or ventrolateral location, large tumors, T2 cord signal changes, and poor preoperative functional status were associated with poor functional outcome at 1-year follow-up. CONCLUSIONS Spine surgeons must be aware of the natural history and risk factors of spinal meningiomas to establish a prognosis for their patients.

  12. Predicting conversion from mild cognitive impairment to Alzheimer's disease using neuropsychological tests and multivariate methods.

    PubMed

    Chapman, Robert M; Mapstone, Mark; McCrary, John W; Gardner, Margaret N; Porsteinsson, Anton; Sandoval, Tiffany C; Guillily, Maria D; Degrush, Elizabeth; Reilly, Lindsey A

    2011-02-01

    Behavioral markers measured through neuropsychological testing in mild cognitive impairment (MCI) were analyzed and combined in multivariate ways to predict conversion to Alzheimer's disease (AD) in a longitudinal study of 43 MCI patients. The test measures taken at a baseline evaluation were first reduced to underlying components (principal component analysis, PCA), and then the component scores were used in discriminant analysis to classify MCI individuals as likely to convert or not. When empirically weighted and combined, episodic memory, speeded executive functioning, recognition memory (false and true positives), visuospatial memory processing speed, and visuospatial episodic memory were together strong predictors of conversion to AD. These multivariate combinations of the test measures achieved through the PCA were good, statistically significant predictors of MCI conversion to AD (84% accuracy, 86% sensitivity, and 83% specificity). Importantly, the posterior probabilities of group membership that accompanied the binary prediction for each participant indicated the confidence of the prediction. Most of the participants (81%) were in the highly confident probability bins (.70-1.00), where the obtained prediction accuracy was more than 90%. The strength and reliability of this multivariate prediction method were tested by cross-validation and randomized resampling.

  13. Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers

    PubMed Central

    Kwon, Andrew T.; Chou, Alice Yi; Arenillas, David J.; Wasserman, Wyeth W.

    2011-01-01

    We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions. PMID:22144875

  14. Sorting Test, Tower Test, and BRIEF-SR do not predict school performance of healthy adolescents in preuniversity education

    PubMed Central

    Boschloo, Annemarie; Krabbendam, Lydia; Aben, Aukje; de Groot, Renate; Jolles, Jelle

    2014-01-01

    Executive functions (EF) such as self-monitoring, planning, and organizing are known to develop through childhood and adolescence. They are of potential importance for learning and school performance. Earlier research into the relation between EF and school performance did not provide clear results possibly because confounding factors such as educational track, boy-girl differences, and parental education were not taken into account. The present study therefore investigated the relation between executive function tests and school performance in a highly controlled sample of 173 healthy adolescents aged 12–18. Only students in the pre-university educational track were used and the performance of boys was compared to that of girls. Results showed that there was no relation between the report marks obtained and the performance on executive function tests, notably the Sorting Test and the Tower Test of the Delis-Kaplan Executive Functions System (D-KEFS). Likewise, no relation was found between the report marks and the scores on the Behavior Rating Inventory of Executive Function—Self-Report Version (BRIEF-SR) after these were controlled for grade, sex, and level of parental education. The findings indicate that executive functioning as measured with widely used instruments such as the BRIEF-SR does not predict school performance of adolescents in preuniversity education any better than a student's grade, sex, and level of parental education. PMID:24782794

  15. Prediction of postoperative pulmonary function following thoracic operations. Value of ventilation-perfusion scanning

    SciTech Connect

    Bria, W.F.; Kanarek, D.J.; Kazemi, H.

    1983-08-01

    Surgical resection of lung cancer is frequently required in patients with severely impaired lung function resulting from chronic obstructive pulmonary disease. Twenty patients with obstructive lung disease and cancer (mean preoperative forced expiratory volume in 1 second (FEV1) . 1.73 L) were studied preoperatively and postoperatively by spirometry and radionuclide perfusion, single-breath ventilation, and washout techniques to test the ability of these methods to predict preoperatively the partial loss of lung function by the resection. Postoperative FEV1 and forced vital capacity (FVC) were accurately predicted by the formula: postoperative FEV1 (or FVC) . preoperative FEV1 X percent function of regions of lung not to be resected (r . 0.88 and 0.95, respectively). Ventilation and perfusion scans are equally effective in prediction. Washout data add to the sophistication of the method by permitting the qualitative evaluation of ventilation during tidal breathing. Criteria for patients requiring the study are suggested.

  16. Models for predicting objective function weights in prostate cancer IMRT

    SciTech Connect

    Boutilier, Justin J. Lee, Taewoo; Craig, Tim; Sharpe, Michael B.; Chan, Timothy C. Y.

    2015-04-15

    Purpose: To develop and evaluate the clinical applicability of advanced machine learning models that simultaneously predict multiple optimization objective function weights from patient geometry for intensity-modulated radiation therapy of prostate cancer. Methods: A previously developed inverse optimization method was applied retrospectively to determine optimal objective function weights for 315 treated patients. The authors used an overlap volume ratio (OV) of bladder and rectum for different PTV expansions and overlap volume histogram slopes (OVSR and OVSB for the rectum and bladder, respectively) as explanatory variables that quantify patient geometry. Using the optimal weights as ground truth, the authors trained and applied three prediction models: logistic regression (LR), multinomial logistic regression (MLR), and weighted K-nearest neighbor (KNN). The population average of the optimal objective function weights was also calculated. Results: The OV at 0.4 cm and OVSR at 0.1 cm features were found to be the most predictive of the weights. The authors observed comparable performance (i.e., no statistically significant difference) between LR, MLR, and KNN methodologies, with LR appearing to perform the best. All three machine learning models outperformed the population average by a statistically significant amount over a range of clinical metrics including bladder/rectum V53Gy, bladder/rectum V70Gy, and dose to the bladder, rectum, CTV, and PTV. When comparing the weights directly, the LR model predicted bladder and rectum weights that had, on average, a 73% and 74% relative improvement over the population average weights, respectively. The treatment plans resulting from the LR weights had, on average, a rectum V70Gy that was 35% closer to the clinical plan and a bladder V70Gy that was 29% closer, compared to the population average weights. Similar results were observed for all other clinical metrics. Conclusions: The authors demonstrated that the KNN and MLR

  17. Multiscale prediction of patient-specific platelet function under flow.

    PubMed

    Flamm, Matthew H; Colace, Thomas V; Chatterjee, Manash S; Jing, Huiyan; Zhou, Songtao; Jaeger, Daniel; Brass, Lawrence F; Sinno, Talid; Diamond, Scott L

    2012-07-01

    During thrombotic or hemostatic episodes, platelets bind collagen and release ADP and thromboxane A(2), recruiting additional platelets to a growing deposit that distorts the flow field. Prediction of clotting function under hemodynamic conditions for a patient's platelet phenotype remains a challenge. A platelet signaling phenotype was obtained for 3 healthy donors using pairwise agonist scanning, in which calcium dye-loaded platelets were exposed to pairwise combinations of ADP, U46619, and convulxin to activate the P2Y(1)/P2Y(12), TP, and GPVI receptors, respectively, with and without the prostacyclin receptor agonist iloprost. A neural network model was trained on each donor's pairwise agonist scanning experiment and then embedded into a multiscale Monte Carlo simulation of donor-specific platelet deposition under flow. The simulations were compared directly with microfluidic experiments of whole blood flowing over collagen at 200 and 1000/s wall shear rate. The simulations predicted the ranked order of drug sensitivity for indomethacin, aspirin, MRS-2179 (a P2Y(1) inhibitor), and iloprost. Consistent with measurement and simulation, one donor displayed larger clots and another presented with indomethacin resistance (revealing a novel heterozygote TP-V241G mutation). In silico representations of a subject's platelet phenotype allowed prediction of blood function under flow, essential for identifying patient-specific risks, drug responses, and novel genotypes.

  18. Prediction of functional regulatory SNPs in monogenic and complex disease

    PubMed Central

    Zhao, Yiqiang; Clark, Wyatt T.; Mort, Matthew; Cooper, David N.; Radivojac, Predrag; Mooney, Sean D.

    2013-01-01

    Next-Generation Sequencing (NGS) technologies are yielding ever-higher volumes of human genome sequence data. Given this large amount of data, it has become both a possibility and a priority to determine how disease-causing single nucleotide polymorphisms (SNPs) detected within gene regulatory regions (rSNPs) exert their effects on gene expression. Recently, several studies have explored whether disease-causing polymorphisms have attributes that can distinguish them from those that are neutral, attaining moderate success at discriminating between functional and putatively neutral regulatory SNPs. Here, we have extended this work by assessing the utility of both SNP-based features (those associated only with the polymorphism site and the surrounding DNA) and Gene-based features (those derived from the associated gene in whose regulatory region the SNP lies) in the identification of functional regulatory polymorphisms involved in either monogenic or complex disease. Gene-based features were found to be capable of both augmenting and enhancing the utility of SNP-based features in the prediction of known regulatory mutations. Adopting this approach, we achieved an AUC of 0.903 for predicting regulatory SNPs. Finally, our tool predicted 225 new regulatory SNPs with a high degree of confidence, with 105 of the 225 falling into linkage disequilibrium blocks of reported disease-associated GWAS SNPs. PMID:21796725

  19. Cognitive Function and Prediction of Dementia in Old Age.

    ERIC Educational Resources Information Center

    La Rue, Asenath; Jarvik, Lissy F.

    1987-01-01

    Examined longitudinal changes in cognitive functioning for aging twins. Found that those who were considered demented in old age had achieved lower test scores 20 years prior to diagnosis and experienced greater declines in vocabulary and forward digit span over time than those without dementia. Suggests that dementia may develop very slowly.…

  20. Electrocortical indices of selective attention predict adolescent executive functioning.

    PubMed

    Lackner, Christine L; Santesso, Diane L; Dywan, Jane; Wade, Terrance J; Segalowitz, Sidney J

    2013-05-01

    Executive functioning is considered a powerful predictor of behavioral and mental health outcomes during adolescence. Our question was whether executive functioning skills, normally considered "top-down" processes, are related to automatic aspects of selective attention. Event-related potentials (ERPs) were recorded from typically-developing 12-14-year-old adolescents as they responded to tones presented in attended and unattended channels in an auditory selective attention task. Examining these ERPs in relation to parental reports on the Behavior Rating Inventory of Executive Function (BRIEF) revealed that an early frontal positivity (EFP) elicited by to-be-ignored/unattended tones was larger in those with poorer executive functions, driven by scores on the BRIEF Metacognition Index. As is traditionally found, N1 amplitudes were more negative for the to-be-attended rather than unattended tones. Additionally, N1 latencies to unattended tones correlated with parent-ratings on the BRIEF Behavior Regulation Index, where shorter latencies predicted better executive functions. Results suggest that the ability to disengage attention from distractor information in the early stages of stimulus processing is associated with adolescent executive functioning skills. PMID:23528784

  1. Electrocortical indices of selective attention predict adolescent executive functioning.

    PubMed

    Lackner, Christine L; Santesso, Diane L; Dywan, Jane; Wade, Terrance J; Segalowitz, Sidney J

    2013-05-01

    Executive functioning is considered a powerful predictor of behavioral and mental health outcomes during adolescence. Our question was whether executive functioning skills, normally considered "top-down" processes, are related to automatic aspects of selective attention. Event-related potentials (ERPs) were recorded from typically-developing 12-14-year-old adolescents as they responded to tones presented in attended and unattended channels in an auditory selective attention task. Examining these ERPs in relation to parental reports on the Behavior Rating Inventory of Executive Function (BRIEF) revealed that an early frontal positivity (EFP) elicited by to-be-ignored/unattended tones was larger in those with poorer executive functions, driven by scores on the BRIEF Metacognition Index. As is traditionally found, N1 amplitudes were more negative for the to-be-attended rather than unattended tones. Additionally, N1 latencies to unattended tones correlated with parent-ratings on the BRIEF Behavior Regulation Index, where shorter latencies predicted better executive functions. Results suggest that the ability to disengage attention from distractor information in the early stages of stimulus processing is associated with adolescent executive functioning skills.

  2. The predictability of molecular evolution during functional innovation.

    PubMed

    Blank, Diana; Wolf, Luise; Ackermann, Martin; Silander, Olin K

    2014-02-25

    Determining the molecular changes that give rise to functional innovations is a major unresolved problem in biology. The paucity of examples has served as a significant hindrance in furthering our understanding of this process. Here we used experimental evolution with the bacterium Escherichia coli to quantify the molecular changes underlying functional innovation in 68 independent instances ranging over 22 different metabolic functions. Using whole-genome sequencing, we show that the relative contribution of regulatory and structural mutations depends on the cellular context of the metabolic function. In addition, we find that regulatory mutations affect genes that act in pathways relevant to the novel function, whereas structural mutations affect genes that act in unrelated pathways. Finally, we use population genetic modeling to show that the relative contributions of regulatory and structural mutations during functional innovation may be affected by population size. These results provide a predictive framework for the molecular basis of evolutionary innovation, which is essential for anticipating future evolutionary trajectories in the face of rapid environmental change.

  3. Early functional magnetic resonance imaging activations predict language outcome after stroke.

    PubMed

    Saur, Dorothee; Ronneberger, Olaf; Kümmerer, Dorothee; Mader, Irina; Weiller, Cornelius; Klöppel, Stefan

    2010-04-01

    An accurate prediction of system-specific recovery after stroke is essential to provide rehabilitation therapy based on the individual needs. We explored the usefulness of functional magnetic resonance imaging scans from an auditory language comprehension experiment to predict individual language recovery in 21 aphasic stroke patients. Subjects with an at least moderate language impairment received extensive language testing 2 weeks and 6 months after left-hemispheric stroke. A multivariate machine learning technique was used to predict language outcome 6 months after stroke. In addition, we aimed to predict the degree of language improvement over 6 months. 76% of patients were correctly separated into those with good and bad language performance 6 months after stroke when based on functional magnetic resonance imaging data from language relevant areas. Accuracy further improved (86% correct assignments) when age and language score were entered alongside functional magnetic resonance imaging data into the fully automatic classifier. A similar accuracy was reached when predicting the degree of language improvement based on imaging, age and language performance. No prediction better than chance level was achieved when exploring the usefulness of diffusion weighted imaging as well as functional magnetic resonance imaging acquired two days after stroke. This study demonstrates the high potential of current machine learning techniques to predict system-specific clinical outcome even for a disease as heterogeneous as stroke. Best prediction of language recovery is achieved when the brain activation potential after system-specific stimulation is assessed in the second week post stroke. More intensive early rehabilitation could be provided for those with a predicted poor recovery and the extension to other systems, for example, motor and attention seems feasible. PMID:20299389

  4. Non-invasive pulmonary function test on Morquio Patients

    PubMed Central

    Kubaski, Francyne; Tomatsu, Shunji; Patel, Pravin; Shimada, Tsutomu; Xie, Li; Yasuda, Eriko; Mason, Robert; Mackenzie, William G.; Theroux, Mary; Bober, Michael B.; Oldham, Helen M.; Orii, Tadao; Shaffer, Thomas H.

    2015-01-01

    In clinical practice, respiratory function tests are difficult to perform in Morquio syndrome patients due to their characteristic skeletal dysplasia, small body size and lack of cooperation of young patients, where in some cases, conventional spirometry for pulmonary function is too challenging. To establish feasible clinical pulmonary endpoints and determine whether age impacts lung function in Morquio patients non-invasive pulmonary tests and conventional spirometry were evaluated. The non-invasive pulmonary tests: impulse oscillometry system, pneumotachography, and respiratory inductance plethysmography in conjunction with conventional spirometry were evaluated in twenty-two Morquio patients (18 Morquio A and 4 Morquio B) (7 males), ranging from 3 and 40 years of age. Twenty-two patients were compliant with non-invasive tests (100%) with exception of IOS (81.8%–18 patients). Seventeen patients (77.3%) were compliant with spirometry testing. All subjects had normal vital signs at rest including > 95% oxygen saturation, end tidal CO2 (38–44 mmHg), and age-appropriate heart rate (mean=98.3, standard deviation=19) (two patients were deviated). All patients preserved normal values in impulse oscillometry system, pneumotachography, and respiratory inductance plethysmography, although predicted forced expiratory volume total (72.8 ± 6.9 SE%) decreased with age and was below normal; phase angle (35.5 ± 16.5 Degrees), %Rib Cage (41.6 ± 12.7%), resonant frequency, and forced expiratory volume in one second/forced expiratory volume total (110.0 ± 3.2 SE%) were normal and not significantly impacted by age. The proposed non-invasive pulmonary function tests are able to cover a greater number of patients (young patients and/or wheel-chair bound), thus providing a new diagnostic approach for the assessment of lung function in Morquio syndrome which in many cases may be difficult to evaluate. Morquio patients studied herein demonstrated no clinical or functional signs

  5. Non-invasive pulmonary function test on Morquio patients.

    PubMed

    Kubaski, Francyne; Tomatsu, Shunji; Patel, Pravin; Shimada, Tsutomu; Xie, Li; Yasuda, Eriko; Mason, Robert; Mackenzie, William G; Theroux, Mary; Bober, Michael B; Oldham, Helen M; Orii, Tadao; Shaffer, Thomas H

    2015-08-01

    In clinical practice, respiratory function tests are difficult to perform in Morquio syndrome patients due to their characteristic skeletal dysplasia, small body size and lack of cooperation of young patients, where in some cases, conventional spirometry for pulmonary function is too challenging. To establish feasible clinical pulmonary endpoints and determine whether age impacts lung function in Morquio patients non-invasive pulmonary tests and conventional spirometry were evaluated. The non-invasive pulmonary tests: impulse oscillometry system, pneumotachography, and respiratory inductance plethysmography in conjunction with conventional spirometry were evaluated in twenty-two Morquio patients (18 Morquio A and 4 Morquio B) (7 males), ranging from 3 to 40 years of age. Twenty-two patients were compliant with non-invasive tests (100%) with the exception of IOS (81.8%-18 patients). Seventeen patients (77.3%) were compliant with spirometry testing. All subjects had normal vital signs at rest including >95% oxygen saturation, end tidal CO2 (38-44 mmHg), and age-appropriate heart rate (mean=98.3, standard deviation=19) (two patients were deviated). All patients preserved normal values in the impulse oscillometry system, pneumotachography, and respiratory inductance plethysmography, although predicted forced expiratory total (72.8±6.9 SE%) decreased with age and was below normal; phase angle (35.5±16.5°), %rib cage (41.6±12.7%), resonant frequency, and forced expiratory volume in 1 s/forced expiratory volume total (110.0±3.2 SE%) were normal and not significantly impacted by age. The proposed non-invasive pulmonary function tests are able to cover a greater number of patients (young patients and/or wheel-chair bound), thus providing a new diagnostic approach for the assessment of lung function in Morquio syndrome which in many cases may be difficult to evaluate. Morquio patients studied herein demonstrated no clinical or functional signs of restrictive and

  6. The Wedensky test predicts malignant ventricular arrhythmias after myocardial infarction

    PubMed Central

    2013-01-01

    Objectives. Better tools are needed for detection of future malignant ventricular arrhythmias post myocardial infarct (MI). Wedensky Modulation (WM) is a new semi-invasive method: A short low-amplitude electrical impulse is applied synchronized to the QRS between a precordial and dorsal thoracic patch, and changes in the following QRS-T are registered. Design. A total of 357 (MI) ICD patients underwent WM testing. QRS-T wavelet analysis provided WM Indexes for the QRS complex (WMI-R) and T wave (WMI-T). Outcome was the time to first occurrence of appropriate device therapy for ventricular arrhythmia. Patients were followed at 6-month intervals for 2 years. Results. No arrhythmia was induced by the testing. Two-year appropriate arrhythmia treatment occurred in 35% (WMI-R positive) versus 25% (WMI-R negative, p = 0.014), and. 45% versus 26% (p = 0.001) for WMI-T positive versus negative. Two-year event rates of WMI-R or WMI-T positive versus WMI-R and WMI-T negative were 36% versus 22% (p = 0.004). In Cox proportional hazard model, the combination of WMI-R and WMI-T was the only statistically significant event predictor (p = 0.003). Conclusion. Potentially life-threatening ventricular arrhythmic events could be predicted by the WM test. In combination with other risk factors WMI may be useful in these patients. PMID:24050376

  7. PuFT: Computer-Assisted Program for Pulmonary Function Tests.

    ERIC Educational Resources Information Center

    Boyle, Joseph

    1983-01-01

    PuFT computer program (Microsoft Basic) is designed to help in understanding/interpreting pulmonary function tests (PFT). The program provides predicted values for common PFT after entry of patient data, calculates/plots graph simulating force vital capacity (FVC), and allows observations of effects on predicted PFT values and FVC curve when…

  8. Can infant lung function predict respiratory morbidity during the first year of life in preterm infants?

    PubMed

    Proietti, Elena; Riedel, Thomas; Fuchs, Oliver; Pramana, Isabelle; Singer, Florian; Schmidt, Anne; Kuehni, Claudia; Latzin, Philipp; Frey, Urs

    2014-06-01

    Compared with term-born infants, preterm infants have increased respiratory morbidity in the first year of life. We investigated whether lung function tests performed near term predict subsequent respiratory morbidity during the first year of life and compared this to standard clinical parameters in preterms. The prospective birth cohort included randomly selected preterm infants with and without bronchopulmonary dysplasia. Lung function (tidal breathing and multiple-breath washout) was measured at 44 weeks post-menstrual age during natural sleep. We assessed respiratory morbidity (wheeze, hospitalisation, inhalation and home oxygen therapy) after 1 year using a standardised questionnaire. We first assessed the association between lung function and subsequent respiratory morbidity. Secondly, we compared the predictive power of standard clinical predictors with and without lung function data. In 166 preterm infants, tidal volume, time to peak tidal expiratory flow/expiratory time ratio and respiratory rate were significantly associated with subsequent wheeze. In comparison with standard clinical predictors, lung function did not improve the prediction of later respiratory morbidity in an individual child. Although associated with later wheeze, noninvasive infant lung function shows large physiological variability and does not add to clinically relevant risk prediction for subsequent respiratory morbidity in an individual preterm.

  9. Predicting predation through prey ontogeny using size-dependent functional response models.

    PubMed

    McCoy, Michael W; Bolker, Benjamin M; Warkentin, Karen M; Vonesh, James R

    2011-06-01

    The functional response is a critical link between consumer and resource dynamics, describing how a consumer's feeding rate varies with prey density. Functional response models often assume homogenous prey size and size-independent feeding rates. However, variation in prey size due to ontogeny and competition is ubiquitous, and predation rates are often size dependent. Thus, functional responses that ignore prey size may not effectively predict predation rates through ontogeny or in heterogeneous populations. Here, we use short-term response-surface experiments and statistical modeling to develop and test prey size-dependent functional responses for water bugs and dragonfly larvae feeding on red-eyed treefrog tadpoles. We then extend these models through simulations to predict mortality through time for growing prey. Both conventional and size-dependent functional response models predicted average overall mortality in short-term mixed-cohort experiments, but only the size-dependent models accurately captured how mortality was spread across sizes. As a result, simulations that extrapolated these results through prey ontogeny showed that differences in size-specific mortality are compounded as prey grow, causing predictions from conventional and size-dependent functional response models to diverge dramatically through time. Our results highlight the importance of incorporating prey size when modeling consumer-prey dynamics in size-structured, growing prey populations. PMID:21597252

  10. Comparative study of biodegradability prediction of chemicals using decision trees, functional trees, and logistic regression.

    PubMed

    Chen, Guangchao; Li, Xuehua; Chen, Jingwen; Zhang, Ya-Nan; Peijnenburg, Willie J G M

    2014-12-01

    Biodegradation is the principal environmental dissipation process of chemicals. As such, it is a dominant factor determining the persistence and fate of organic chemicals in the environment, and is therefore of critical importance to chemical management and regulation. In the present study, the authors developed in silico methods assessing biodegradability based on a large heterogeneous set of 825 organic compounds, using the techniques of the C4.5 decision tree, the functional inner regression tree, and logistic regression. External validation was subsequently carried out by 2 independent test sets of 777 and 27 chemicals. As a result, the functional inner regression tree exhibited the best predictability with predictive accuracies of 81.5% and 81.0%, respectively, on the training set (825 chemicals) and test set I (777 chemicals). Performance of the developed models on the 2 test sets was subsequently compared with that of the Estimation Program Interface (EPI) Suite Biowin 5 and Biowin 6 models, which also showed a better predictability of the functional inner regression tree model. The model built in the present study exhibits a reasonable predictability compared with existing models while possessing a transparent algorithm. Interpretation of the mechanisms of biodegradation was also carried out based on the models developed.

  11. Prediction and assessment of splicing alterations: implications for clinical testing.

    PubMed

    Spurdle, Amanda B; Couch, Fergus J; Hogervorst, Frans B L; Radice, Paolo; Sinilnikova, Olga M

    2008-11-01

    Sequence variants that may result in splicing alterations are a particular class of inherited variants for which consequences can be more readily assessed, using a combination of bioinformatic prediction methods and in vitro assays. There is also a general agreement that a variant would invariably be considered pathogenic on the basis of convincing evidence that it results in transcript(s) carrying a premature stop codon or an in-frame deletion disrupting known functional domain(s). This commentary discusses current practices used to assess the clinical significance of this class of variants, provides suggestions to improve assessment, and highlights the issues involved in routine assessment of potential splicing aberrations. We conclude that classification of sequence variants that may alter splicing is greatly enhanced by supporting in vitro analysis. Additional studies that assess large numbers of variants for induction of splicing aberrations and exon skipping are needed to define the contribution of splicing/exon skipping to cancer and disease. These studies will also provide the impetus for development of algorithms that better predict splicing patterns. To facilitate variant classification and development of more specific bioinformatic tools, we call for the deposition of all laboratory data from splicing analyses into national and international databases. PMID:18951448

  12. Flight Tests of the Turbulence Prediction and Warning System (TPAWS)

    NASA Technical Reports Server (NTRS)

    Hamilton, David W.; Proctor, Fred H.; Ahmad, Nashat N.

    2012-01-01

    Flight tests of the National Aeronautics and Space Administration's Turbulence Prediction And Warning System (TPAWS) were conducted in the Fall of 2000 and Spring of 2002. TPAWS is a radar-based airborne turbulence detection system. During twelve flights, NASA's B-757 tallied 53 encounters with convectively induced turbulence. Analysis of data collected during 49 encounters in the Spring of 2002 showed that the TPAWS Airborne Turbulence Detection System (ATDS) successfully detected 80% of the events at least 30 seconds prior to the encounter, achieving FAA recommended performance criteria. Details of the flights, the prevailing weather conditions, and each of the turbulence events are presented in this report. Sensor and environmental characterizations are also provided.

  13. Predicting Run Distances for a Modified Wedge Test

    NASA Astrophysics Data System (ADS)

    Dorgan, Robert J.; Lee, Richard; Sutherland, Gerrit

    2012-03-01

    Simulations were used to aid in the development of a modified wedge test (MWT). This explosive sensitivity experiment allows the shockwave curvature to be defined in order to investigate the effect of combined shock-shear loading on sensitivity. Various widths of PBXN-110 donor slabs were used to define the shockwave curvature introduced to wedge samples of the same explosive. The donor slabs were initiated with a linewave generator and a Detasheet booster, and the shock wave was attenuated using a slab of PMMA. In developing simulations for these three material experiments, calibrations of the PBXN-110 ignition and growth model and of the PMMA constitutive model were investigated in order to choose between several models found in the literature. A calibration shot from the MWT was also used to demonstrate the appropriateness of the models selected. Experimental results were compared to CTH calculations to indicate if there were effects associated with highly curved shock fronts that could not be adequately predicted. The run distances predicted in CTH for the thicker donor slab compare very favorably with the actual experiments; however, for thinner donor slabs, the actual experimental results seem to suggest a more sensitive behavior than the simulations are able to capture.

  14. Predicting Run Distances for a Modified Wedge Test

    NASA Astrophysics Data System (ADS)

    Dorgan, Robert; Lee, Richard; Sutherland, Gerrit

    2011-06-01

    Simulations were used to aid in the development of a modified wedge test (MWT). This explosive sensitivity experiment allows the shockwave curvature to be defined in order to investigate the effect of combined shock-shear loading on sensitivity. Various widths of PBXN-110 donor slabs were used to define the shockwave curvature introduced to wedge samples of the same explosive. The donor slabs were initiated with a linewave generator and a Detasheet booster, and the shock wave was attenuated using a slab of PMMA. In developing simulations for these three material experiments, calibrations of the PBXN-110 ignition and growth model and of the PMMA constitutive model were investigated in order to choose between several models found in the literature. A calibration shot from the MWT was also used to demonstrate the appropriateness of the models selected. Experimental results were compared to CTH calculations to indicate if there were effects associated with highly curved shock fronts that could not be adequately predicted. The run distances predicted in CTH for the thicker donor slab compare very favorably with the actual experiments; however, for thinner donor slabs, the actual experimental results seem to suggest a more sensitive behavior than the simulations are able to capture. DISTRIBUTION A. Approved for public release, distribution unlimited. (96ABW-2011-0053)

  15. Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

    PubMed Central

    Bardwell, David A.; Adjiman, Claire S.; Arnautova, Yelena A.; Bartashevich, Ekaterina; Boerrigter, Stephan X. M.; Braun, Doris E.; Cruz-Cabeza, Aurora J.; Day, Graeme M.; Della Valle, Raffaele G.; Desiraju, Gautam R.; van Eijck, Bouke P.; Facelli, Julio C.; Ferraro, Marta B.; Grillo, Damian; Habgood, Matthew; Hofmann, Detlef W. M.; Hofmann, Fridolin; Jose, K. V. Jovan; Karamertzanis, Panagiotis G.; Kazantsev, Andrei V.; Kendrick, John; Kuleshova, Liudmila N.; Leusen, Frank J. J.; Maleev, Andrey V.; Misquitta, Alston J.; Mohamed, Sharmarke; Needs, Richard J.; Neumann, Marcus A.; Nikylov, Denis; Orendt, Anita M.; Pal, Rumpa; Pantelides, Constantinos C.; Pickard, Chris J.; Price, Louise S.; Price, Sarah L.; Scheraga, Harold A.; van de Streek, Jacco; Thakur, Tejender S.; Tiwari, Siddharth; Venuti, Elisabetta; Zhitkov, Ilia K.

    2011-01-01

    Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome. PMID:22101543

  16. Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

    PubMed

    Bardwell, David A; Adjiman, Claire S; Arnautova, Yelena A; Bartashevich, Ekaterina; Boerrigter, Stephan X M; Braun, Doris E; Cruz-Cabeza, Aurora J; Day, Graeme M; Della Valle, Raffaele G; Desiraju, Gautam R; van Eijck, Bouke P; Facelli, Julio C; Ferraro, Marta B; Grillo, Damian; Habgood, Matthew; Hofmann, Detlef W M; Hofmann, Fridolin; Jose, K V Jovan; Karamertzanis, Panagiotis G; Kazantsev, Andrei V; Kendrick, John; Kuleshova, Liudmila N; Leusen, Frank J J; Maleev, Andrey V; Misquitta, Alston J; Mohamed, Sharmarke; Needs, Richard J; Neumann, Marcus A; Nikylov, Denis; Orendt, Anita M; Pal, Rumpa; Pantelides, Constantinos C; Pickard, Chris J; Price, Louise S; Price, Sarah L; Scheraga, Harold A; van de Streek, Jacco; Thakur, Tejender S; Tiwari, Siddharth; Venuti, Elisabetta; Zhitkov, Ilia K

    2011-12-01

    Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome. PMID:22101543

  17. Predicting (17)O NMR chemical shifts of polyoxometalates using density functional theory.

    PubMed

    Sharma, Rupali; Zhang, Jie; Ohlin, C André

    2016-03-21

    We have investigated the computation of (17)O NMR chemical shifts of a wide range of polyoxometalates using density functional theory. The effects of basis sets and exchange-correlation functionals are explored, and whereas pure DFT functionals generally predict the chemical shifts of terminal oxygen sites quite well, hybrid functionals are required for the prediction of accurate chemical shifts in conjunction with linear regression. By using PBE0/def2-tzvp//PBE0/cc-pvtz(H-Ar), lanl2dz(K-) we have computed the chemical shifts of 37 polyoxometalates, corresponding to 209 (17)O NMR signals. We also show that at this level of theory the protonation-induced pH dependence of the chemical shift of the triprotic hexaniobate Lindqvist anion, [HxNb6O19]((8-x)), can be reproduced, which suggests that hypotheses regarding loci of protonation can be confidently tested. PMID:26925832

  18. Organization of intrinsic functional brain connectivity predicts decisions to reciprocate social behavior.

    PubMed

    Cáceda, Ricardo; James, G Andrew; Gutman, David A; Kilts, Clinton D

    2015-10-01

    Reciprocation of trust exchanges is central to the development of interpersonal relationships and societal well-being. Understanding how humans make pro-social and self-centered decisions in dyadic interactions and how to predict these choices has been an area of great interest in social neuroscience. A functional magnetic resonance imaging (fMRI) based technology with potential clinical application is the study of resting state brain connectivity. We tested if resting state connectivity may predict choice behavior in a social context. Twenty-nine healthy adults underwent resting state fMRI before performing the Trust Game, a two person monetary exchange game. We assessed the ability of patterns of resting-state functional brain organization, demographic characteristics and a measure of moral development, the Defining Issues Test (DIT-2), to predict individuals' decisions to reciprocate money during the Trust Game. Subjects reciprocated in 74.9% of the trials. Independent component analysis identified canonical resting-state networks. Increased functional connectivity between the salience (bilateral insula/anterior cingulate) and central executive (dorsolateral prefrontal cortex/ posterior parietal cortex) networks significantly predicted the choice to reciprocate pro-social behavior (R(2) = 0.20, p = 0.015). Stepwise linear regression analysis showed that functional connectivity between these two networks (p = 0.002), age (p = 0.007) and DIT-2 personal interest schema score (p = 0.032) significantly predicted reciprocity behavior (R(2) = 0.498, p = 0.001). Intrinsic functional connectivity between neural networks in conjunction with other individual characteristics may be a valuable tool for predicting performance during social interactions. Future replication and temporal extension of these findings may bolster the understanding of decision making in clinical, financial and marketing settings.

  19. Organization of intrinsic functional brain connectivity predicts decisions to reciprocate social behavior.

    PubMed

    Cáceda, Ricardo; James, G Andrew; Gutman, David A; Kilts, Clinton D

    2015-10-01

    Reciprocation of trust exchanges is central to the development of interpersonal relationships and societal well-being. Understanding how humans make pro-social and self-centered decisions in dyadic interactions and how to predict these choices has been an area of great interest in social neuroscience. A functional magnetic resonance imaging (fMRI) based technology with potential clinical application is the study of resting state brain connectivity. We tested if resting state connectivity may predict choice behavior in a social context. Twenty-nine healthy adults underwent resting state fMRI before performing the Trust Game, a two person monetary exchange game. We assessed the ability of patterns of resting-state functional brain organization, demographic characteristics and a measure of moral development, the Defining Issues Test (DIT-2), to predict individuals' decisions to reciprocate money during the Trust Game. Subjects reciprocated in 74.9% of the trials. Independent component analysis identified canonical resting-state networks. Increased functional connectivity between the salience (bilateral insula/anterior cingulate) and central executive (dorsolateral prefrontal cortex/ posterior parietal cortex) networks significantly predicted the choice to reciprocate pro-social behavior (R(2) = 0.20, p = 0.015). Stepwise linear regression analysis showed that functional connectivity between these two networks (p = 0.002), age (p = 0.007) and DIT-2 personal interest schema score (p = 0.032) significantly predicted reciprocity behavior (R(2) = 0.498, p = 0.001). Intrinsic functional connectivity between neural networks in conjunction with other individual characteristics may be a valuable tool for predicting performance during social interactions. Future replication and temporal extension of these findings may bolster the understanding of decision making in clinical, financial and marketing settings. PMID:26166191

  20. Defining Predictive Probability Functions for Species Sampling Models

    PubMed Central

    Lee, Jaeyong; Quintana, Fernando A.; Müller, Peter; Trippa, Lorenzo

    2013-01-01

    We review the class of species sampling models (SSM). In particular, we investigate the relation between the exchangeable partition probability function (EPPF) and the predictive probability function (PPF). It is straightforward to define a PPF from an EPPF, but the converse is not necessarily true. In this paper we introduce the notion of putative PPFs and show novel conditions for a putative PPF to define an EPPF. We show that all possible PPFs in a certain class have to define (unnormalized) probabilities for cluster membership that are linear in cluster size. We give a new necessary and sufficient condition for arbitrary putative PPFs to define an EPPF. Finally, we show posterior inference for a large class of SSMs with a PPF that is not linear in cluster size and discuss a numerical method to derive its PPF. PMID:24368874

  1. Predicting Infrared Spectra of Nerve Agents Using Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Zhang, Y.-P.; Wang, H.-T.; Zheng, W.-P.; Sun, C.; Bai, Y.; Guo, X.-D.; Sun, H.

    2016-09-01

    Vibration frequencies of four nerve agents and two simulators are calculated using B3LYP coupled with ten basis sets. To evaluate the accuracy of calculated spectra, root mean square error (RMSE) and weighted cross-correlation average (WCCA) are considered. The evaluation shows that B3LYP/6-311+g(d,p) performs best in predicting infrared spectra, and polarization functions are found to be more important than diffusion functions in spectra simulation. Moreover, B3LYP calculation underestimates frequencies related to the P atom. The WCCA metric derives 1.008 as a unique scaling factor for calculated frequencies. The results indicate that the WCCA metric can identify six agents based on calculated spectra.

  2. Predictions for the ARPES spectral function of kagome antiferromagnetic insulators

    NASA Astrophysics Data System (ADS)

    Pujari, Sumiran; Lawler, Michael J.

    2011-03-01

    There are now a number of spin liquid candidate materials possibly with exotic spin-1/2 ``spinon'' excitations. Motivation by these discoveries, we consider the scaling properties of the hole spectral function for the frustrated Kagome Heisenberg antiferromagnet assuming Dirac Spin Liquid(DSL) ground state proposed for Herbertsmithite [ 2 ] . We predict a sublinear in energy power law dependence of the ARPES spectral function at certain wave vectors. Using Renormalization group techniques, we show how (gauge) fluctuations of the DSL mean field give an anomalous exponent to spinons [ 2 ] and no anomalous exponent to holons thereby leading to the sublinear power law. If this behavior is observed in experiments, they would provide strong evidence for the existence of spinons in highly frustrated magnets. S.P. gratefully acknowledges support from NSF grant DMR-1005466.

  3. Experimental design in phylogenetics: testing predictions from expected information.

    PubMed

    San Mauro, Diego; Gower, David J; Cotton, James A; Zardoya, Rafael; Wilkinson, Mark; Massingham, Tim

    2012-07-01

    Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well

  4. Can clinical colour vision tests be used to predict the results of the Farnsworth lantern test?

    PubMed

    Cole, B L; Maddocks, J D

    1998-11-01

    Clinicians usually do not have access to a lantern test when making an occupational assessment of the ability of a person with defective colour vision to recognise signal light colours: they must rely on the results of ordinary clinical tests. While all colour vision defectives fail the Holmes Wright Type B lantern test and most fail the Holmes Wright Type A lantern, 35% of colour vision defectives pass the Farnsworth lantern. Can clinical tests predict who will pass and fail the Farnsworth lantern? We find that a pass (less than two or more diametrical crossings) at the Farnsworth Panel D 15 Dichotomous test has a sensitivity of 0.67 and specificity of 0.94 in predicting a pass or fail at the Farnsworth lantern test: a Nagel range of > 10 has a sensitivity of 0.87 and a specificity of 0.57. We conclude that neither the D 15 nor the Nagel Anomaloscope matching range are satisfactory predictors of performance on the Farnsworth Lantern.

  5. Predicting activity approach based on new atoms similarity kernel function.

    PubMed

    Abu El-Atta, Ahmed H; Moussa, M I; Hassanien, Aboul Ella

    2015-07-01

    Drug design is a high cost and long term process. To reduce time and costs for drugs discoveries, new techniques are needed. Chemoinformatics field implements the informational techniques and computer science like machine learning and graph theory to discover the chemical compounds properties, such as toxicity or biological activity. This is done through analyzing their molecular structure (molecular graph). To overcome this problem there is an increasing need for algorithms to analyze and classify graph data to predict the activity of molecules. Kernels methods provide a powerful framework which combines machine learning with graph theory techniques. These kernels methods have led to impressive performance results in many several chemoinformatics problems like biological activity prediction. This paper presents a new approach based on kernel functions to solve activity prediction problem for chemical compounds. First we encode all atoms depending on their neighbors then we use these codes to find a relationship between those atoms each other. Then we use relation between different atoms to find similarity between chemical compounds. The proposed approach was compared with many other classification methods and the results show competitive accuracy with these methods.

  6. Predictive tests to evaluate oxidative potential of engineered nanomaterials

    NASA Astrophysics Data System (ADS)

    Ghiazza, Mara; Carella, Emanuele; Oliaro-Bosso, Simonetta; Corazzari, Ingrid; Viola, Franca; Fenoglio, Ivana

    2013-04-01

    Oxidative stress constitutes one of the principal injury mechanisms through which particulate toxicants (asbestos, crystalline silica, hard metals) and engineered nanomaterials can induce adverse health effects. ROS may be generated indirectly by activated cells and/or directly at the surface of the material. The occurrence of these processes depends upon the type of material. Many authors have recently demonstrated that metal oxides and carbon-based nanoparticles may influence (increasing or decreasing) the generation of oxygen radicals in a cell environment. Metal oxide, such as iron oxides, crystalline silica, and titanium dioxide are able to generate free radicals via different mechanisms causing an imbalance within oxidant species. The increase of ROS species may lead to inflammatory responses and in some cases to the development of cancer. On the other hand carbon-based nanomaterials, such as fullerene, carbon nanotubes, carbon black as well as cerium dioxide are able to scavenge the free radicals generated acting as antioxidant. The high numbers of new-engineered nanomaterials, which are introduced in the market, are exponentially increasing. Therefore the definition of toxicological strategies is urgently needed. The development of acellular screening tests will make possible the reduction of the number of in vitro and in vivo tests to be performed. An integrated protocol that may be used to predict the oxidant/antioxidant potential of engineered nanoparticles will be here presented.

  7. Graphlet kernels for prediction of functional residues in protein structures.

    PubMed

    Vacic, Vladimir; Iakoucheva, Lilia M; Lonardi, Stefano; Radivojac, Predrag

    2010-01-01

    We introduce a novel graph-based kernel method for annotating functional residues in protein structures. A structure is first modeled as a protein contact graph, where nodes correspond to residues and edges connect spatially neighboring residues. Each vertex in the graph is then represented as a vector of counts of labeled non-isomorphic subgraphs (graphlets), centered on the vertex of interest. A similarity measure between two vertices is expressed as the inner product of their respective count vectors and is used in a supervised learning framework to classify protein residues. We evaluated our method on two function prediction problems: identification of catalytic residues in proteins, which is a well-studied problem suitable for benchmarking, and a much less explored problem of predicting phosphorylation sites in protein structures. The performance of the graphlet kernel approach was then compared against two alternative methods, a sequence-based predictor and our implementation of the FEATURE framework. On both tasks, the graphlet kernel performed favorably; however, the margin of difference was considerably higher on the problem of phosphorylation site prediction. While there is data that phosphorylation sites are preferentially positioned in intrinsically disordered regions, we provide evidence that for the sites that are located in structured regions, neither the surface accessibility alone nor the averaged measures calculated from the residue microenvironments utilized by FEATURE were sufficient to achieve high accuracy. The key benefit of the graphlet representation is its ability to capture neighborhood similarities in protein structures via enumerating the patterns of local connectivity in the corresponding labeled graphs.

  8. Reliability of predicted renal function in Japanese patients on cisplatin therapy.

    PubMed

    Yajima, A; Ogawa, C; Yatabe, M; Kondo, N; Saito, S; Suzuki, Y; Uesawa, Y

    2013-09-01

    Cisplatin, cis-Dichlorodiammine platinum (II) (CDDP) remains a major antineoplastic drug for the treatment of solid tumors. Its chief dose-limiting side effect is nephrotoxicity. To make a safe and effective dosing regimen of a drug excreted mainly by the renal route, evaluation of patients' renal function is essential. Creatinine clearance (CLcr) or glomerular filtration rate (GFR) is considered to be a standard renal-function test. Several equations have been used in clinical settings, to predict CLcr and GFR using serum creatinine concentration. We carried out a retrospective analysis of the correlation between 24-hour CLcr measured by a urine collection method; and the predicted CLcr and GFR estimated by various equations such as Jelliffe, Yasuda, Orita, Mawer, Mawer, MDRD and modified MDRD, and Cockcroft-Gault. This study used data from Japanese head-and-neck cancer patients, before and after chemotherapy with CDDP. Slopes of regression lines of scatter plots between measured CLcr and predicted renal function in post-CDDP patients were less compared to pre-CDDP patients. On the other hand, Y-intercepts were noted in the scatter plots on renal function from all equations. These results suggest that evaluation of renal function using predictive formulae may have been over-/under-estimated after CDDP administration. PMID:24147348

  9. Ongoing dynamics in large-scale functional connectivity predict perception

    PubMed Central

    Sadaghiani, Sepideh; Poline, Jean-Baptiste; Kleinschmidt, Andreas; D’Esposito, Mark

    2015-01-01

    Most brain activity occurs in an ongoing manner not directly locked to external events or stimuli. Regional ongoing activity fluctuates in unison with some brain regions but not others, and the degree of long-range coupling is called functional connectivity, often measured with correlation. Strength and spatial distributions of functional connectivity dynamically change in an ongoing manner over seconds to minutes, even when the external environment is held constant. Direct evidence for any behavioral relevance of these continuous large-scale dynamics has been limited. Here, we investigated whether ongoing changes in baseline functional connectivity correlate with perception. In a continuous auditory detection task, participants perceived the target sound in roughly one-half of the trials. Very long (22–40 s) interstimulus intervals permitted investigation of baseline connectivity unaffected by preceding evoked responses. Using multivariate classification, we observed that functional connectivity before the target predicted whether it was heard or missed. Using graph theoretical measures, we characterized the difference in functional connectivity between states that lead to hits vs. misses. Before misses compared with hits and task-free rest, connectivity showed reduced modularity, a measure of integrity of modular network structure. This effect was strongest in the default mode and visual networks and caused by both reduced within-network connectivity and enhanced across-network connections before misses. The relation of behavior to prestimulus connectivity was dissociable from that of prestimulus activity amplitudes. In conclusion, moment to moment dynamic changes in baseline functional connectivity may shape subsequent behavioral performance. A highly modular network structure seems beneficial to perceptual efficiency. PMID:26106164

  10. Ongoing dynamics in large-scale functional connectivity predict perception.

    PubMed

    Sadaghiani, Sepideh; Poline, Jean-Baptiste; Kleinschmidt, Andreas; D'Esposito, Mark

    2015-07-01

    Most brain activity occurs in an ongoing manner not directly locked to external events or stimuli. Regional ongoing activity fluctuates in unison with some brain regions but not others, and the degree of long-range coupling is called functional connectivity, often measured with correlation. Strength and spatial distributions of functional connectivity dynamically change in an ongoing manner over seconds to minutes, even when the external environment is held constant. Direct evidence for any behavioral relevance of these continuous large-scale dynamics has been limited. Here, we investigated whether ongoing changes in baseline functional connectivity correlate with perception. In a continuous auditory detection task, participants perceived the target sound in roughly one-half of the trials. Very long (22-40 s) interstimulus intervals permitted investigation of baseline connectivity unaffected by preceding evoked responses. Using multivariate classification, we observed that functional connectivity before the target predicted whether it was heard or missed. Using graph theoretical measures, we characterized the difference in functional connectivity between states that lead to hits vs. misses. Before misses compared with hits and task-free rest, connectivity showed reduced modularity, a measure of integrity of modular network structure. This effect was strongest in the default mode and visual networks and caused by both reduced within-network connectivity and enhanced across-network connections before misses. The relation of behavior to prestimulus connectivity was dissociable from that of prestimulus activity amplitudes. In conclusion, moment to moment dynamic changes in baseline functional connectivity may shape subsequent behavioral performance. A highly modular network structure seems beneficial to perceptual efficiency. PMID:26106164

  11. Ongoing dynamics in large-scale functional connectivity predict perception.

    PubMed

    Sadaghiani, Sepideh; Poline, Jean-Baptiste; Kleinschmidt, Andreas; D'Esposito, Mark

    2015-07-01

    Most brain activity occurs in an ongoing manner not directly locked to external events or stimuli. Regional ongoing activity fluctuates in unison with some brain regions but not others, and the degree of long-range coupling is called functional connectivity, often measured with correlation. Strength and spatial distributions of functional connectivity dynamically change in an ongoing manner over seconds to minutes, even when the external environment is held constant. Direct evidence for any behavioral relevance of these continuous large-scale dynamics has been limited. Here, we investigated whether ongoing changes in baseline functional connectivity correlate with perception. In a continuous auditory detection task, participants perceived the target sound in roughly one-half of the trials. Very long (22-40 s) interstimulus intervals permitted investigation of baseline connectivity unaffected by preceding evoked responses. Using multivariate classification, we observed that functional connectivity before the target predicted whether it was heard or missed. Using graph theoretical measures, we characterized the difference in functional connectivity between states that lead to hits vs. misses. Before misses compared with hits and task-free rest, connectivity showed reduced modularity, a measure of integrity of modular network structure. This effect was strongest in the default mode and visual networks and caused by both reduced within-network connectivity and enhanced across-network connections before misses. The relation of behavior to prestimulus connectivity was dissociable from that of prestimulus activity amplitudes. In conclusion, moment to moment dynamic changes in baseline functional connectivity may shape subsequent behavioral performance. A highly modular network structure seems beneficial to perceptual efficiency.

  12. Test-Anchored Vibration Response Predictions for an Acoustically Energized Curved Orthogrid Panel with Mounted Components

    NASA Technical Reports Server (NTRS)

    Frady, Gregory P.; Duvall, Lowery D.; Fulcher, Clay W. G.; Laverde, Bruce T.; Hunt, Ronald A.

    2011-01-01

    A rich body of vibroacoustic test data was recently generated at Marshall Space Flight Center for a curved orthogrid panel typical of launch vehicle skin structures. Several test article configurations were produced by adding component equipment of differing weights to the flight-like vehicle panel. The test data were used to anchor computational predictions of a variety of spatially distributed responses including acceleration, strain and component interface force. Transfer functions relating the responses to the input pressure field were generated from finite element based modal solutions and test-derived damping estimates. A diffuse acoustic field model was employed to describe the assumed correlation of phased input sound pressures across the energized panel. This application demonstrates the ability to quickly and accurately predict a variety of responses to acoustically energized skin panels with mounted components. Favorable comparisons between the measured and predicted responses were established. The validated models were used to examine vibration response sensitivities to relevant modeling parameters such as pressure patch density, mesh density, weight of the mounted component and model form. Convergence metrics include spectral densities and cumulative root-mean squared (RMS) functions for acceleration, velocity, displacement, strain and interface force. Minimum frequencies for response convergence were established as well as recommendations for modeling techniques, particularly in the early stages of a component design when accurate structural vibration requirements are needed relatively quickly. The results were compared with long-established guidelines for modeling accuracy of component-loaded panels. A theoretical basis for the Response/Pressure Transfer Function (RPTF) approach provides insight into trends observed in the response predictions and confirmed in the test data. The software modules developed for the RPTF method can be easily adapted for

  13. Food allergy--towards predictive testing for novel foods.

    PubMed

    Oehlschlager, S; Reece, P; Brown, A; Hughson, E; Hird, H; Chisholm, J; Atkinson, H; Meredith, C; Pumphrey, R; Wilson, P; Sunderland, J

    2001-12-01

    The risks associated with IgE-mediated food allergy highlight the need for methods to screen for potential food allergens. Clinical and immunological tests are available for the diagnosis of food allergy to known food allergens, but this does not extend to the evaluation, or prediction of allergenicity in novel foods. This category, includes foods produced using novel processes genetically modified (GM) foods, and foods that might be used as alternatives to traditional foods. Through the collation and analysis of the protein sequences of known allergens and their epitopes, it is possible to identify related groups which correlate with observed clinical cross-reactivities. 3-D modelling extends the use of sequence data and can be used to display eptiopes on the surface of a molecule. Experimental models support sequence analysis and 3-D modelling. Observed cross-reactivities can be examined by Western blots prepared from native 2-D gels of a whole food preparation (e.g. hazelnut, peanut), and common proteins identified. IgEs to novel proteins can be raised in Brown Norway rat (a high IgE responder strain) and the proteins tested in simulated digest to determine epitope stability. Using the CSL serum bank, epitope binding can be examined through the ability of an allergen to cross-link the high affinity IgE receptor and thereby release mediators using in vitro cell-based models. This range of methods, in combination with data mining, provides a variety of screening options for testing the potential of a novel food to be allergenic, which does not involve prior exposure to the consumer.

  14. Food allergy--towards predictive testing for novel foods.

    PubMed

    Oehlschlager, S; Reece, P; Brown, A; Hughson, E; Hird, H; Chisholm, J; Atkinson, H; Meredith, C; Pumphrey, R; Wilson, P; Sunderland, J

    2001-12-01

    The risks associated with IgE-mediated food allergy highlight the need for methods to screen for potential food allergens. Clinical and immunological tests are available for the diagnosis of food allergy to known food allergens, but this does not extend to the evaluation, or prediction of allergenicity in novel foods. This category, includes foods produced using novel processes genetically modified (GM) foods, and foods that might be used as alternatives to traditional foods. Through the collation and analysis of the protein sequences of known allergens and their epitopes, it is possible to identify related groups which correlate with observed clinical cross-reactivities. 3-D modelling extends the use of sequence data and can be used to display eptiopes on the surface of a molecule. Experimental models support sequence analysis and 3-D modelling. Observed cross-reactivities can be examined by Western blots prepared from native 2-D gels of a whole food preparation (e.g. hazelnut, peanut), and common proteins identified. IgEs to novel proteins can be raised in Brown Norway rat (a high IgE responder strain) and the proteins tested in simulated digest to determine epitope stability. Using the CSL serum bank, epitope binding can be examined through the ability of an allergen to cross-link the high affinity IgE receptor and thereby release mediators using in vitro cell-based models. This range of methods, in combination with data mining, provides a variety of screening options for testing the potential of a novel food to be allergenic, which does not involve prior exposure to the consumer. PMID:11761121

  15. Predicting Functional Performance and Range of Motion Outcomes After Total Knee Arthroplasty

    PubMed Central

    Bade, Michael J.; Kittelson, John M.; Kohrt, Wendy M.; Stevens-Lapsley, Jennifer E.

    2015-01-01

    Objective The aim of this study was to assess the predictive value of functional performance and range of motion measures on outcomes after total knee arthroplasty. Design This is a secondary analysis of two pooled prospective randomized controlled trials. Sixty-four subjects (32 men and 32 women) with end-stage knee osteoarthritis scheduled to undergo primary total knee arthroplasty were enrolled. Active knee flexion and extension range of motion, Timed Up and Go (TUG) test time, and 6-min walk test distance were assessed. Results Preoperative measures of knee flexion and extension were predictive of long-term flexion (β = 0.44, P < 0.001) and extension (β = 0.46, P < 0.001). Acute measures of knee flexion and extension were not predictive of long-term flexion (β= 0.09, P = 0.26) or extension (β = 0.04, P = 0.76). Preoperative TUG performance was predictive of long-term 6-min walk performance (β = −21, P < 0.001). Acute TUG performance was predictive of long-term functional performance on the 6-min walk test, after adjusting for the effects of sex and age (P = 0.02); however, once adjusted for preoperative TUG performance, acute TUG was no longer related to long-term 6-min walk performance (P = 0.65). Conclusions Acute postoperative measures of knee range of motion are of limited prognostic value, although preoperative measures have some prognostic value. However, acute measures of functional performance are of useful prognostic value, especially when preoperative functional performance data are unavailable. PMID:24508937

  16. Orion Pad Abort 1 Flight Test: Simulation Predictions Versus Flight Data

    NASA Technical Reports Server (NTRS)

    Stillwater, Ryan Allanque; Merritt, Deborah S.

    2011-01-01

    The presentation covers the pre-flight simulation predictions of the Orion Pad Abort 1. The pre-flight simulation predictions are compared to the Orion Pad Abort 1 flight test data. Finally the flight test data is compared to the updated simulation predictions, which show a ove rall improvement in the accuracy of the simulation predictions.

  17. Gap Test Modeling to Predict Wedge Tests Initiation of PBXN-103

    NASA Astrophysics Data System (ADS)

    Richmond, Clinton Thomas

    1997-07-01

    The experimental Initiation of PBXN-103 by the standard wedge test has been modeled by using the HVRB initiation and growth model in the CTH code. The P-081 plane wave lens was used as initiator in these experiments. The wedge test was converted to a gap test by replacing the PBXN-103 wedge by a PBXN-103 cylinder. By modeling this gap test, shock initiation in the PBXN-103 was calculated. The results of these calculations are in agreement with the experimental results of the wedge tests. Comparison of the CTH code calculations with the wedge test data was accomplished by using an auxiliary program to the CTH code called the BCAT code. In particular, it computes the ``pop plot'' and compares it to the wedge test data. It also predicts other fundamental results of the wedge test. Shock initiation of PBX-9404 was also calculated by the HVRB model and compared to the same calculation using the Lee-Tarver model. Comparison of the two calculations indicate that the HVRB model is apparently as good as the Lee-Tarver model.

  18. Prediction of cloud condensation nuclei activity for organic compounds using functional group contribution methods

    DOE PAGESBeta

    Petters, M. D.; Kreidenweis, S. M.; Ziemann, P. J.

    2016-01-19

    A wealth of recent laboratory and field experiments demonstrate that organic aerosol composition evolves with time in the atmosphere, leading to changes in the influence of the organic fraction to cloud condensation nuclei (CCN) spectra. There is a need for tools that can realistically represent the evolution of CCN activity to better predict indirect effects of organic aerosol on clouds and climate. This work describes a model to predict the CCN activity of organic compounds from functional group composition. Following previous methods in the literature, we test the ability of semi-empirical group contribution methods in Köhler theory to predict themore » effective hygroscopicity parameter, kappa. However, in our approach we also account for liquid–liquid phase boundaries to simulate phase-limited activation behavior. Model evaluation against a selected database of published laboratory measurements demonstrates that kappa can be predicted within a factor of 2. Simulation of homologous series is used to identify the relative effectiveness of different functional groups in increasing the CCN activity of weakly functionalized organic compounds. Hydroxyl, carboxyl, aldehyde, hydroperoxide, carbonyl, and ether moieties promote CCN activity while methylene and nitrate moieties inhibit CCN activity. The model can be incorporated into scale-bridging test beds such as the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) to evaluate the evolution of kappa for a complex mix of organic compounds and to develop suitable parameterizations of CCN evolution for larger-scale models.« less

  19. Prediction of cloud condensation nuclei activity for organic compounds using functional group contribution methods

    NASA Astrophysics Data System (ADS)

    Petters, M. D.; Kreidenweis, S. M.; Ziemann, P. J.

    2016-01-01

    A wealth of recent laboratory and field experiments demonstrate that organic aerosol composition evolves with time in the atmosphere, leading to changes in the influence of the organic fraction to cloud condensation nuclei (CCN) spectra. There is a need for tools that can realistically represent the evolution of CCN activity to better predict indirect effects of organic aerosol on clouds and climate. This work describes a model to predict the CCN activity of organic compounds from functional group composition. Following previous methods in the literature, we test the ability of semi-empirical group contribution methods in Köhler theory to predict the effective hygroscopicity parameter, kappa. However, in our approach we also account for liquid-liquid phase boundaries to simulate phase-limited activation behavior. Model evaluation against a selected database of published laboratory measurements demonstrates that kappa can be predicted within a factor of 2. Simulation of homologous series is used to identify the relative effectiveness of different functional groups in increasing the CCN activity of weakly functionalized organic compounds. Hydroxyl, carboxyl, aldehyde, hydroperoxide, carbonyl, and ether moieties promote CCN activity while methylene and nitrate moieties inhibit CCN activity. The model can be incorporated into scale-bridging test beds such as the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) to evaluate the evolution of kappa for a complex mix of organic compounds and to develop suitable parameterizations of CCN evolution for larger-scale models.

  20. Predicting Gene-Regulation Functions: Lessons from Temperate Bacteriophages

    PubMed Central

    Teif, Vladimir B.

    2010-01-01

    Gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). The challenge is to predict GRFs from the sequence. Here we systematically consider the lysogeny-lysis CRMs of different temperate bacteriophages such as the Lactobacillus casei phage A2, Escherichia coli phages λ, and 186 and Lactococcal phage TP901-1. This study allowed explaining a recent experimental puzzle on the role of Cro protein in the lambda switch. Several general conclusions have been drawn: 1), long-range interactions, multilayer assembly and DNA looping may lead to complex GRFs that cannot be described by linear functions of binding site occupancies; 2), in general, GRFs cannot be described by the Boolean logic, whereas a three-state non-Boolean logic suffices for the studied examples; 3), studied CRMs of the intact phages seemed to have a similar GRF topology (the number of plateaus and peaks corresponding to different expression regimes); we hypothesize that functionally equivalent CRMs might have topologically equivalent GRFs for a larger class of genetic systems; and 4) within a given GRF class, a set of mechanistic-to-mathematical transformations has been identified, which allows shaping the GRF before carrying out a system-level analysis. PMID:20371324

  1. Vestibular Function Tests for Vestibular Migraine: Clinical Implication of Video Head Impulse and Caloric Tests

    PubMed Central

    Kang, Woo Seok; Lee, Sang Hun; Yang, Chan Joo; Ahn, Joong Ho; Chung, Jong Woo; Park, Hong Ju

    2016-01-01

    Vestibular migraine (VM) is one of the most common causes of episodic vertigo. We reviewed the results of multiple vestibular function tests in a cohort of VM patients who were diagnosed with VM according to the diagnostic criteria of the Barany Society and the International Headache Society and assessed the efficacy of each for predicting the prognosis in VM patients. A retrospective chart analysis was performed on 81 VM patients at a tertiary care center from June 2014 to July 2015. Patients were assessed by the video head impulse test (vHIT), caloric test, vestibular-evoked myogenic potentials (VEMPs), and sensory organization test (SOT) at the initial visit and then evaluated for symptomatic improvement after 6 months. Complete response (CR) was defined as no need for continued medication, partial response (PR) as improved symptoms but need for continued medication, and no response (NR) as no symptomatic improvement and requiring increased dosage or change in medications. At the initial evaluation, 9 of 81 patients (11%) exhibited abnormal vHIT results, 14 of 73 (19%) exhibited abnormal caloric test results, 25 of 65 (38%) exhibited abnormal SOT results, 8 of 75 (11%) exhibited abnormal cervical VEMP results, and 20 of 75 (27%) exhibited abnormal ocular VEMP results. Six months later, 63 of 81 patients (78%) no longer required medication (CR), while 18 (22%) still required medication, including 7 PR and 11 NR patients. Abnormal vHIT gain and abnormal caloric results were significantly related to the necessity for continued medication at 6-month follow-up (OR = 5.67 and 4.36, respectively). Abnormal vHIT and caloric test results revealed semicircular canal dysfunction in VM patients and predicted prolonged preventive medication requirement. These results suggest that peripheral vestibular abnormalities are closely related to the development of vertigo in VM patients. PMID:27746761

  2. Functional Network Architecture Predicts Psychologically Mediated Analgesia Related to Treatment in Chronic Knee Pain Patients

    PubMed Central

    Kong, Jian; Spaeth, Rosa; Khan, Sheraz; Kaptchuk, Ted J.

    2014-01-01

    Placebo analgesia is an indicator of how efficiently the brain translates psychological signals conveyed by a treatment procedure into pain relief. It has been demonstrated that functional connectivity between distributed brain regions predicts placebo analgesia in chronic back pain patients. Greater network efficiency in baseline brain networks may allow better information transfer and facilitate adaptive physiological responses to psychological aspects of treatment. Here, we theorized that topological network alignments in resting state scans predict psychologically conditioned analgesic responses to acupuncture treatment in chronic knee osteoarthritis pain patients (n = 45). Analgesia was induced by building positive expectations toward acupuncture treatment with verbal suggestion and heat pain conditioning on a test site of the arm. This procedure induced significantly more analgesia after sham or real acupuncture on the test site than in a control site. The psychologically conditioned analgesia was invariant to sham versus real treatment. Efficiency of information transfer within local networks calculated with graph-theoretic measures (local efficiency and clustering coefficients) significantly predicted conditioned analgesia. Clustering coefficients in regions associated with memory, motivation, and pain modulation were closely involved in predicting analgesia. Moreover, women showed higher clustering coefficients and marginally greater pain reduction than men. Overall, analgesic response to placebo cues can be predicted from a priori resting state data by observing local network topology. Such low-cost synchronizations may represent preparatory resources that facilitate subsequent performance of brain circuits in responding to adaptive environmental cues. This suggests a potential utility of network measures in predicting placebo response for clinical use. PMID:24623770

  3. Test-Anchored Vibration Response Predictions for an Acoustically Energized Curved Orthogrid Panel with Mounted Components

    NASA Technical Reports Server (NTRS)

    Frady, Gregory P.; Duvall, Lowery D.; Fulcher, Clay W. G.; Laverde, Bruce T.; Hunt, Ronald A.

    2011-01-01

    rich body of vibroacoustic test data was recently generated at Marshall Space Flight Center for component-loaded curved orthogrid panels typical of launch vehicle skin structures. The test data were used to anchor computational predictions of a variety of spatially distributed responses including acceleration, strain and component interface force. Transfer functions relating the responses to the input pressure field were generated from finite element based modal solutions and test-derived damping estimates. A diffuse acoustic field model was applied to correlate the measured input sound pressures across the energized panel. This application quantifies the ability to quickly and accurately predict a variety of responses to acoustically energized skin panels with mounted components. Favorable comparisons between the measured and predicted responses were established. The validated models were used to examine vibration response sensitivities to relevant modeling parameters such as pressure patch density, mesh density, weight of the mounted component and model form. Convergence metrics include spectral densities and cumulative root-mean squared (RMS) functions for acceleration, velocity, displacement, strain and interface force. Minimum frequencies for response convergence were established as well as recommendations for modeling techniques, particularly in the early stages of a component design when accurate structural vibration requirements are needed relatively quickly. The results were compared with long-established guidelines for modeling accuracy of component-loaded panels. A theoretical basis for the Response/Pressure Transfer Function (RPTF) approach provides insight into trends observed in the response predictions and confirmed in the test data. The software developed for the RPTF method allows easy replacement of the diffuse acoustic field with other pressure fields such as a turbulent boundary layer (TBL) model suitable for vehicle ascent. Structural responses

  4. Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study

    PubMed Central

    2011-01-01

    Next-generation sequencing has opened up new avenues for the genetic study of complex traits. However, because of the small number of observations for any given rare allele and high sequencing error, it is a challenge to identify functional rare variants associated with the phenotype of interest. Recent research shows that grouping variants by gene and incorporating computationally predicted functions of variants may provide higher statistical power. On the other hand, many algorithms are available for predicting the damaging effects of nonsynonymous variants. Here, we use the simulated mini-exome data of Genetic Analysis Workshop 17 to study and compare the effects of incorporating the functional predictions of single-nucleotide polymorphisms using two popular algorithms, SIFT and PolyPhen-2, into a gene-based association test. We also propose a simple mixture model that can effectively combine test results based on different functional prediction algorithms. PMID:22373178

  5. Predicted equations for ventilatory function among Kuching (Sarawak, Malaysia) population.

    PubMed

    Djojodibroto, R D; Pratibha, G; Kamaluddin, B; Manjit, S S; Sumitabha, G; Kumar, A Deva; Hashami, B

    2009-12-01

    Spirometry data of 869 individuals (males and females) between the ages of 10 to 60 years were analyzed. The analysis yielded the following conclusions: 1. The pattern of Forced Vital Capacity (FVC) and Forced Expiratory Volume in One Second (FEV1) for the selected subgroups seems to be gender dependant: in males, the highest values were seen in the Chinese, followed by the Malay, and then the Dayak; in females, the highest values were seen in the Chinese, followed by the Dayak, and then the Malay. 2. Smoking that did not produce respiratory symptom was not associated with a decline in lung function, in fact we noted higher values in smokers as compared to nonsmokers. 3. Prediction formulae (54 in total) are worked out for FVC & FEV1 for the respective gender and each of the selected subgroups.

  6. The evolution of genomic imprinting: theories, predictions and empirical tests.

    PubMed

    Patten, M M; Ross, L; Curley, J P; Queller, D C; Bonduriansky, R; Wolf, J B

    2014-08-01

    The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues' kinship theory; Day and Bonduriansky's sexual antagonism theory; and Wolf and Hager's maternal-offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternal-offspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted. PMID:24755983

  7. The evolution of genomic imprinting: theories, predictions and empirical tests

    PubMed Central

    Patten, M M; Ross, L; Curley, J P; Queller, D C; Bonduriansky, R; Wolf, J B

    2014-01-01

    The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues' kinship theory; Day and Bonduriansky's sexual antagonism theory; and Wolf and Hager's maternal–offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternal–offspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted. PMID:24755983

  8. The evolution of genomic imprinting: theories, predictions and empirical tests.

    PubMed

    Patten, M M; Ross, L; Curley, J P; Queller, D C; Bonduriansky, R; Wolf, J B

    2014-08-01

    The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues' kinship theory; Day and Bonduriansky's sexual antagonism theory; and Wolf and Hager's maternal-offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternal-offspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted.

  9. Spatiotemporal properties of microsaccades: Model predictions and experimental tests

    NASA Astrophysics Data System (ADS)

    Zhou, Jian-Fang; Yuan, Wu-Jie; Zhou, Zhao

    2016-10-01

    Microsaccades are involuntary and very small eye movements during fixation. Recently, the microsaccade-related neural dynamics have been extensively investigated both in experiments and by constructing neural network models. Experimentally, microsaccades also exhibit many behavioral properties. It’s well known that the behavior properties imply the underlying neural dynamical mechanisms, and so are determined by neural dynamics. The behavioral properties resulted from neural responses to microsaccades, however, are not yet understood and are rarely studied theoretically. Linking neural dynamics to behavior is one of the central goals of neuroscience. In this paper, we provide behavior predictions on spatiotemporal properties of microsaccades according to microsaccade-induced neural dynamics in a cascading network model, which includes both retinal adaptation and short-term depression (STD) at thalamocortical synapses. We also successfully give experimental tests in the statistical sense. Our results provide the first behavior description of microsaccades based on neural dynamics induced by behaving activity, and so firstly link neural dynamics to behavior of microsaccades. These results indicate strongly that the cascading adaptations play an important role in the study of microsaccades. Our work may be useful for further investigations of the microsaccadic behavioral properties and of the underlying neural dynamical mechanisms responsible for the behavioral properties.

  10. Spatiotemporal properties of microsaccades: Model predictions and experimental tests

    PubMed Central

    Zhou, Jian-Fang; Yuan, Wu-Jie; Zhou, Zhao

    2016-01-01

    Microsaccades are involuntary and very small eye movements during fixation. Recently, the microsaccade-related neural dynamics have been extensively investigated both in experiments and by constructing neural network models. Experimentally, microsaccades also exhibit many behavioral properties. It’s well known that the behavior properties imply the underlying neural dynamical mechanisms, and so are determined by neural dynamics. The behavioral properties resulted from neural responses to microsaccades, however, are not yet understood and are rarely studied theoretically. Linking neural dynamics to behavior is one of the central goals of neuroscience. In this paper, we provide behavior predictions on spatiotemporal properties of microsaccades according to microsaccade-induced neural dynamics in a cascading network model, which includes both retinal adaptation and short-term depression (STD) at thalamocortical synapses. We also successfully give experimental tests in the statistical sense. Our results provide the first behavior description of microsaccades based on neural dynamics induced by behaving activity, and so firstly link neural dynamics to behavior of microsaccades. These results indicate strongly that the cascading adaptations play an important role in the study of microsaccades. Our work may be useful for further investigations of the microsaccadic behavioral properties and of the underlying neural dynamical mechanisms responsible for the behavioral properties. PMID:27739541

  11. Cognitive functioning differentially predicts different dimensions of older drivers' on-road safety.

    PubMed

    Aksan, Nazan; Anderson, Steve W; Dawson, Jeffrey; Uc, Ergun; Rizzo, Matthew

    2015-02-01

    The extent to which deficits in specific cognitive domains contribute to older drivers' safety risk in complex real-world driving tasks is not well understood. We selected 148 drivers older than 70 years of age both with and without neurodegenerative diseases (Alzheimer disease-AD and Parkinson disease-PD) from an existing driving database of older adults. Participant assessments included on-road driving safety and cognitive functioning in visuospatial construction, speed of processing, memory, and executive functioning. The standardized on-road drive test was designed to examine multiple facets of older driver safety including navigation performance (e.g., following a route, identifying landmarks), safety errors while concurrently performing secondary navigation tasks ("on-task" safety errors), and safety errors in the absence of any secondary navigation tasks ("baseline" safety errors). The inter-correlations of these outcome measures were fair to moderate supporting their distinctiveness. Participants with diseases performed worse than the healthy aging group on all driving measures and differences between those with AD and PD were minimal. In multivariate analyses, different domains of cognitive functioning predicted distinct facets of driver safety on road. Memory and set-shifting predicted performance in navigation-related secondary tasks, speed of processing predicted on-task safety errors, and visuospatial construction predicted baseline safety errors. These findings support broad assessments of cognitive functioning to inform decisions regarding older driver safety on the road and suggest navigation performance may be useful in evaluating older driver fitness and restrictions in licensing. PMID:25525974

  12. A yeast functional screen predicts new candidate ALS disease genes

    PubMed Central

    Couthouis, Julien; Hart, Michael P.; Shorter, James; DeJesus-Hernandez, Mariely; Erion, Renske; Oristano, Rachel; Liu, Annie X.; Ramos, Daniel; Jethava, Niti; Hosangadi, Divya; Epstein, James; Chiang, Ashley; Diaz, Zamia; Nakaya, Tadashi; Ibrahim, Fadia; Kim, Hyung-Jun; Solski, Jennifer A.; Williams, Kelly L.; Mojsilovic-Petrovic, Jelena; Ingre, Caroline; Boylan, Kevin; Graff-Radford, Neill R.; Dickson, Dennis W.; Clay-Falcone, Dana; Elman, Lauren; McCluskey, Leo; Greene, Robert; Kalb, Robert G.; Lee, Virginia M.-Y.; Trojanowski, John Q.; Ludolph, Albert; Robberecht, Wim; Andersen, Peter M.; Nicholson, Garth A.; Blair, Ian P.; King, Oliver D.; Bonini, Nancy M.; Van Deerlin, Vivianna; Rademakers, Rosa; Mourelatos, Zissimos; Gitler, Aaron D.

    2011-01-01

    Amyotrophic lateral sclerosis (ALS) is a devastating and universally fatal neurodegenerative disease. Mutations in two related RNA-binding proteins, TDP-43 and FUS, that harbor prion-like domains, cause some forms of ALS. There are at least 213 human proteins harboring RNA recognition motifs, including FUS and TDP-43, raising the possibility that additional RNA-binding proteins might contribute to ALS pathogenesis. We performed a systematic survey of these proteins to find additional candidates similar to TDP-43 and FUS, followed by bioinformatics to predict prion-like domains in a subset of them. We sequenced one of these genes, TAF15, in patients with ALS and identified missense variants, which were absent in a large number of healthy controls. These disease-associated variants of TAF15 caused formation of cytoplasmic foci when expressed in primary cultures of spinal cord neurons. Very similar to TDP-43 and FUS, TAF15 aggregated in vitro and conferred neurodegeneration in Drosophila, with the ALS-linked variants having a more severe effect than wild type. Immunohistochemistry of postmortem spinal cord tissue revealed mislocalization of TAF15 in motor neurons of patients with ALS. We propose that aggregation-prone RNA-binding proteins might contribute very broadly to ALS pathogenesis and the genes identified in our yeast functional screen, coupled with prion-like domain prediction analysis, now provide a powerful resource to facilitate ALS disease gene discovery. PMID:22065782

  13. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    DOE PAGESBeta

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0more » to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

  14. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    SciTech Connect

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.

  15. The use of model-test data for predicting full-scale ACV resistance

    NASA Astrophysics Data System (ADS)

    Forstell, B. G.; Harry, C. W.

    The paper summarizes the analysis of test data obtained with a 1/12-scale model of the Amphibious Assault Landing Craft (AALC) JEFF(B). The analysis was conducted with the objective of improving the accuracy of drag predictions for a JEFF(B)-type air-cushion vehicle (ACV). Model test results, scaled to full-scale, are compared with full-scale drag obtained in various sea states during JEFF(B) trials. From the results of this comparison, it is found that the Froude-scale model rough-water drag data is consistently greater than full-scale derived drag, and is a function of both wave height and craft forward speed. Results are presented indicating that Froude scaling model data obtained in calm water also causes an over-prediction of calm-water drag at full-scale. An empirical correction that was developed for use on a JEFF(B)-type craft is discussed.

  16. Prediction of glass durability as a function of environmental conditions

    SciTech Connect

    Jantzen, C M

    1988-01-01

    A thermodynamic model of glass durability is applied to natural, ancient, and nuclear waste glasses. The durabilities of over 150 different natural and man-made glasses, including actual ancient Roman and Islamic glasses (Jalame ca. 350 AD, Nishapur 10-11th century AD and Gorgon 9-11th century AD), are compared. Glass durability is a function of the thermodynamic hydration free energy, ..delta..G/sub hyd/, which can be calculated from glass composition and solution pH. The durability of the most durable nuclear waste glasses examined was /approximately/10/sup 6/ years. The least durable waste glass formulations were comparable in durability to the most durable simulated medieval window glasses of /approximately/10/sup 3/ years. In this manner, the durability of nuclear waste glasses has been interpolated to be /approximately/10/sup 6/ years and no less than 10/sup 3/ years. Hydration thermodynamics have been shown to be applicable to the dissolution of glass in various natural environments. Groundwater-glass interactions relative to geologic disposal of nuclear waste, hydration rind dating of obsidians, andor other archeological studies can be modeled, e.g., the relative durabilities of six simulated medieval window glasses have been correctly predicted for both laboratory (one month) and burial (5 years) experiments. Effects of solution pH on glass dissolution has been determined experimentally for the 150 different glasses and can be predicted theoretically by hydration thermodynamics. The effects of solution redox on dissolution of glass matrix elements such as SI and B have shown to be minimal. The combined effects of solution pH and Eh have been described and unified by construction of thermodynamically calculated Pourbaix (pH-Eh) diagrams for glass dissolution. The Pourbaix diagrams have been quantified to describe glass dissolution as a function of environmental conditions by use of the data derived from hydration thermodynamics. 56 refs., 7 figs.

  17. Predicting the Effects of Test Media in Ground-Based Propulsion Testing

    NASA Technical Reports Server (NTRS)

    Drummond, J. Philip; Danehy, Paul M.; Bivolaru, Daniel; Gaffney, Richard L.; Parker, Peter A.; Chelliah, Harsha K.; Cutler, Andrew D.; Givi, Peyman; Hassan, Hassan, A.

    2006-01-01

    This paper discusses the progress of work which began in mid-2004 sponsored by the Office of the Secretary of Defense (OSD) Test & Evaluation/Science & Technology (T&E/S&T) Program. The purpose of the work is to improve the state of the art of CFD capabilities for predicting the effects of the test media on the flameholding characteristics in scramjet engines. The program has several components including the development of advance algorithms and models for simulating engine flowpaths as well as a fundamental experimental and diagnostic development effort to support the formulation and validation of the mathematical models. The paper will provide details of current work involving the development of phenomenological models for Reynolds averaged Navier-Stokes codes, large-eddy simulation techniques and reduced-kinetics models. Experiments that will provide data for the modeling efforts will also be described, along with with the associated nonintrusive diagnostics used to collect the data.

  18. Development of Methods to Predict the Effects of Test Media in Ground-Based Propulsion Testing

    NASA Technical Reports Server (NTRS)

    Drummond, J. Philip; Danehy, Paul M.; Gaffney, Richard L., Jr.; Parker, Peter A.; Tedder, Sarah A.; Chelliah, Harsha K.; Cutler, Andrew D.; Bivolaru, Daniel; Givi, Peyman; Hassan, Hassan A.

    2009-01-01

    This report discusses work that began in mid-2004 sponsored by the Office of the Secretary of Defense (OSD) Test & Evaluation/Science & Technology (T&E/S&T) Program. The work was undertaken to improve the state of the art of CFD capabilities for predicting the effects of the test media on the flameholding characteristics in scramjet engines. The program had several components including the development of advanced algorithms and models for simulating engine flowpaths as well as a fundamental experimental and diagnostic development effort to support the formulation and validation of the mathematical models. This report provides details of the completed work, involving the development of phenomenological models for Reynolds averaged Navier-Stokes codes, large-eddy simulation techniques and reduced-kinetics models. Experiments that provided data for the modeling efforts are also described, along with with the associated nonintrusive diagnostics used to collect the data.

  19. Resting-state functional connectivity predicts longitudinal change in autistic traits and adaptive functioning in autism.

    PubMed

    Plitt, Mark; Barnes, Kelly Anne; Wallace, Gregory L; Kenworthy, Lauren; Martin, Alex

    2015-12-01

    Although typically identified in early childhood, the social communication symptoms and adaptive behavior deficits that are characteristic of autism spectrum disorder (ASD) persist throughout the lifespan. Despite this persistence, even individuals without cooccurring intellectual disability show substantial heterogeneity in outcomes. Previous studies have found various behavioral assessments [such as intelligence quotient (IQ), early language ability, and baseline autistic traits and adaptive behavior scores] to be predictive of outcome, but most of the variance in functioning remains unexplained by such factors. In this study, we investigated to what extent functional brain connectivity measures obtained from resting-state functional connectivity MRI (rs-fcMRI) could predict the variance left unexplained by age and behavior (follow-up latency and baseline autistic traits and adaptive behavior scores) in two measures of outcome--adaptive behaviors and autistic traits at least 1 y postscan (mean follow-up latency = 2 y, 10 mo). We found that connectivity involving the so-called salience network (SN), default-mode network (DMN), and frontoparietal task control network (FPTCN) was highly predictive of future autistic traits and the change in autistic traits and adaptive behavior over the same time period. Furthermore, functional connectivity involving the SN, which is predominantly composed of the anterior insula and the dorsal anterior cingulate, predicted reliable improvement in adaptive behaviors with 100% sensitivity and 70.59% precision. From rs-fcMRI data, our study successfully predicted heterogeneity in outcomes for individuals with ASD that was unaccounted for by simple behavioral metrics and provides unique evidence for networks underlying long-term symptom abatement.

  20. Functional Literacy in Schoolchildren. Definition and Criteria of Test Selection.

    ERIC Educational Resources Information Center

    Bessemer, David W.; Spencer, Mary L.

    As part of the development of a functional literacy test for fourth through eigth grade children in Title I compensatory education programs, this report defines functional literacy for children and enumerates criteria for evaluating existing tests. Criteria for selection of a test include: (1) content, empirical, and construct validity; (2)…

  1. First State Fitness Test. A Measurement of Functional Health.

    ERIC Educational Resources Information Center

    Brown, Timothy; And Others

    This test is designed to measure the functional health of young people. Functional health refers to those factors relating to personal health that can be improved with regular exercise. This test is unique in comparison to other physical fitness tests because of the absence of motor skill items which have no relationship to an individual's…

  2. Balance assessments for predicting functional ankle instability and stable ankles.

    PubMed

    Ross, Scott E; Linens, Shelley W; Wright, Cynthia J; Arnold, Brent L

    2011-10-01

    A number of instrumented and non-instrumented measures are used to detect balance deficits associated with functional ankle instability (FAI). Determining outcome measures that detect balance deficits associated with FAI might assist clinicians in identifying impairments that may otherwise go undetected with less responsive balance measures. Thus, our objective was to determine the balance measure that best predicted ankle group membership (FAI or stable ankle). Participants included 17 subjects without a history of ankle sprains (168±9 cm, 66±14 kg, 24±5 yr) and 17 subjects with FAI (172±9 cm, 71±11 kg, 22±3 yr). Balance trials were performed without vision and subjects stood on a single leg as motionless as possible for 20s. Balance was quantified with center-of-pressure measures (velocity, area) and error score. Measures were positively correlated with each other (r range: 0.60-0.76). The multifactorial model with all three measures best predicted group membership (F((3,30))=7.20, P=0.001; R(2)=0.42; percent classified correctly=77%), and was followed by the multifactorial model with resultant center-of-pressure velocity and error score (F((2,31))=8.73, P=0.001; R(2)=0.36; percent classified correctly=74%). The resultant center-of-pressure velocity (F((1,32))=13.46, P=0.001; R(2)=0.30; percent classified correctly=74%; unique variance=12.7%) and error score (F((1,32))=12.51, P=0.001; R(2)=0.28; percent classified correctly=71%; unique variance=12.0%) predicted group membership; however, 95th percentile center-of-pressure area ellipse did not (F((1,32))=4.16, P=0.05; R(2)=0.12; percent classified correctly=65%; unique variance=5.8%). A multifactorial single leg balance assessment is best for predicting group membership. COPV is the best single predictor of group membership, but clinicians may use error score to identify deficits associated with FAI if force plates are not available. PMID:21868225

  3. "Teaching to the Test" in the NCLB Era: How Test Predictability Affects Our Understanding of Student Performance

    ERIC Educational Resources Information Center

    Jennings, Jennifer L.; Bearak, Jonathan Marc

    2014-01-01

    What is "teaching to the test," and can one detect evidence of this practice in state test scores? This paper unpacks this concept and empirically investigates one variant of it by analyzing test item--level data from three states' mathematics and reading tests. We show that NCLB-era state tests predictably emphasized some state…

  4. Testing the performance of technical trading rules in the Chinese markets based on superior predictive test

    NASA Astrophysics Data System (ADS)

    Wang, Shan; Jiang, Zhi-Qiang; Li, Sai-Ping; Zhou, Wei-Xing

    2015-12-01

    Technical trading rules have a long history of being used by practitioners in financial markets. The profitable ability and efficiency of technical trading rules are yet controversial. In this paper, we test the performance of more than seven thousand traditional technical trading rules on the Shanghai Securities Composite Index (SSCI) from May 21, 1992 through June 30, 2013 and China Securities Index 300 (CSI 300) from April 8, 2005 through June 30, 2013 to check whether an effective trading strategy could be found by using the performance measurements based on the return and Sharpe ratio. To correct for the influence of the data-snooping effect, we adopt the Superior Predictive Ability test to evaluate if there exists a trading rule that can significantly outperform the benchmark. The result shows that for SSCI, technical trading rules offer significant profitability, while for CSI 300, this ability is lost. We further partition the SSCI into two sub-series and find that the efficiency of technical trading in sub-series, which have exactly the same spanning period as that of CSI 300, is severely weakened. By testing the trading rules on both indexes with a five-year moving window, we find that during the financial bubble from 2005 to 2007, the effectiveness of technical trading rules is greatly improved. This is consistent with the predictive ability of technical trading rules which appears when the market is less efficient.

  5. Cost-Sensitive Radial Basis Function Neural Network Classifier for Software Defect Prediction

    PubMed Central

    Venkatesan, R.

    2016-01-01

    Effective prediction of software modules, those that are prone to defects, will enable software developers to achieve efficient allocation of resources and to concentrate on quality assurance activities. The process of software development life cycle basically includes design, analysis, implementation, testing, and release phases. Generally, software testing is a critical task in the software development process wherein it is to save time and budget by detecting defects at the earliest and deliver a product without defects to the customers. This testing phase should be carefully operated in an effective manner to release a defect-free (bug-free) software product to the customers. In order to improve the software testing process, fault prediction methods identify the software parts that are more noted to be defect-prone. This paper proposes a prediction approach based on conventional radial basis function neural network (RBFNN) and the novel adaptive dimensional biogeography based optimization (ADBBO) model. The developed ADBBO based RBFNN model is tested with five publicly available datasets from the NASA data program repository. The computed results prove the effectiveness of the proposed ADBBO-RBFNN classifier approach with respect to the considered metrics in comparison with that of the early predictors available in the literature for the same datasets. PMID:27738649

  6. Spatial weighting functions: transient hydraulic tests and heterogeneous media.

    PubMed

    Molz, Fred J; Guan, Jianyong; Wang, Jinjun

    2005-01-01

    To improve understanding of property measurements in heterogeneous media, an energy-based weighting function concept is developed. In (assumed) homogeneous media, the instrument spatial weighting function (ISWF) depends only on the energy dissipation distribution set up by the measurement procedure and it reduces to simply inverse sample volume (uniform weighting) for 1-D parallel flow case (ideal permeameter). For 1-D transient flow in homogeneous media, such as with slug tests, the ISWF varies with position and time, with 95% of the total weighting contained within 115 well radii, even late in the test. In the heterogeneous case, the determination of the ISWF is connected to the problem of determining an equivalent hydraulic conductivity (K), where the criterion for equivalence is based on equal energy dissipation rate rather than equal volume discharge. The discharge-based equivalent K (K(E)) and the energy-based equivalent K in heterogeneous media (K(eh)) are not equal in general, with K(eh) typically above the nodal arithmetic mean K. The possibly more fundamental problem is that as one makes K measurements in heterogeneous media at different locations or on different cores of heterogeneous materials, the ISWF will be heterogeneity dependent, implying that the averaging process resulting in the equivalent K value also varies with position. If the testing procedure is transient, then the averaging process varies with time. This suggests a fundamental ambiguity in the interpretation of hydraulic conductivity measurements in heterogeneous media that may impact how we approach modeling and prediction in a practical sense (Molz 2003). Further research is suggested.

  7. Testing process predictions of models of risky choice: a quantitative model comparison approach

    PubMed Central

    Pachur, Thorsten; Hertwig, Ralph; Gigerenzer, Gerd; Brandstätter, Eduard

    2013-01-01

    This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or non-linear functions thereof) and the separate evaluation of risky options (expectation models). Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models). We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter et al., 2006), and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up) and direction of search (i.e., gamble-wise vs. reason-wise). In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly); acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988) called “similarity.” In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies. PMID:24151472

  8. Efficacy of functional movement screening for predicting injuries in coast guard cadets.

    PubMed

    Knapik, Joseph J; Cosio-Lima, Ludimila M; Reynolds, Katy L; Shumway, Richard S

    2015-05-01

    Functional movement screening (FMS) examines the ability of individuals to perform highly specific movements with the aim of identifying individuals who have functional limitations or asymmetries. It is assumed that individuals who can more effectively accomplish the required movements have a lower injury risk. This study determined the ability of FMS to predict injuries in the United States Coast Guard (USCG) cadets. Seven hundred seventy male and 275 female USCG freshman cadets were administered the 7 FMS tests before the physically intense 8-week Summer Warfare Annual Basic (SWAB) training. Physical training-related injuries were recorded during SWAB training. Cumulative injury incidence was calculated at various FMS cutpoint scores. The ability of the FMS total score to predict injuries was examined by calculating sensitivity and specificity. Determination of the FMS cutpoint that maximized specificity and sensitivity was determined from the Youden's index (sensitivity + specificity - 1). For men, FMS scores ≤ 12 were associated with higher injury risk than scores >12; for women, FMS scores ≤ 15 were associated with higher injury risk than scores >15. The Youden's Index indicated that the optimal FMS cutpoint was ≤ 11 for men (22% sensitivity, 87% specificity) and ≤ 14 for women (60% sensitivity, 61% specificity). Functional movement screening demonstrated moderate prognostic accuracy for determining injury risk among female Coast Guard cadets but relatively low accuracy among male cadets. Attempting to predict injury risk based on the FMS test seems to have some limited promise based on the present and past investigations.

  9. Efficacy of functional movement screening for predicting injuries in coast guard cadets.

    PubMed

    Knapik, Joseph J; Cosio-Lima, Ludimila M; Reynolds, Katy L; Shumway, Richard S

    2015-05-01

    Functional movement screening (FMS) examines the ability of individuals to perform highly specific movements with the aim of identifying individuals who have functional limitations or asymmetries. It is assumed that individuals who can more effectively accomplish the required movements have a lower injury risk. This study determined the ability of FMS to predict injuries in the United States Coast Guard (USCG) cadets. Seven hundred seventy male and 275 female USCG freshman cadets were administered the 7 FMS tests before the physically intense 8-week Summer Warfare Annual Basic (SWAB) training. Physical training-related injuries were recorded during SWAB training. Cumulative injury incidence was calculated at various FMS cutpoint scores. The ability of the FMS total score to predict injuries was examined by calculating sensitivity and specificity. Determination of the FMS cutpoint that maximized specificity and sensitivity was determined from the Youden's index (sensitivity + specificity - 1). For men, FMS scores ≤ 12 were associated with higher injury risk than scores >12; for women, FMS scores ≤ 15 were associated with higher injury risk than scores >15. The Youden's Index indicated that the optimal FMS cutpoint was ≤ 11 for men (22% sensitivity, 87% specificity) and ≤ 14 for women (60% sensitivity, 61% specificity). Functional movement screening demonstrated moderate prognostic accuracy for determining injury risk among female Coast Guard cadets but relatively low accuracy among male cadets. Attempting to predict injury risk based on the FMS test seems to have some limited promise based on the present and past investigations. PMID:25264669

  10. A Comparison of Statistical Significance Tests for Selecting Equating Functions

    ERIC Educational Resources Information Center

    Moses, Tim

    2009-01-01

    This study compared the accuracies of nine previously proposed statistical significance tests for selecting identity, linear, and equipercentile equating functions in an equivalent groups equating design. The strategies included likelihood ratio tests for the loglinear models of tests' frequency distributions, regression tests, Kolmogorov-Smirnov…

  11. Handgrip Strength Predicts Functional Decline at Discharge in Hospitalized Male Elderly: A Hospital Cohort Study

    PubMed Central

    García-Peña, Carmen; García-Fabela, Luis C.; Gutiérrez-Robledo, Luis M.; García-González, Jose J.; Arango-Lopera, Victoria E.; Pérez-Zepeda, Mario U.

    2013-01-01

    Functional decline after hospitalization is a common adverse outcome in elderly. An easy to use, reproducible and accurate tool to identify those at risk would aid focusing interventions in those at higher risk. Handgrip strength has been shown to predict adverse outcomes in other settings. The aim of this study was to determine if handgrip strength measured upon admission to an acute care facility would predict functional decline (either incident or worsening of preexisting) at discharge among older Mexican, stratified by gender. In addition, cutoff points as a function of specificity would be determined. A cohort study was conducted in two hospitals in Mexico City. The primary endpoint was functional decline on discharge, defined as a 30-point reduction in the Barthel Index score from that of the baseline score. Handgrip strength along with other variables was measured at initial assessment, including: instrumental activities of daily living, cognition, depressive symptoms, delirium, hospitalization length and quality of life. All analyses were stratified by gender. Logistic regression to test independent association between handgrip strength and functional decline was performed, along with estimation of handgrip strength test values (specificity, sensitivity, area under the curve, etc.). A total of 223 patients admitted to an acute care facility between 2007 and 2009 were recruited. A total of 55 patients (24.7%) had functional decline, 23.46% in male and 25.6% in women. Multivariate analysis showed that only males with low handgrip strength had an increased risk of functional decline at discharge (OR 0.88, 95% CI 0.79–0.98, p = 0.01), with a specificity of 91.3% and a cutoff point of 20.65 kg for handgrip strength. Females had not a significant association between handgrip strength and functional decline. Measurement of handgrip strength on admission to acute care facilities may identify male elderly patients at risk of having functional decline, and

  12. Can Brief Tests of Mental Status Predict Functional Behavioral Impairment?

    ERIC Educational Resources Information Center

    Hershey, Douglas A.; And Others

    Although criteria for the diagnosis, prognosis, and treatment of Alzheimer's disease (AD) have become better defined, few research findings have appeared in the literature which characterize the degenerative course of the disease. Of particular interest to both clinicians and researchers would be a study focusing on changes in the patient's…

  13. Predicting Invasive Fungal Pathogens Using Invasive Pest Assemblages: Testing Model Predictions in a Virtual World

    PubMed Central

    Paini, Dean R.; Bianchi, Felix J. J. A.; Northfield, Tobin D.; De Barro, Paul J.

    2011-01-01

    Predicting future species invasions presents significant challenges to researchers and government agencies. Simply considering the vast number of potential species that could invade an area can be insurmountable. One method, recently suggested, which can analyse large datasets of invasive species simultaneously is that of a self organising map (SOM), a form of artificial neural network which can rank species by establishment likelihood. We used this method to analyse the worldwide distribution of 486 fungal pathogens and then validated the method by creating a virtual world of invasive species in which to test the SOM. This novel validation method allowed us to test SOM's ability to rank those species that can establish above those that can't. Overall, we found the SOM highly effective, having on average, a 96–98% success rate (depending on the virtual world parameters). We also found that regions with fewer species present (i.e. 1–10 species) were more difficult for the SOM to generate an accurately ranked list, with success rates varying from 100% correct down to 0% correct. However, we were able to combine the numbers of species present in a region with clustering patterns in the SOM, to further refine confidence in lists generated from these sparsely populated regions. We then used the results from the virtual world to determine confidences for lists generated from the fungal pathogen dataset. Specifically, for lists generated for Australia and its states and territories, the reliability scores were between 84–98%. We conclude that a SOM analysis is a reliable method for analysing a large dataset of potential invasive species and could be used by biosecurity agencies around the world resulting in a better overall assessment of invasion risk. PMID:22016773

  14. An online study combining the constructs from the theory of planned behaviour and protection motivation theory in predicting intention to test for chlamydia in two testing contexts.

    PubMed

    Powell, Rachael; Pattison, Helen M; Francis, Jill J

    2016-01-01

    Chlamydia is a common sexually transmitted infection that has potentially serious consequences unless detected and treated early. The health service in the UK offers clinic-based testing for chlamydia but uptake is low. Identifying the predictors of testing behaviours may inform interventions to increase uptake. Self-tests for chlamydia may facilitate testing and treatment in people who avoid clinic-based testing. Self-testing and being tested by a health care professional (HCP) involve two contrasting contexts that may influence testing behaviour. However, little is known about how predictors of behaviour differ as a function of context. In this study, theoretical models of behaviour were used to assess factors that may predict intention to test in two different contexts: self-testing and being tested by a HCP. Individuals searching for or reading about chlamydia testing online were recruited using Google Adwords. Participants completed an online questionnaire that addressed previous testing behaviour and measured constructs of the Theory of Planned Behaviour and Protection Motivation Theory, which propose a total of eight possible predictors of intention. The questionnaire was completed by 310 participants. Sufficient data for multiple regression were provided by 102 and 118 respondents for self-testing and testing by a HCP respectively. Intention to self-test was predicted by vulnerability and self-efficacy, with a trend-level effect for response efficacy. Intention to be tested by a HCP was predicted by vulnerability, attitude and subjective norm. Thus, intentions to carry out two testing behaviours with very similar goals can have different predictors depending on test context. We conclude that interventions to increase self-testing should be based on evidence specifically related to test context.

  15. An online study combining the constructs from the theory of planned behaviour and protection motivation theory in predicting intention to test for chlamydia in two testing contexts.

    PubMed

    Powell, Rachael; Pattison, Helen M; Francis, Jill J

    2016-01-01

    Chlamydia is a common sexually transmitted infection that has potentially serious consequences unless detected and treated early. The health service in the UK offers clinic-based testing for chlamydia but uptake is low. Identifying the predictors of testing behaviours may inform interventions to increase uptake. Self-tests for chlamydia may facilitate testing and treatment in people who avoid clinic-based testing. Self-testing and being tested by a health care professional (HCP) involve two contrasting contexts that may influence testing behaviour. However, little is known about how predictors of behaviour differ as a function of context. In this study, theoretical models of behaviour were used to assess factors that may predict intention to test in two different contexts: self-testing and being tested by a HCP. Individuals searching for or reading about chlamydia testing online were recruited using Google Adwords. Participants completed an online questionnaire that addressed previous testing behaviour and measured constructs of the Theory of Planned Behaviour and Protection Motivation Theory, which propose a total of eight possible predictors of intention. The questionnaire was completed by 310 participants. Sufficient data for multiple regression were provided by 102 and 118 respondents for self-testing and testing by a HCP respectively. Intention to self-test was predicted by vulnerability and self-efficacy, with a trend-level effect for response efficacy. Intention to be tested by a HCP was predicted by vulnerability, attitude and subjective norm. Thus, intentions to carry out two testing behaviours with very similar goals can have different predictors depending on test context. We conclude that interventions to increase self-testing should be based on evidence specifically related to test context. PMID:25929700

  16. Prediction of Frequency for Simulation of Asphalt Mix Fatigue Tests Using MARS and ANN

    PubMed Central

    Fakhri, Mansour

    2014-01-01

    Fatigue life of asphalt mixes in laboratory tests is commonly determined by applying a sinusoidal or haversine waveform with specific frequency. The pavement structure and loading conditions affect the shape and the frequency of tensile response pulses at the bottom of asphalt layer. This paper introduces two methods for predicting the loading frequency in laboratory asphalt fatigue tests for better simulation of field conditions. Five thousand (5000) four-layered pavement sections were analyzed and stress and strain response pulses in both longitudinal and transverse directions was determined. After fitting the haversine function to the response pulses by the concept of equal-energy pulse, the effective length of the response pulses were determined. Two methods including Multivariate Adaptive Regression Splines (MARS) and Artificial Neural Network (ANN) methods were then employed to predict the effective length (i.e., frequency) of tensile stress and strain pulses in longitudinal and transverse directions based on haversine waveform. It is indicated that, under controlled stress and strain modes, both methods (MARS and ANN) are capable of predicting the frequency of loading in HMA fatigue tests with very good accuracy. The accuracy of ANN method is, however, more than MARS method. It is furthermore shown that the results of the present study can be generalized to sinusoidal waveform by a simple equation. PMID:24688400

  17. Defensive activation to (un)predictable interoceptive threat: The NPU respiratory threat test (NPUr).

    PubMed

    Schroijen, Mathias; Fantoni, Simona; Rivera, Carmen; Vervliet, Bram; Schruers, Koen; van den Bergh, Omer; van Diest, Ilse

    2016-06-01

    Potentially life-threatening interoceptive sensations easily engage the behavioral defensive system. Resulting fear and anxiety toward interoceptive threat are functionally distinct states that are hypothesized to play a prominent role in the etiology of panic disorder. The present study aimed to investigate whether fear- and anxiety-potentiated startle responses occur to predictable and unpredictable interoceptive threat, respectively. Therefore, we modified the NPU threat test (Schmitz & Grillon, ) and replaced the aversive electrocutaneous stimulus with an aversive interoceptive stimulus (a breathing occlusion, making it briefly impossible to breathe). Healthy participants (N = 48) underwent three instructed conditions. A visual cue signaled the occlusion in the predictable condition (P), whereas another cue was unrelated to the occurrence of the occlusion in the unpredictable condition (U). The safe condition (N) also had a visual cue, but no occlusion. Both fear- and anxiety-potentiated startle blink responses were observed in response to predictable and unpredictable respiratory threat, respectively. The current study presents and validates the NPU respiratory threat test (NPUr) as an ecologically valid paradigm to study both anxiety and fear in response to a panic-relevant interoceptive threat. The paradigm allows future testing of contextual generalization, investigation of different clinical groups, and more explicit comparisons of defensive responding to interoceptive versus exteroceptive threats.

  18. Defensive activation to (un)predictable interoceptive threat: The NPU respiratory threat test (NPUr).

    PubMed

    Schroijen, Mathias; Fantoni, Simona; Rivera, Carmen; Vervliet, Bram; Schruers, Koen; van den Bergh, Omer; van Diest, Ilse

    2016-06-01

    Potentially life-threatening interoceptive sensations easily engage the behavioral defensive system. Resulting fear and anxiety toward interoceptive threat are functionally distinct states that are hypothesized to play a prominent role in the etiology of panic disorder. The present study aimed to investigate whether fear- and anxiety-potentiated startle responses occur to predictable and unpredictable interoceptive threat, respectively. Therefore, we modified the NPU threat test (Schmitz & Grillon, ) and replaced the aversive electrocutaneous stimulus with an aversive interoceptive stimulus (a breathing occlusion, making it briefly impossible to breathe). Healthy participants (N = 48) underwent three instructed conditions. A visual cue signaled the occlusion in the predictable condition (P), whereas another cue was unrelated to the occurrence of the occlusion in the unpredictable condition (U). The safe condition (N) also had a visual cue, but no occlusion. Both fear- and anxiety-potentiated startle blink responses were observed in response to predictable and unpredictable respiratory threat, respectively. The current study presents and validates the NPU respiratory threat test (NPUr) as an ecologically valid paradigm to study both anxiety and fear in response to a panic-relevant interoceptive threat. The paradigm allows future testing of contextual generalization, investigation of different clinical groups, and more explicit comparisons of defensive responding to interoceptive versus exteroceptive threats. PMID:26879710

  19. Multiloop Integral System Test (MIST): MIST Facility Functional Specification

    SciTech Connect

    Habib, T F; Koksal, C G; Moskal, T E; Rush, G C; Gloudemans, J R

    1991-04-01

    The Multiloop Integral System Test (MIST) is part of a multiphase program started in 1983 to address small-break loss-of-coolant accidents (SBLOCAs) specific to Babcock and Wilcox designed plants. MIST is sponsored by the US Nuclear Regulatory Commission, the Babcock Wilcox Owners Group, the Electric Power Research Institute, and Babcock and Wilcox. The unique features of the Babcock and Wilcox design, specifically the hot leg U-bends and steam generators, prevented the use of existing integral system data or existing integral facilities to address the thermal-hydraulic SBLOCA questions. MIST was specifically designed and constructed for this program, and an existing facility -- the Once Through Integral System (OTIS) -- was also used. Data from MIST and OTIS are used to benchmark the adequacy of system codes, such as RELAP5 and TRAC, for predicting abnormal plant transients. The MIST Functional Specification documents as-built design features, dimensions, instrumentation, and test approach. It also presents the scaling basis for the facility and serves to define the scope of work for the facility design and construction. 13 refs., 112 figs., 38 tabs.

  20. Cosmological tests with the FSRQ gamma-ray luminosity function

    NASA Astrophysics Data System (ADS)

    Zeng, Houdun; Melia, Fulvio; Zhang, Li

    2016-11-01

    The extensive catalogue of gamma-ray selected flat-spectrum radio quasars (FSRQs) produced by Fermi during a four-year survey has generated considerable interest in determining their gamma-ray luminosity function (GLF) and its evolution with cosmic time. In this paper, we introduce the novel idea of using this extensive database to test the differential volume expansion rate predicted by two specific models, the concordance Λ cold dark matter (ΛCDM) and Rh = ct cosmologies. For this purpose, we use two well-studied formulations of the GLF, one based on pure luminosity evolution (PLE) and the other on a luminosity-dependent density evolution (LDDE). Using a Kolmogorov-Smirnov test on one-parameter cumulative distributions (in luminosity, redshift, photon index and source count), we confirm the results of earlier works showing that these data somewhat favour LDDE over PLE; we show that this is the case for both ΛCDM and Rh = ct. Regardless of which GLF one chooses, however, we also show that model selection tools very strongly favour Rh = ct over ΛCDM. We suggest that such population studies, though featuring a strong evolution in redshift, may none the less be used as a valuable independent check of other model comparisons based solely on geometric considerations.

  1. RELAP5 Prediction of Transient Tests in the RD-14 Test Facility

    SciTech Connect

    Lee, Sukho; Kim, Manwoong; Kim, Hho-Jung; Lee, John C.

    2005-09-15

    Although the RELAP5 computer code has been developed for best-estimate transient simulation of a pressurized water reactor and its associated systems, it could not assess the thermal-hydraulic behavior of a Canada deuterium uranium (CANDU) reactor adequately. However, some studies have been initiated to explore the applicability for simulating a large-break loss-of-coolant accident in CANDU reactors. In the present study, the small-reactor inlet header break test and the steam generator secondary-side depressurization test conducted in the RD-14 test facility were simulated with the RELAP5/MOD3.2.2 code to examine its extended capability for all the postulated transients and accidents in CANDU reactors. The results were compared with experimental data and those of the CATHENA code performed by Atomic Energy of Canada Limited.In the RELAP5 analyses, the heated sections in the facility were simulated as a multichannel with five pipe models, which have identical flow areas and hydraulic elevations, as well as a single-pipe model.The results of the small-reactor inlet header break and the steam generator secondary-side depressurization simulations predicted experimental data reasonably well. However, some discrepancies in the depressurization of the primary heat transport system after the header break and consequent time delay of the major phenomena were observed in the simulation of the small-reactor inlet header break test.

  2. Aptitude Tests and Successful College Students: The Predictive Validity of the General Aptitude Test (GAT) in Saudi Arabia

    ERIC Educational Resources Information Center

    Alnahdi, Ghaleb Hamad

    2015-01-01

    Aptitude tests should predict student success at the university level. This study examined the predictive validity of the General Aptitude Test (GAT) in Saudi Arabia. Data for 27420 students enrolled at Prince Sattam bin Abdulaziz University were analyzed. Of these students, 17565 were male students, and 9855 were female students. Multiple…

  3. Imaging memory and predicting postoperative memory decline in temporal lobe epilepsy: Insights from functional imaging.

    PubMed

    Dupont, S

    2015-03-01

    After medial temporal lobe epilepsy (MTLE) surgery, there is considerable individual variation in the extent, nature and direction of postoperative memory change. Before surgery, epileptic patients who are surgery candidates need precise information about the potential cognitive after effects, and particularly in temporal lobe epilepsy, postoperative memory changes. Clinical and neuropsychological data may bring useful information to predict the postoperative memory outcome, but, these data are not always sufficient to replace the Wada test, considered for a long time, as the gold standard to predict postoperative decline following surgery. In any case, numerous studies demonstrate that the Wada procedure can be nowadays reliably replaced by functional MRI (fMRI) activation studies. A vast majority of fMRI studies suggest that it is the functional adequacy of the resected hippocampus rather than the functional reserve of the contralateral hippocampus that determines the extent of postoperative memory decline. In addition, new functional neuroimaging procedures that explore more widespread network disruptions commonly found in MTLE such as diffusion-tensor imaging (DTI) or connectivity studies could in the future constitute a reliable approach combined with fMRI activation studies to significantly improve the prediction of postsurgical memory decline.

  4. Prediction of Functional Outcome in Axonal Guillain-Barre Syndrome

    PubMed Central

    2016-01-01

    Objective To identify the factors that could predict the functional outcome in patients with the axonal type of Guillain-Barre syndrome (GBS). Methods Two hundred and two GBS patients admitted to our university hospital between 2003 and 2014 were reviewed retrospectively. We defined a good outcome as being "able to walk independently at 1 month after onset" and a poor outcome as being "unable to walk independently at 1 month after onset". We evaluated the factors that differed between the good and poor outcome groups. Results Twenty-four patients were classified into the acute motor axonal neuropathy type. There was a statistically significant difference between the good and poor outcome groups in terms of the GBS disability score at admission, and GBS disability score and Medical Research Council sum score at 1 month after admission. In an electrophysiologic analysis, the good outcome group showed greater amplitude of median, ulnar, deep peroneal, and posterior tibial nerve compound muscle action potentials (CMAP) and greater amplitude of median, ulnar, and superficial peroneal sensory nerve action potentials (SNAP) than the poor outcome group. Conclusion A lower GBS disability score at admission, high amplitude of median, ulnar, deep peroneal, and posterior tibial CMAPs, and high amplitude of median, ulnar, and superficial peroneal SNAPs were associated with being able to walk at 1 month in patients with axonal GBS. PMID:27446785

  5. Anisotropic yield function capable of predicting eight ears

    NASA Astrophysics Data System (ADS)

    Yoon, J. H.; Cazacu, O.

    2011-08-01

    Deep drawing of a cylindrical cup from a rolled sheet is one of the typical forming operations where the effect of this anisotropy is most evident. Indeed, it is well documented in the literature that the number of ears and the shape of the earing pattern correlate with the r-values profile. For the strongly textured aluminum alloy AA 5042 (Numisheet Benchmark 2011), the experimental r-value distribution has two minima between the rolling and transverse direction data provided for this show that the r-value along the transverse direction (TD) is five times larger than the value corresponding to the rolling direction. Therefore, it is expected that there are more that the earing profile has more than four ears. The main objective of this paper is to assess whether a new form of CPB06ex2 yield function (Plunkett et al. (2008)) tailored for metals with no tension-compression asymmetry is capable of predicting more than four ears for this material.

  6. FunPred-1: protein function prediction from a protein interaction network using neighborhood analysis.

    PubMed

    Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Kundu, Mahantapas; Nasipuri, Mita

    2014-12-01

    Proteins are responsible for all biological activities in living organisms. Thanks to genome sequencing projects, large amounts of DNA and protein sequence data are now available, but the biological functions of many proteins are still not annotated in most cases. The unknown function of such non-annotated proteins may be inferred or deduced from their neighbors in a protein interaction network. In this paper, we propose two new methods to predict protein functions based on network neighborhood properties. FunPred 1.1 uses a combination of three simple-yet-effective scoring techniques: the neighborhood ratio, the protein path connectivity and the relative functional similarity. FunPred 1.2 applies a heuristic approach using the edge clustering coefficient to reduce the search space by identifying densely connected neighborhood regions. The overall accuracy achieved in FunPred 1.2 over 8 functional groups involving hetero-interactions in 650 yeast proteins is around 87%, which is higher than the accuracy with FunPred 1.1. It is also higher than the accuracy of many of the state-of-the-art protein function prediction methods described in the literature. The test datasets and the complete source code of the developed software are now freely available at http://code.google.com/p/cmaterbioinfo/ . PMID:25424913

  7. FunPred-1: protein function prediction from a protein interaction network using neighborhood analysis.

    PubMed

    Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Kundu, Mahantapas; Nasipuri, Mita

    2014-12-01

    Proteins are responsible for all biological activities in living organisms. Thanks to genome sequencing projects, large amounts of DNA and protein sequence data are now available, but the biological functions of many proteins are still not annotated in most cases. The unknown function of such non-annotated proteins may be inferred or deduced from their neighbors in a protein interaction network. In this paper, we propose two new methods to predict protein functions based on network neighborhood properties. FunPred 1.1 uses a combination of three simple-yet-effective scoring techniques: the neighborhood ratio, the protein path connectivity and the relative functional similarity. FunPred 1.2 applies a heuristic approach using the edge clustering coefficient to reduce the search space by identifying densely connected neighborhood regions. The overall accuracy achieved in FunPred 1.2 over 8 functional groups involving hetero-interactions in 650 yeast proteins is around 87%, which is higher than the accuracy with FunPred 1.1. It is also higher than the accuracy of many of the state-of-the-art protein function prediction methods described in the literature. The test datasets and the complete source code of the developed software are now freely available at http://code.google.com/p/cmaterbioinfo/ .

  8. Chemical testing strategies for predicting health hazards to children.

    PubMed

    Lamb, J C; Brown, S M

    2000-01-01

    The United States Environmental Protection Agency has proposed the development of a Children's Health Test Program under the Toxic Substances Control Act. The Environmental Protection Agency's proposal for the children's health test battery has 12 different assays including general toxicity, genotoxicity, carcinogenicity, neurotoxicity, and developmental and reproductive toxicity. The current Environmental Protection Agency testing proposal is an "all or nothing" test battery. An alternative and preferable approach would be to use a science-based, tiered testing scheme. It is proposed that the Screening Information Dataset program, currently used by the Organization for Economic Co-operation and Development (OECD) for the Screening Information Dataset-High Production Volume test battery, or equivalent, be considered for the first step. Step 1 would include acute and repeat dose toxicity testing, developmental toxicity testing (first species OECD 414 or OECD 422), reproductive toxicity screening (OECD 415 or 422), and genetic toxicity testing. For this step, the rat would be the initial and only species tested unless the mouse was used for in vivo genetic toxicity. Step 2 of the proposed children's health test battery would include developmental testing (second species OECD 414) or special mode of action studies performed for those chemicals that proved to be developmental toxicants in Step 1. Those chemicals that tested positive as reproductive toxicants in Step 1 would be tested in a two-generation reproduction study (OECD 416) or a special mode of action study. Steps 1 and 2 provide information on whether oncogenicity or developmental neurotoxicity testing is useful. Step 3 would include chronic toxicity/oncogenicity testing for those chemicals that tested positive for genetic toxicity in Step 1, and positive for developmental concerns in Step 2. In this step, chemicals would also be tested for developmental neurotoxicity if they showed evidence of neuropathy

  9. Functional Testing Protocols for Commercial Building Efficiency Baseline Modeling Software

    SciTech Connect

    Jump, David; Price, Phillip N.; Granderson, Jessica; Sohn, Michael

    2013-09-06

    This document describes procedures for testing and validating proprietary baseline energy modeling software accuracy in predicting energy use over the period of interest, such as a month or a year. The procedures are designed according to the methodology used for public domain baselining software in another LBNL report that was (like the present report) prepared for Pacific Gas and Electric Company: ?Commercial Building Energy Baseline Modeling Software: Performance Metrics and Method Testing with Open Source Models and Implications for Proprietary Software Testing Protocols? (referred to here as the ?Model Analysis Report?). The test procedure focuses on the quality of the software?s predictions rather than on the specific algorithms used to predict energy use. In this way the software vendor is not required to divulge or share proprietary information about how their software works, while enabling stakeholders to assess its performance.

  10. Factor analysis and predictive validity of microcomputer-based tests

    NASA Technical Reports Server (NTRS)

    Kennedy, R. S.; Baltzley, D. R.; Turnage, J. J.; Jones, M. B.

    1989-01-01

    11 tests were selected from two microcomputer-based performance test batteries because previously these tests exhibited rapid stability (less than 10 min, of practice) and high retest reliability efficiencies (r greater than 0.707 for each 3 min. of testing). The battery was administered three times to each of 108 college students (48 men and 60 women) and a factor analysis was performed. Two of the three identified factors appear to be related to information processing ("encoding" and "throughput/decoding"), and the third named an "output/speed" factor. The spatial, memory, and verbal tests loaded on the "encoding" factor and included Grammatical Reasoning, Pattern Comparison, Continuous Recall, and Matrix Rotation. The "throughput/decoding" tests included perceptual/numerical tests like Math Processing, Code Substitution, and Pattern Comparison. The output speed factor was identified by Tapping and Reaction Time tests. The Wonderlic Personnel Test was group administered before the first and after the last administration of the performance tests. The multiple Rs in the total sample between combined Wonderlic as a criterion and less than 5 min. of microcomputer testing on Grammatical Reasoning and Math Processing as predictors ranged between 0.41 and 0.52 on the three test administrations. Based on these results, the authors recommend a core battery which, if time permits, would consist of two tests from each factor. Such a battery is now known to permit stable, reliable, and efficient assessment.

  11. Functional traits predict relationship between plant abundance dynamic and long-term climate warming.

    PubMed

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G; Onipchenko, Vladimir G; Shidakov, Islam I; Salpagarova, Fatima S; Khubiev, Anzor B; Tekeev, Dzhamal K; Cornelissen, Johannes H C

    2013-11-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change. PMID:24145400

  12. Functional traits predict relationship between plant abundance dynamic and long-term climate warming

    PubMed Central

    Soudzilovskaia, Nadejda A.; Elumeeva, Tatiana G.; Onipchenko, Vladimir G.; Shidakov, Islam I.; Salpagarova, Fatima S.; Khubiev, Anzor B.; Tekeev, Dzhamal K.; Cornelissen, Johannes H. C.

    2013-01-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year’s shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change. PMID:24145400

  13. Functional traits predict relationship between plant abundance dynamic and long-term climate warming.

    PubMed

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G; Onipchenko, Vladimir G; Shidakov, Islam I; Salpagarova, Fatima S; Khubiev, Anzor B; Tekeev, Dzhamal K; Cornelissen, Johannes H C

    2013-11-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change.

  14. 33 CFR 157.12f - Workshop functional test requirements.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... CARRYING OIL IN BULK Design, Equipment, and Installation § 157.12f Workshop functional test requirements... the specific design of equipment. A completed workshop certificate including the delivery test...; (2) A check of the correct function of the signal processor and the recording equipment...

  15. In silico predicted structural and functional robustness of piscine steroidogenesis.

    PubMed

    Hala, D; Huggett, D B

    2014-03-21

    Assessments of metabolic robustness or susceptibility are inherently dependent on quantitative descriptions of network structure and associated function. In this paper a stoichiometric model of piscine steroidogenesis was constructed and constrained with productions of selected steroid hormones. Structural and flux metrics of this in silico model were quantified by calculating extreme pathways and optimal flux distributions (using linear programming). Extreme pathway analysis showed progestin and corticosteroid synthesis reactions to be highly participant in extreme pathways. Furthermore, reaction participation in extreme pathways also fitted a power law distribution (degree exponent γ=2.3), which suggested that progestin and corticosteroid reactions act as 'hubs' capable of generating other functionally relevant pathways required to maintain steady-state functionality of the network. Analysis of cofactor usage (O2 and NADPH) showed progestin synthesis reactions to exhibit high robustness, whereas estrogen productions showed highest energetic demands with low associated robustness to maintain such demands. Linear programming calculated optimal flux distributions showed high heterogeneity of flux values with a near-random power law distribution (degree exponent γ≥2.7). Subsequently, network robustness was tested by assessing maintenance of metabolite flux-sum subject to targeted deletions of rank-ordered (low to high metric) extreme pathway participant and optimal flux reactions. Network robustness was susceptible to deletions of extreme pathway participant reactions, whereas minimal impact of high flux reaction deletion was observed. This analysis shows that the steroid network is susceptible to perturbation of structurally relevant (extreme pathway) reactions rather than those carrying high flux. PMID:24333207

  16. Fibrosis with Inflammation at One Year Predicts Transplant Functional Decline

    PubMed Central

    Park, Walter D.; Griffin, Matthew D.; Cornell, Lynn D.; Cosio, Fernando G.

    2010-01-01

    Lack of knowledge regarding specific causes for late loss of kidney transplants hampers improvements in long-term allograft survival. Kidney transplants with both interstitial fibrosis and subclinical inflammation but not fibrosis alone after 1 year have reduced survival. This study tested whether fibrosis with inflammation at 1 year associates with decline of renal function in a low-risk cohort and characterized the nature of the inflammation. We studied 151 living-donor, tacrolimus/mycophenolate-treated recipients without overt risk factors for reduced graft survival. Transplants with normal histology (n = 86) or fibrosis alone (n = 45) on 1-year protocol biopsy had stable renal function between 1 and 5 years, whereas those with both fibrosis and inflammation (n = 20) exhibited a decline in GFR and reduced graft survival. Immunohistochemistry confirmed increased interstitial T cells and macrophages/dendritic cells in the group with both fibrosis and inflammation, and there was increased expression of transcripts related to innate and cognate immunity. Pathway- and pathologic process–specific analyses of microarray profiles revealed that potentially damaging immunologic activities were enriched among the overexpressed transcripts (e.g., Toll-like receptor signaling, antigen presentation/dendritic cell maturation, IFN-γ–inducible response, cytotoxic T lymphocyte–associated and acute rejection–associated genes). Therefore, the combination of fibrosis and inflammation in 1-year protocol biopsies associates with reduced graft function and survival as well as a rejection-like gene expression signature, even among recipients with no clinical risk factors for poor outcomes. Early interventions aimed at altering rejection-like inflammation may improve long-term survival of kidney allografts. PMID:20813870

  17. Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?

    PubMed Central

    Fetrow, Jacquelyn S.; Siew, Naomi; Di Gennaro, Jeannine A.; Martinez-Yamout, Maria; Dyson, H. Jane; Skolnick, Jeffrey

    2001-01-01

    A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone. PMID:11316881

  18. The Predictive Value of the Watson-Barker Listening Test.

    ERIC Educational Resources Information Center

    Vander Kooi, Daryl

    Using the Watson-Barker Listening Test Form A and Form B as pretest and posttest at the freshman level, this research attempted to determine whether the two forms of the test and the differences between pretest and posttest would be significant predictors of students' final grade point average (GPA). Each form of the test was taken by 190 students…

  19. Structural habitat predicts functional dispersal habitat of a large carnivore: how leopards change spots.

    PubMed

    Fattebert, Julien; Robinson, Hugh S; Balme, Guy; Slotow, Rob; Hunter, Luke

    2015-10-01

    Natal dispersal promotes inter-population linkage, and is key to spatial distribution of populations. Degradation of suitable landscape structures beyond the specific threshold of an individual's ability to disperse can therefore lead to disruption of functional landscape connectivity and impact metapopulation function. Because it ignores behavioral responses of individuals, structural connectivity is easier to assess than functional connectivity and is often used as a surrogate for landscape connectivity modeling. However using structural resource selection models as surrogate for modeling functional connectivity through dispersal could be erroneous. We tested how well a second-order resource selection function (RSF) models (structural connectivity), based on GPS telemetry data from resident adult leopard (Panthera pardus L.), could predict subadult habitat use during dispersal (functional connectivity). We created eight non-exclusive subsets of the subadult data based on differing definitions of dispersal to assess the predictive ability of our adult-based RSF model extrapolated over a broader landscape. Dispersing leopards used habitats in accordance with adult selection patterns, regardless of the definition of dispersal considered. We demonstrate that, for a wide-ranging apex carnivore, functional connectivity through natal dispersal corresponds to structural connectivity as modeled by a second-order RSF. Mapping of the adult-based habitat classes provides direct visualization of the potential linkages between populations, without the need to model paths between a priori starting and destination points. The use of such landscape scale RSFs may provide insight into predicting suitable dispersal habitat peninsulas in human-dominated landscapes where mitigation of human-wildlife conflict should be focused. We recommend the use of second-order RSFs for landscape conservation planning and propose a similar approach to the conservation of other wide-ranging large

  20. Coaching patients during pulmonary function testing: A practical guide

    PubMed Central

    Cheung, Heidi J; Cheung, Lawrence

    2015-01-01

    Pulmonary function tests are an important tool to assist in the diagnosis and management of patients with respiratory disease. Ensuring that the tests are of acceptable quality is vital. Acceptable pulmonary function test quality requires, among others, optimal patient performance. Optimal patient performance, in turn, requires adequate coaching from registered respiratory therapists (RRTs) and other pulmonary function laboratory personnel. The present article provides techniques and tips to help RRTs coach patients during testing. The authors briefly review the components of pulmonary function testing, then describe factors that may hinder a patient’s performance, list common mistakes that patients make during testing, and provide tips that RRTs can use to help patients optimize their performance. PMID:26283871

  1. Predicting objective function weights from patient anatomy in prostate IMRT treatment planning

    SciTech Connect

    Lee, Taewoo Hammad, Muhannad; Chan, Timothy C. Y.; Craig, Tim; Sharpe, Michael B.

    2013-12-15

    Purpose: Intensity-modulated radiation therapy (IMRT) treatment planning typically combines multiple criteria into a single objective function by taking a weighted sum. The authors propose a statistical model that predicts objective function weights from patient anatomy for prostate IMRT treatment planning. This study provides a proof of concept for geometry-driven weight determination. Methods: A previously developed inverse optimization method (IOM) was used to generate optimal objective function weights for 24 patients using their historical treatment plans (i.e., dose distributions). These IOM weights were around 1% for each of the femoral heads, while bladder and rectum weights varied greatly between patients. A regression model was developed to predict a patient's rectum weight using the ratio of the overlap volume of the rectum and bladder with the planning target volume at a 1 cm expansion as the independent variable. The femoral head weights were fixed to 1% each and the bladder weight was calculated as one minus the rectum and femoral head weights. The model was validated using leave-one-out cross validation. Objective values and dose distributions generated through inverse planning using the predicted weights were compared to those generated using the original IOM weights, as well as an average of the IOM weights across all patients. Results: The IOM weight vectors were on average six times closer to the predicted weight vectors than to the average weight vector, usingl{sub 2} distance. Likewise, the bladder and rectum objective values achieved by the predicted weights were more similar to the objective values achieved by the IOM weights. The difference in objective value performance between the predicted and average weights was statistically significant according to a one-sided sign test. For all patients, the difference in rectum V54.3 Gy, rectum V70.0 Gy, bladder V54.3 Gy, and bladder V70.0 Gy values between the dose distributions generated by the

  2. A Generalized DIF Effect Variance Estimator for Measuring Unsigned Differential Test Functioning in Mixed Format Tests

    ERIC Educational Resources Information Center

    Penfield, Randall D.; Algina, James

    2006-01-01

    One approach to measuring unsigned differential test functioning is to estimate the variance of the differential item functioning (DIF) effect across the items of the test. This article proposes two estimators of the DIF effect variance for tests containing dichotomous and polytomous items. The proposed estimators are direct extensions of the…

  3. Criterion function for predicting freckles in CMSX-4 during directional solidification

    NASA Astrophysics Data System (ADS)

    Pustal, B.; Ma, D.; Warnken, N.; Subasic, E.; Jakumeit, J.; Bührig-Polaczek, A.

    2016-03-01

    In the present work the impact of curvature effects on freckle formation in CMSX-4 during directional solidification was modelled and simulated. Modelling work is based on a four-step criterion function for predicting freckles. First, only surface elements are taken into account. Second, critical cross-sectional areas are identified where freckle formation is possible. As a new aspect, third, curvature effects are taken into account for predicting freckles in radiation shadow. Fourth, the Rayleigh number is calculated based on a permeability function of dendrite arm spacing and fraction of liquid. In the thus identified areas sufficient thermo-solutal convection takes place to initiate freckle formation. With the new model freckles can only appear in areas where the thermal temperature profile is concave, that is, at locations where the temperature gradient is positive against the surface normal. The present model was tested simulating step samples. For that, the individual parts of our industrial Bridgman furnace were input and joined in one FEM model. The thermal results clearly show concave solidus isothermal at the shadow faces of the step sample in the cluster. Freckles are predicted at the corresponding locations. When comparing simulated freckle formation with experimental findings, good correlation was found. Furthermore, we could predict both the transition length that occurs when the cross-sectional area increases stepwise and the run length when the cross-sectional area is reduced.

  4. Predicting Gene Structures from Multiple RT-PCR Tests

    NASA Astrophysics Data System (ADS)

    Kováč, Jakub; Vinař, Tomáš; Brejová, Broňa

    It has been demonstrated that the use of additional information such as ESTs and protein homology can significantly improve accuracy of gene prediction. However, many sources of external information are still being omitted from consideration. Here, we investigate the use of product lengths from RT-PCR experiments in gene finding. We present hardness results and practical algorithms for several variants of the problem and apply our methods to a real RT-PCR data set in the Drosophila genome. We conclude that the use of RT-PCR data can improve the sensitivity of gene prediction and locate novel splicing variants.

  5. Memory Hazard Functions: A Vehicle for Theory Development and Test

    ERIC Educational Resources Information Center

    Chechile, Richard A.

    2006-01-01

    A framework is developed to rigorously test an entire class of memory retention functions by examining hazard properties. Evidence is provided that the memory hazard function is not monotonically decreasing. Yet most of the proposals for retention functions, which have emerged from the psychological literature, imply that memory hazard is…

  6. Structure activity relationships: their function in biological prediction

    SciTech Connect

    Schultz, T.W.

    1982-01-01

    Quantitative structure activity relationships provide a means of ranking or predicting biological effects based on chemical structure. For each compound used to formulate a structure activity model two kinds of quantitative information are required: (1) biological activity and (2) molecular properties. Molecular properties are of three types: (1) molecular shape, (2) physiochemical parameters, and (3) abstract quantitations of molecular structure. Currently the two best descriptors are the hydrophobic parameter, log 1-octanol/water partition coefficient (log P), and the /sup 1/X/sup v/(one-chi-v) molecular connectivity index. Biological responses can be divided into three main categories: (1) non-specific effects due to membrane perturbation, (2) non-specific effects due to interaction with functional groups of proteins, and (3) specific effects due to interaction with receptors. Twenty-six synthetic fossil fuel-related nitrogen-containing aromatic compounds were examined to determine the quantitative correlation between log P and /sup 1/X/sup v/ and population growth impairment of Tetrahymena pyriformis. Nitro-containing compounds are the most active, followed by amino-containing compounds and azaarenes. Within each analog series activity increases with alkyl substitution and ring addition. The planar model log BR = 0.5564 log P + 0.3000 /sup 1/X/sup v/ -2.0138 was determined using mono-nitrogen substituted compounds. Attempts to extrapolate this model to dinitrogen-containing molecules were, for the most part, unsuccessful because of a change in mode of action from membrane perturbation to uncoupling of oxidative phosphoralation.

  7. Effect of Multiple Testing Adjustment in Differential Item Functioning Detection

    ERIC Educational Resources Information Center

    Kim, Jihye; Oshima, T. C.

    2013-01-01

    In a typical differential item functioning (DIF) analysis, a significance test is conducted for each item. As a test consists of multiple items, such multiple testing may increase the possibility of making a Type I error at least once. The goal of this study was to investigate how to control a Type I error rate and power using adjustment…

  8. Modelling snow cover duration improves predictions of functional and taxonomic diversity for alpine plant communities

    PubMed Central

    Carlson, Bradley Z.; Choler, Philippe; Renaud, Julien; Dedieu, Jean-Pierre; Thuiller, Wilfried

    2015-01-01

    Background and Aims Quantifying relationships between snow cover duration and plant community properties remains an important challenge in alpine ecology. This study develops a method to estimate spatial variation in energy availability in the context of a topographically complex, high-elevation watershed, which was used to test the explanatory power of environmental gradients both with and without snow cover in relation to taxonomic and functional plant diversity. Methods Snow cover in the French Alps was mapped at 15-m resolution using Landsat imagery for five recent years, and a generalized additive model (GAM) was fitted for each year linking snow to time and topography. Predicted snow cover maps were combined with air temperature and solar radiation data at daily resolution, summed for each year and averaged across years. Equivalent growing season energy gradients were also estimated without accounting for snow cover duration. Relationships were tested between environmental gradients and diversity metrics measured for 100 plots, including species richness, community-weighted mean traits, functional diversity and hyperspectral estimates of canopy chlorophyll content. Key Results Accounting for snow cover in environmental variables consistently led to improved predictive power as well as more ecologically meaningful characterizations of plant diversity. Model parameters differed significantly when fitted with and without snow cover. Filtering solar radiation with snow as compared without led to an average gain in R2 of 0·26 and reversed slope direction to more intuitive relationships for several diversity metrics. Conclusions The results show that in alpine environments high-resolution data on snow cover duration are pivotal for capturing the spatial heterogeneity of both taxonomic and functional diversity. The use of climate variables without consideration of snow cover can lead to erroneous predictions of plant diversity. The results further indicate that

  9. Simple analytical test and a formula to predict the potential for dermal carcinogenicity from petroleum oils

    SciTech Connect

    Haas, J.M.; Dimeler, G.R.; Basil, E.W.; Wilkins, G.W.; Nutter, J.S.

    1987-11-01

    A correlation for predicting dermal carcinogenicity of petroleum oils in laboratory animals has been developed using two simple analytical tests. The tests are the Food and Drug Administration test (FDA) commonly used to measure white oil purity, and a viscosity test. In the correlation, FDA is a measure of aromaticity, and viscosity is used to account for molecular weight. The FDA test alone appears to be comparable to other predictors now in use, but incorporating viscosity significantly increases the accuracy of predicting dermal carcinogenicity. A formula is proposed, using both the FDA test results and viscosity, that predicts the percentage of mice which will develop neoplastic skin tumors.

  10. Testing the Predictions of the Central Capacity Sharing Model

    ERIC Educational Resources Information Center

    Tombu, Michael; Jolicoeur, Pierre

    2005-01-01

    The divergent predictions of 2 models of dual-task performance are investigated. The central bottleneck and central capacity sharing models argue that a central stage of information processing is capacity limited, whereas stages before and after are capacity free. The models disagree about the nature of this central capacity limitation. The…

  11. Prediction of In-Season Shoulder Injury From Preseason Testing in Division I Collegiate Football Players

    PubMed Central

    Pontillo, Marisa; Spinelli, Bryan A.; Sennett, Brian J.

    2014-01-01

    Background: Collegiate football is a high-demand sport in which shoulder injuries are common. Research has described the incidence of these injuries, with little focus on causative factors or injury prevention. Hypothesis: Football athletes who score lower on preseason strength and functional testing are more likely to sustain an in-season shoulder injury. Study Design: Prospective, cohort study. Level of Evidence: Level 2. Methods: Twenty-six collegiate football players underwent preseason testing with a rotational profile for shoulder range of motion, isometric strength of the rotator cuff at 90° elevation and external rotation in the 90/90 position, fatigue testing (prone-Y, scaption, and standing cable press), and the Closed Kinetic Chain Upper Extremity Stability Test (CKCUEST). Data collected postseason included the type of shoulder injury and the side injured. Logistic regression was used to determine if the testing measures predicted injury, and a receiver operating characteristic curve was constructed to examine the relationship of CKCUEST to injury. Results: Six athletes sustained shoulder injuries during the season. Predictor variables could significantly predict whether that player would sustain an injury during the season for both the right and left shoulders (P < 0.05). The variables that were significantly correlated with injury of the right side were forward elevation strength, prone-Y to fatigue, and the CKCUEST (P < 0.05); on the left, only the CKCUEST was significant (P < 0.05). The area under the receiver operating characteristic curve for the CKCUEST was 0.86 (ϵ = 0.87, P = 0.01). Using a score of 21 touches, the CKCUEST had a sensitivity of 0.83, a specificity of 0.79, and an odds ratio of 18.75 in determining whether a player sustained a shoulder injury. Conclusion: For this sample, the combination of preseason strength, fatigue, and functional testing was able to identify football players who would sustain a shoulder injury during the

  12. Report on the sixth blind test of organic crystal structure prediction methods

    PubMed Central

    Reilly, Anthony M.; Cooper, Richard I.; Adjiman, Claire S.; Bhattacharya, Saswata; Boese, A. Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J.; Bylsma, Rita; Campbell, Josh E.; Car, Roberto; Case, David H.; Chadha, Renu; Cole, Jason C.; Cosburn, Katherine; Cuppen, Herma M.; Curtis, Farren; Day, Graeme M.; DiStasio Jr, Robert A.; Dzyabchenko, Alexander; van Eijck, Bouke P.; Elking, Dennis M.; van den Ende, Joost A.; Facelli, Julio C.; Ferraro, Marta B.; Fusti-Molnar, Laszlo; Gatsiou, Christina-Anna; Gee, Thomas S.; de Gelder, René; Ghiringhelli, Luca M.; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W. M.; Hoja, Johannes; Hylton, Rebecca K.; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T.; Kendrick, John; de Klerk, Niek J. J.; Ko, Hsin-Yu; Kuleshova, Liudmila N.; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J. J.; Lund, Albert M.; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E.; McCabe, Patrick; McMahon, David P.; Meekes, Hugo; Metz, Michael P.; Misquitta, Alston J.; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J.; Neumann, Marcus A.; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R.; Orendt, Anita M.; Pagola, Gabriel I.; Pantelides, Constantinos C.; Pickard, Chris J.; Podeszwa, Rafal; Price, Louise S.; Price, Sarah L.; Pulido, Angeles; Read, Murray G.; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P.; Singh, Pawanpreet; Sugden, Isaac J.; Szalewicz, Krzysztof; Taylor, Christopher R.; Tkatchenko, Alexandre; Tuckerman, Mark E.; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E.; de Wijs, Gilles A.; Yang, Jack; Zhu, Qiang; Groom, Colin R.

    2016-01-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and ‘best practices’ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z′ = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. PMID:27484368

  13. Report on the sixth blind test of organic crystal structure prediction methods.

    PubMed

    Reilly, Anthony M; Cooper, Richard I; Adjiman, Claire S; Bhattacharya, Saswata; Boese, A Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J; Bylsma, Rita; Campbell, Josh E; Car, Roberto; Case, David H; Chadha, Renu; Cole, Jason C; Cosburn, Katherine; Cuppen, Herma M; Curtis, Farren; Day, Graeme M; DiStasio, Robert A; Dzyabchenko, Alexander; van Eijck, Bouke P; Elking, Dennis M; van den Ende, Joost A; Facelli, Julio C; Ferraro, Marta B; Fusti-Molnar, Laszlo; Gatsiou, Christina Anna; Gee, Thomas S; de Gelder, René; Ghiringhelli, Luca M; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W M; Hoja, Johannes; Hylton, Rebecca K; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T; Kendrick, John; de Klerk, Niek J J; Ko, Hsin Yu; Kuleshova, Liudmila N; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J J; Lund, Albert M; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E; McCabe, Patrick; McMahon, David P; Meekes, Hugo; Metz, Michael P; Misquitta, Alston J; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J; Neumann, Marcus A; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R; Orendt, Anita M; Pagola, Gabriel I; Pantelides, Constantinos C; Pickard, Chris J; Podeszwa, Rafal; Price, Louise S; Price, Sarah L; Pulido, Angeles; Read, Murray G; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P; Singh, Pawanpreet; Sugden, Isaac J; Szalewicz, Krzysztof; Taylor, Christopher R; Tkatchenko, Alexandre; Tuckerman, Mark E; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E; de Wijs, Gilles A; Yang, Jack; Zhu, Qiang; Groom, Colin R

    2016-08-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. PMID:27484368

  14. Report on the sixth blind test of organic crystal structure prediction methods.

    PubMed

    Reilly, Anthony M; Cooper, Richard I; Adjiman, Claire S; Bhattacharya, Saswata; Boese, A Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J; Bylsma, Rita; Campbell, Josh E; Car, Roberto; Case, David H; Chadha, Renu; Cole, Jason C; Cosburn, Katherine; Cuppen, Herma M; Curtis, Farren; Day, Graeme M; DiStasio, Robert A; Dzyabchenko, Alexander; van Eijck, Bouke P; Elking, Dennis M; van den Ende, Joost A; Facelli, Julio C; Ferraro, Marta B; Fusti-Molnar, Laszlo; Gatsiou, Christina Anna; Gee, Thomas S; de Gelder, René; Ghiringhelli, Luca M; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W M; Hoja, Johannes; Hylton, Rebecca K; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T; Kendrick, John; de Klerk, Niek J J; Ko, Hsin Yu; Kuleshova, Liudmila N; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J J; Lund, Albert M; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E; McCabe, Patrick; McMahon, David P; Meekes, Hugo; Metz, Michael P; Misquitta, Alston J; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J; Neumann, Marcus A; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R; Orendt, Anita M; Pagola, Gabriel I; Pantelides, Constantinos C; Pickard, Chris J; Podeszwa, Rafal; Price, Louise S; Price, Sarah L; Pulido, Angeles; Read, Murray G; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P; Singh, Pawanpreet; Sugden, Isaac J; Szalewicz, Krzysztof; Taylor, Christopher R; Tkatchenko, Alexandre; Tuckerman, Mark E; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E; de Wijs, Gilles A; Yang, Jack; Zhu, Qiang; Groom, Colin R

    2016-08-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

  15. Playing off the curve - testing quantitative predictions of skill acquisition theories in development of chess performance

    PubMed Central

    Gaschler, Robert; Progscha, Johanna; Smallbone, Kieran; Ram, Nilam; Bilalić, Merim

    2014-01-01

    Learning curves have been proposed as an adequate description of learning processes, no matter whether the processes manifest within minutes or across years. Different mechanisms underlying skill acquisition can lead to differences in the shape of learning curves. In the current study, we analyze the tournament performance data of 1383 chess players who begin competing at young age and play tournaments for at least 10 years. We analyze the performance development with the goal to test the adequacy of learning curves, and the skill acquisition theories they are based on, for describing and predicting expertise acquisition. On the one hand, we show that the skill acquisition theories implying a negative exponential learning curve do a better job in both describing early performance gains and predicting later trajectories of chess performance than those theories implying a power function learning curve. On the other hand, the learning curves of a large proportion of players show systematic qualitative deviations from the predictions of either type of skill acquisition theory. While skill acquisition theories predict larger performance gains in early years and smaller gains in later years, a substantial number of players begin to show substantial improvements with a delay of several years (and no improvement in the first years), deviations not fully accounted for by quantity of practice. The current work adds to the debate on how learning processes on a small time scale combine to large-scale changes. PMID:25202292

  16. Playing off the curve - testing quantitative predictions of skill acquisition theories in development of chess performance.

    PubMed

    Gaschler, Robert; Progscha, Johanna; Smallbone, Kieran; Ram, Nilam; Bilalić, Merim

    2014-01-01

    Learning curves have been proposed as an adequate description of learning processes, no matter whether the processes manifest within minutes or across years. Different mechanisms underlying skill acquisition can lead to differences in the shape of learning curves. In the current study, we analyze the tournament performance data of 1383 chess players who begin competing at young age and play tournaments for at least 10 years. We analyze the performance development with the goal to test the adequacy of learning curves, and the skill acquisition theories they are based on, for describing and predicting expertise acquisition. On the one hand, we show that the skill acquisition theories implying a negative exponential learning curve do a better job in both describing early performance gains and predicting later trajectories of chess performance than those theories implying a power function learning curve. On the other hand, the learning curves of a large proportion of players show systematic qualitative deviations from the predictions of either type of skill acquisition theory. While skill acquisition theories predict larger performance gains in early years and smaller gains in later years, a substantial number of players begin to show substantial improvements with a delay of several years (and no improvement in the first years), deviations not fully accounted for by quantity of practice. The current work adds to the debate on how learning processes on a small time scale combine to large-scale changes.

  17. Dual-orthogonal radial basis function networks for nonlinear time series prediction.

    PubMed

    Hong, X; Billings, Steve A.

    1998-04-01

    A new structure of Radial Basis Function (RBF) neural network called the Dual-orthogonal RBF Network (DRBF) is introduced for nonlinear time series prediction. The hidden nodes of a conventional RBF network compare the Euclidean distance between the network input vector and the centres, and the node responses are radially symmetrical. But in time series prediction where the system input vectors are lagged system outputs, which are usually highly correlated, the Euclidean distance measure may not be appropriate. The DRBF network modifies the distance metric by introducing a classification function which is based on the estimation data set. Training the DRBF networks consists of two stages. Learning the classification related basis functions and the important input nodes, followed by selecting the regressors and learning the weights of the hidden nodes. In both cases, a forward Orthogonal Least Squares (OLS) selection procedure is applied, initially to select the important input nodes and then to select the important centres. Simulation results of single-step and multi-step ahead predictions over a test data set are included to demonstrate the effectiveness of the new approach.

  18. Critical Flicker Fusion Predicts Executive Function in Younger and Older Adults.

    PubMed

    Mewborn, Catherine; Renzi, Lisa M; Hammond, Billy R; Miller, L Stephen

    2015-11-01

    Critical flicker fusion (CFF), a measure of visual processing speed, has often been regarded as a basic metric underlying a number of higher cognitive functions. To test this, we measured CFF, global cognition, and several cognitive subdomains. Because age is a strong covariate for most of these variables, both younger (n = 72) and older (n = 57) subjects were measured. Consistent with expectations, age was inversely related to CFF and performance on all of the cognitive measures except for visual memory. In contrast, age-adjusted CFF thresholds were only positively related to executive function. Results showed that CFF predicted executive function across both age groups and accounted for unique variance in performance above and beyond age and global cognitive status. The current findings suggest that CFF may be a unique predictor of executive dysfunction. PMID:26370250

  19. Locomotor Tests Predict Community Mobility in Children and Youth with Cerebral Palsy

    ERIC Educational Resources Information Center

    Ferland, Chantale; Moffet, Helene; Maltais, Desiree

    2012-01-01

    Ambulatory children and youth with cerebral palsy have limitations in locomotor capacities and in community mobility. The ability of three locomotor tests to predict community mobility in this population (N = 49, 27 boys, 6-16 years old) was examined. The tests were a level ground walking test, the 6-min-Walk-Test (6MWT), and two tests of advanced…

  20. Do Laboratory Tests Predict Everyday Memory? A Neuropsychological Study.

    ERIC Educational Resources Information Center

    Sunderland, Alan; And Others

    1983-01-01

    The relationship between memory performance in everyday life and performance on laboratory tests was investigated with normal-memory and previously severely head-injured subjects. Correlation of the two test types was found in normal-memory and long-term head-injured, but not with the recently-injured. Highest correlations were with prose recall…

  1. UTILIZATION OF TREATABILITY AND PILOT TESTS TO PREDICT CAH BIOREMEDIATION

    EPA Science Inventory

    Multiple tools have been suggested to help in the design of enhanced anaerobic bioremediation systems for CAHs:
    - Extensive high quality microcosm testing followed by small-scale, thoroughly observed field pilot tests (i.e., RABITT Protocol, Morse 1998)
    - More limited ...

  2. Cognitive functioning differentially predicts different dimensions of older drivers’ on-road safety

    PubMed Central

    Aksan, Nazan; Anderson, Steve W; Dawson, Jeffrey; Uc, Ergun; Rizzo, Matthew

    2015-01-01

    The extent to which deficits in specific cognitive domains contribute to older drivers’ safety risk in complex real-world driving tasks is not well understood. We selected 148 drivers older than 70 years of age both with and without neurodegenerative diseases (Alzheimer disease-AD and Parkinson disease-PD) from an existing driving database of older adults. Participant assessments included on-road driving safety and cognitive functioning in visuospatial construction, speed of processing, memory, and executive functioning. The standardized on-road drive test was designed to examine multiple facets of older driver safety including navigation performance (e.g. following a route, identifying landmarks), safety errors while concurrently performing secondary navigation tasks (“on-task” safety errors), and safety errors in the absence of any secondary navigation tasks (“baseline” safety errors). The inter-correlations of these outcome measures were fair to moderate supporting their distinctiveness. Participants with diseases performed worse than the healthy aging group on all driving measures, and differences between those with AD and PD were minimal. In multivariate analyses, different domains of cognitive functioning predicted distinct facets of driver safety on road. Memory and set-shifting predicted performance in navigation-related secondary tasks, speed of processing predicted on-task safety errors, and visuospatial construction predicted baseline safety errors. These findings support broad assessments of cognitive functioning to inform decisions regarding older driver safety on the road and suggest navigation performance may be useful in evaluating older driver fitness and restrictions in licensing. PMID:25525974

  3. Implications of the International Classification of Functioning, Disability and Health (ICF) for Test Development and Use

    ERIC Educational Resources Information Center

    Carlson, Janet F.; Benson, Nicholas; Oakland, Thomas

    2010-01-01

    Implications of the International Classification of Functioning, Disability and Health (ICF) on the development and use of tests in school settings are enumerated. We predict increased demand for behavioural assessments that consider a person's activities, participation and person-environment interactions, including measures that: (a) address…

  4. Individual differences in common factors of emotional traits and executive functions predict functional connectivity of the amygdala.

    PubMed

    Rohr, C S; Dreyer, F R; Aderka, I M; Margulies, D S; Frisch, S; Villringer, A; Okon-Singer, H

    2015-10-15

    Evidence suggests that individual differences in emotion control are associated with frontoparietal-limbic networks and linked to emotional traits and executive functions. In a first attempt to directly target the link between emotional traits and executive functions using resting-state fMRI analysis, 43 healthy adults completed a test battery including executive tasks and emotional trait self-assessments that were subjected to a principal component analysis. Of the three factors detected, two explained 40.4% of the variance and were further investigated. Both factors suggest a relation between emotional traits and executive functions. Specifically, the first factor consisted of measures related to inhibitory control and negative affect, and the second factor was related to reward and positive affect. To investigate whether this interplay between emotional traits and executive functions is reflected in neural connectivity, we used resting-state fMRI to explore the functional connectivity of the amygdala as a starting point, and progressed to other seed-based analyses based on the initial findings. We found that the first factor predicted the strength of connectivity between brain regions known to be involved in the cognitive control of emotion, including the amygdala and the dorsolateral prefrontal cortex, whereas the second factor predicted the strength of connectivity between brain regions known to be involved in reward and attention, including the amygdala, the caudate and the thalamus. These findings suggest that individual differences in the ability to inhibit negative affect are mediated by prefrontal-limbic pathways, while the ability to be positive and use rewarding information is mediated by a network that includes the amygdala and thalamostriatal regions.

  5. Caffeine test in predicting flutamide-induced hepatic injury in patients with prostate cancer.

    PubMed

    Ozono, S; Yamaguchi, A; Mochizuki, H; Kawakami, T; Fujimoto, K; Otani, T; Yoshida, K; Ichinei, M; Yamashita, T; Hirao, Y

    2002-01-01

    The caffeine test measures the activity of cytochrome p450 (CYP1A2) which is a major enzyme involved in the activation of flutamide. The usefulness of this test in predicting flutamide-induced hepatic injury in patients with prostate cancer was examined. The subjects were: (1). five patients whose aspartate aminotransferase (AST) or alanine aminotransferase (ALT) level rose to 100 IU/l or higher following the start of flutamide (moderately injured group); (2). four patients whose AST and ALT levels were higher than normal but less than 100 IU/l (mildly injured group); and (3). two patients whose hepatic function remained normal (normal group). The subjects were each given canned coffee to drink. Urinary caffeine (137X), paraxanthine (17X) and 1, 7-dimethyluric acid (17U) levels were measured 4-5 h later. The metabolite ratio, (17U+17X)/137X, was calculated to serve as an indicator of CYP1A2 activity. The metabolite ratio for the moderately injured group (3.98+/-1.56) and the mildly injured group (5.55+/-1.42) were lower than that for the normal group (9.56). The results suggest that a decrease in CYP1A2 activity is involved in the onset of flutamide-induced hepatic injury, and that the caffeine test seems to provide a useful means of its prediction. PMID:12497002

  6. Transient excitation and mechanical admittance test techniques for prediction of payload vibration environments

    NASA Technical Reports Server (NTRS)

    Kana, D. D.; Vargas, L. M.

    1977-01-01

    Transient excitation forces were applied separately to simple beam-and-mass launch vehicle and payload models to develop complex admittance functions for the interface and other appropriate points on the structures. These measured admittances were then analytically combined by a matrix representation to obtain a description of the coupled system dynamic characteristics. Response of the payload model to excitation of the launch vehicle model was predicted and compared with results measured on the combined models. These results are also compared with results of earlier work in which a similar procedure was employed except that steady-state sinusoidal excitation techniques were included. It is found that the method employing transient tests produces results that are better overall than the steady state methods. Furthermore, the transient method requires far less time to implement, and provides far better resolution in the data. However, the data acquisition and handling problem is more complex for this method. It is concluded that the transient test and admittance matrix prediction method can be a valuable tool for development of payload vibration tests.

  7. Commercial predictive testing: the desirability of one overseeing body.

    PubMed

    Hoedemaekers, R

    2000-08-01

    In Europe a process of harmonisation of standards and regulations on genetic testing has started. Public discussion and consultation are recommended, but it is not clear in every European country how the decision making process as regards the further introduction of genetic testing services should be formed. In this paper the usefulness and importance of an overseeing body for genetic screening and testing is founded on four lines of reasoning: (1) analysis of the role of value judgments in the use of the concept of (genetic) abnormality; (2) a balancing of potential benefits for all parties involved; (3) a balancing of potential disadvantages, and (4) the greater availability of commercial genetic tests in the future. It is further argued that such an overseeing body has advantages for all the interested parties.

  8. A multi-label classifier for prediction membrane protein functional types in animal.

    PubMed

    Zou, Hong-Liang

    2014-11-01

    Membrane protein is an important composition of cell membrane. Given a membrane protein sequence, how can we identify its type(s) is very important because the type keeps a close correlation with its functions. According to previous studies, membrane protein can be divided into the following eight types: single-pass type I, single-pass type II, single-pass type III, single-pass type IV, multipass, lipid-anchor, GPI-anchor, peripheral membrane protein. With the avalanche of newly found protein sequences in the post-genomic age, it is urgent to develop an automatic and effective computational method to rapid and reliable prediction of the types of membrane proteins. At present, most of the existing methods were based on the assumption that one membrane protein only belongs to one type. Actually, a membrane protein may simultaneously exist at two or more different functional types. In this study, a new method by hybridizing the pseudo amino acid composition with multi-label algorithm called LIFT (multi-label learning with label-specific features) was proposed to predict the functional types both singleplex and multiplex animal membrane proteins. Experimental result on a stringent benchmark dataset of membrane proteins by jackknife test show that the absolute-true obtained was 0.6342, indicating that our approach is quite promising. It may become a useful high-through tool, or at least play a complementary role to the existing predictors in identifying functional types of membrane proteins.

  9. FFPred 3: feature-based function prediction for all Gene Ontology domains.

    PubMed

    Cozzetto, Domenico; Minneci, Federico; Currant, Hannah; Jones, David T

    2016-01-01

    Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present FFPred 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features. PMID:27561554

  10. FFPred 3: feature-based function prediction for all Gene Ontology domains

    PubMed Central

    Cozzetto, Domenico; Minneci, Federico; Currant, Hannah; Jones, David T.

    2016-01-01

    Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present FFPred 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features. PMID:27561554

  11. Thalamic functional connectivity predicts seizure laterality in individual TLE patients: Application of a biomarker development strategy

    PubMed Central

    Barron, Daniel S.; Fox, Peter T.; Pardoe, Heath; Lancaster, Jack; Price, Larry R.; Blackmon, Karen; Berry, Kristen; Cavazos, Jose E.; Kuzniecky, Ruben; Devinsky, Orrin; Thesen, Thomas

    2014-01-01

    Noninvasive markers of brain function could yield biomarkers in many neurological disorders. Disease models constrained by coordinate-based meta-analysis are likely to increase this yield. Here, we evaluate a thalamic model of temporal lobe epilepsy that we proposed in a coordinate-based meta-analysis and extended in a diffusion tractography study of an independent patient population. Specifically, we evaluated whether thalamic functional connectivity (resting-state fMRI-BOLD) with temporal lobe areas can predict seizure onset laterality, as established with intracranial EEG. Twenty-four lesional and non-lesional temporal lobe epilepsy patients were studied. No significant differences in functional connection strength in patient and control groups were observed with Mann-Whitney Tests (corrected for multiple comparisons). Notwithstanding the lack of group differences, individual patient difference scores (from control mean connection strength) successfully predicted seizure onset zone as shown in ROC curves: discriminant analysis (two-dimensional) predicted seizure onset zone with 85% sensitivity and 91% specificity; logistic regression (four-dimensional) achieved 86% sensitivity and 100% specificity. The strongest markers in both analyses were left thalamo-hippocampal and right thalamo-entorhinal cortex functional connection strength. Thus, this study shows that thalamic functional connections are sensitive and specific markers of seizure onset laterality in individual temporal lobe epilepsy patients. This study also advances an overall strategy for the programmatic development of neuroimaging biomarkers in clinical and genetic populations: a disease model informed by coordinate-based meta-analysis was used to anatomically constrain individual patient analyses. PMID:25610790

  12. Formal Functional Test Designs: Bridging the Gap Between Test Requirements and Test Specifications

    NASA Technical Reports Server (NTRS)

    Hops, Jonathan

    1993-01-01

    This presentation describes the testing life cycle, the purpose of the test design phase, and test design methods and gives an example application. Also included is a description of Test Representation Language (TRL), a summary of the language, and an example of an application of TRL. A sample test requirement and sample test design are included.

  13. Strength prediction of fly ash concretes by accelerated testing

    SciTech Connect

    Tokyay, M.

    1999-11-01

    Relationships between standard compressive strength at 7, 28, and 90 days and early strength attained by (1) autogeneous curing, (2) warm water curing, and (3) boiling water curing were obtained and a regression expression to predict the strength of concretes containing high-lime and low-lime fly ashes as partial cement replacement are proposed. The control concretes were designed for 28-day characteristic compressive strengths, f{sub ck28} = 40, 60, 65, and 70 MPa. All concretes were proportioned to keep the slump at 80--100 mm. The curing methods used were in accordance with the relevant ASTM and Turkish standards.

  14. Smoke alarm tests may not adequately indicate smoke alarm function.

    PubMed

    Peek-Asa, Corinne; Yang, Jingzhen; Hamann, Cara; Young, Tracy

    2011-01-01

    Smoke alarms are one of the most promoted prevention strategies to reduce residential fire deaths, and they can reduce residential fire deaths by half. Smoke alarm function can be measured by two tests: the smoke alarm button test and the chemical smoke test. Using results from a randomized trial of smoke alarms, we compared smoke alarm response to the button test and the smoke test. The smoke alarms found in the study homes at baseline were tested, as well as study alarms placed into homes as part of the randomized trial. Study alarms were tested at 12 and 42 months postinstallation. The proportion of alarms that passed the button test but not the smoke test ranged from 0.5 to 5.8% of alarms; this result was found most frequently among ionization alarms with zinc or alkaline batteries. These alarms would indicate to the owner (through the button test) that the smoke alarm was working, but the alarm would not actually respond in the case of a fire (as demonstrated by failing the smoke test). The proportion of alarms that passed the smoke test but not the button test ranged from 1.0 to 3.0%. These alarms would appear nonfunctional to the owner (because the button test failed), even though the alarm would operate in response to a fire (as demonstrated by passing the smoke test). The general public is not aware of the potential for inaccuracy in smoke alarm tests, and burn professionals can advocate for enhanced testing methods. The optimal test to determine smoke alarm function is the chemical smoke test. PMID:21747329

  15. Exercise testing in severe emphysema: association with quality of life and lung function.

    PubMed

    Brown, Cynthia D; Benditt, Joshua O; Sciurba, Frank C; Lee, Shing M; Criner, Gerard J; Mosenifar, Zab; Shade, David M; Slivka, William A; Wise, Robert A

    2008-04-01

    Six-minute walk testing (6MWT) and cardiopulmonary exercise testing (CPX) are used to evaluate impairment in emphysema. However, the extent of impairment in these tests as well as the correlation of these tests with each other and lung function in advanced emphysema is not well characterized. During screening for the National Emphysema Treatment Trial, maximum ergometer CPX and 6MWT were performed in 1,218 individuals with severe COPD with an average FEV(1) of 26.9 +/- 7.1 % predicted. Predicted values for 6MWT and CPX were calculated from reference equations. Correlation coefficients and multivariable regression models were used to determine the association between lung function, quality of life (QOL) scores, and exercise measures. The two forms of exercise testing were correlated with each other (r = 0.57, p < 0.0001). However, the impairment of performance on CPX was greater than on the 6MWT (27.6 +/- 16.8 vs. 67.9 +/- 18.9 % predicted). Both exercise tests had similar correlation with measures of QOL, but maximum exercise capacity was better correlated with lung function measures than 6-minute walk distance. After adjustment, 6MWD had a slightly greater association with total SGRQ score than maximal exercise (effect size 0.37 +/- 0.04 vs. 0.25 +/- 0.03 %predicted/unit). Despite advanced emphysema, patients are able to maintain 6MWD to a greater degree than maximum exercise capacity. Moreover, the 6MWT may be a better test of functional capacity given its greater association with QOL measures whereas CPX is a better test of physiologic impairment.

  16. Using Accelerated Testing To Predict Module Reliability: Preprint

    SciTech Connect

    Wohlgemuth, J. H.; Kurtz, S.

    2011-07-01

    Long-term reliability is critical to the cost effectiveness and commercial success of photovoltaic (PV) products. Today most PV modules are warranted for 25 years, but there is no accepted test protocol to validate a 25-year lifetime. The qualification tests do an excellent job of identifying design, materials, and process flaws that are likely to lead to premature failure (infant mortality), but they are not designed to test for wear-out mechanisms that limit lifetime. This paper presents a method for evaluating the ability of a new PV module technology to survive long-term exposure to specific stresses. The authors propose the use of baseline technologies with proven long-term field performance as controls in the accelerated stress tests. The performance of new-technology modules can then be evaluated versus that of proven-technology modules. If the new-technology demonstrates equivalent or superior performance to the proven one, there is a high likelihood that they will survive versus the tested stress in the real world.

  17. Two novel prediction models improve predictions of skin corrosive sub-categories by test methods of OECD Test Guideline No. 431.

    PubMed

    Desprez, Bertrand; Barroso, João; Griesinger, Claudius; Kandárová, Helena; Alépée, Nathalie; Fuchs, Horst W

    2015-12-01

    Alternative test methods often use prediction models (PMs) for converting endpoint measurements into predictions. Two PMs are used for the skin corrosion tests (SCTs) of the OECD Test Guideline No. 431 (TG 431). One is specific to EpiSkin™ test method, whereas EpiDerm™, SkinEthic™ RHE and epiCS® share a common PM. These methods are based on reconstructed human epidermis models wherein cell viability values are measured. Their PMs allow translating those values into sub-categories of corrosive chemicals, Category 1A (Cat1A) and a combination of Categories 1B/1C (Cat1BC), and identifying non-corrosive (NC) chemicals. EpiSkin™'s PM already results in sufficiently accurate predictions. The common PM of the three others accurately identifies all corrosive chemicals but, for sub-categorization, an important fraction of Cat1BC chemicals (40-50%) is over-predicted as Cat1A. This paper presents a post-hoc analysis of validation data on a set of n=80 chemicals. It investigates: why this common PM causes these over-predictions and how two novel PMs that we developed (PMvar1 and PMvar2) improve the predictive capacity of these methods. PMvar1 is based on a two-step approach; PMvar2 is based on a single composite indicator of cell viability. Both showed a greater capacity to predict Cat1BC, while Cat1A correct predictions remaining at least at the same level of EpiSkin™. We suggest revising TG 431, to include the novel PMs in view of improving the predictive capacity of its SCTs. PMID:26320836

  18. Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

    PubMed Central

    Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Rost, Burkhard

    2013-01-01

    We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032

  19. Cloud prediction of protein structure and function with PredictProtein for Debian.

    PubMed

    Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

    2013-01-01

    We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

  20. Long-term prediction test procedure for most ICs, based on linear response theory

    NASA Technical Reports Server (NTRS)

    Litovchenko, V.; Ivakhnenko, I.

    1991-01-01

    Experimentally, thermal annealing is known to be a factor which enables a number of different integrated circuits (IC's) to recover their operating characteristics after suffering radiation damage in the space radiation environment; thus, decreasing and limiting long term cumulative total-dose effects. This annealing is also known to be accelerated at elevated temperatures both during and after irradiation. Linear response theory (LRT) was applied, and a linear response function (LRF) to predict the radiation/annealing response of sensitive parameters of IC's for long term (several months or years) exposure to the space radiation environment were constructed. Compressing the annealing process from several years in orbit to just a few hours or days in the laboratory is achieved by subjecting the IC to elevated temperatures or by increasing the typical spaceflight dose rate by several orders of magnitude for simultaneous radiation/annealing only. The accomplishments are as follows: (1) the test procedure to make predictions of the radiation response was developed; (2) the calculation of the shift in the threshold potential due to the charge distribution in the oxide was written; (3) electron tunneling processes from the bulk Si to the oxide region in an MOS IC were estimated; (4) in order to connect the experimental annealing data to the theoretical model, constants of the model of the basic annealing process were established; (5) experimental data obtained at elevated temperatures were analyzed; (6) time compression and reliability of predictions for the long term region were shown; (7) a method to compress test time and to make predictions of response for the nonlinear region was proposed; and (8) nonlinearity of the LRF with respect to log(t) was calculated theoretically from a model.

  1. Safety and Function Test Report for the SWIFT Wind Turbine

    SciTech Connect

    Mendoza, I.; Hur, J.

    2013-01-01

    This test was conducted as part of the U.S. Department of Energy's (DOE) Independent Testing project. This project was established to help reduce the barriers of wind energy expansion by providing independent testing results for small turbines. Three turbines where selected for testing at the National Wind Technology Center (NWTC) as a part of round two of the Small Wind Turbine Independent Testing project. Safety and Function testing is one of up to 5 tests that may be performed on the turbines. Other tests include power performance, duration, noise, and power quality. The results of the testing will provide the manufacturers with reports that may be used for small wind turbine certification.

  2. A Functional Test Platform for the Community Land Model

    SciTech Connect

    Xu, Yang; Thornton, Peter E; King, Anthony Wayne; Steed, Chad A; Gu, Lianhong; Schuchart, Joseph

    2014-01-01

    A functional test platform is presented to create direct linkages between site measurements and the process-based ecosystem model within the Community Earth System Models (CESM). The platform consists of three major parts: 1) interactive user interfaces, 2) functional test model and 3) observational datasets. It provides much needed integration interfaces for both field experimentalists and ecosystem modelers to improve the model s representation of ecosystem processes within the CESM framework without large software overhead.

  3. Attitudes of neurologists, psychiatrists, and psychotherapists towards predictive testing for Huntington's disease in Germany.

    PubMed Central

    Thies, U; Bockel, B; Bochdalofsky, V

    1993-01-01

    Predictive testing for Huntington's disease (HD) in Germany is performed by genetic counsellors, neurologists, psychiatrists, and psychotherapists. In order to evaluate the attitudes of neurologists, psychiatrists, and psychotherapists in Germany towards predictive testing for HD, a postal questionnaire was sent to this group. Two German Bundesländer were chosen, Baden Württemberg (BW) and Niedersachsen (NS). Of 469 persons interviewed the response rate was 32.6%. The questionnaire consisted of 17 items assessing sociodemographic data, acquaintance with HD patients, lay organisations, attitudes towards genetic counselling, presymptomatic and prenatal DNA testing, and reproduction of persons at risk for HD. More than 70% of the subjects were well informed about predictive DNA testing but knowledge about the details of the test procedure, especially the World Federation of Neurology (WFN) and International Huntington Association (IHA)1 recommendations, was quite low (11.8%). Nevertheless, the majority would recommend predictive testing for HD although they anticipated problems for the probands. The majority of our respondents favoured psychological test and post-test counselling for those tested. Concerning reproduction, most subjects favoured prenatal testing or that persons at risk should refrain from having children. We found that the opinions of practitioners and at risk persons differed with respect to the predictive DNA test and, particularly, to prenatal testing. Therefore the testing procedure could be improved if practitioners were better informed about the DNA test in general and about the attitudes and wishes of their patients. PMID:8133501

  4. The Effect of Coaching on the Predictive Validity of Scholastic Aptitude Tests.

    ERIC Educational Resources Information Center

    Allalouf, Avi; Ben-Shakhar, Gershon

    1998-01-01

    Examined how coaching affects the predictive validity and fairness of scholastic aptitude tests. A coached (n=271) and uncoached (n=95) group were compared. Comparison revealed that although coaching enhanced scores on the Israeli Psychometric Entrance Test by about 25% of a standard deviation, it did not create a prediction bias or affect…

  5. Predicting Performance on a Firefighter's Ability Test from Fitness Parameters

    ERIC Educational Resources Information Center

    Michaelides, Marcos A.; Parpa, Koulla M.; Thompson, Jerald; Brown, Barry

    2008-01-01

    The purpose of this project was to identify the relationships between various fitness parameters such as upper body muscular endurance, upper and lower body strength, flexibility, body composition and performance on an ability test (AT) that included simulated firefighting tasks. A second intent was to create a regression model that would predict…

  6. Heat of hydration for fly ash as a predictive test

    SciTech Connect

    Hassett, D.J.

    1995-12-31

    Coal combustion residues are commonly used in construction and for other engineering applications. These materials are complex and exhibit highly variable characteristics. Coal combustion fly ash, the most utilized of these materials, is commonly classified by its pozzolanic or cementitious properties. These properties are generally determined and monitored by empirical physical test procedures required for certification of these materials for use as a mineral admixture in cement. The current classification system does not provide a continuous scale rating for pozzolanic/cementitious behavior for these materials, or adequate information to assess the reactivity of these materials outside of their limited use in cement and concrete products. A test procedure, based on the heat of hydration, has been developed at the Energy and Environmental Research Center to more accurately assess the reactivity and behavior of these materials for utilization. The technique employs either a Dewar flask or a modified oxygen bomb calorimeter to determine the temperature change and rate of change after the addition of water to fly ash. X-ray diffraction is performed on the hydrated material following the hydration test to follow mineralogical changes as a result of the hydration process. A study of coal fly ash samples is underway to determine whether correlations exist between the temperature change and empirical test results. A protocol has been developed to assist in an improved classification scheme for coal fly ash.

  7. Predictive factors for postoperative visual function of primary chronic rhegmatogenous retinal detachment after scleral buckling

    PubMed Central

    Fang, Wei; Li, Jiu-Ke; Jin, Xiao-Hong; Dai, Yuan-Min; Li, Yu-Min

    2016-01-01

    AIM To evaluate predictive factors for postoperative visual function of primary chronic rhegmatgenous retinal detachment (RRD) after sclera buckling (SB). METHODS Totally 48 patients (51 eyes) with primary chronic RRD were included in this prospective interventional clinical cases study, which underwent SB alone from June 2008 to December 2014. Age, sex, symptoms duration, detached extension, retinal hole position, size, type, fovea on/off, proliferative vitreoretinopathy (PVR), posterior vitreous detachment (PVD), baseline best corrected visual acuity (BCVA), operative duration, follow up duration, final BCVA were measured. Pearson correlation analysis, Spearman correlation analysis and multivariate linear stepwise regression were used to confirm predictive factors for better final visual acuity. Student's t-test, Wilcoxon two-sample test, Chi-square test and logistic stepwise regression were used to confirm predictive factors for better vision improvement. RESULTS Baseline BCVA was 0.8313±0.6911 logMAR and final BCVA was 0.4761±0.4956 logMAR. Primary surgical success rate was 92.16% (47/51). Correlation analyses revealed shorter symptoms duration (r=0.3850, P=0.0053), less detached area (r=0.5489, P<0.0001), fovea (r=0.4605, P=0.0007), no PVR (r=0.3138, P=0.0250), better baseline BCVA (r=0.7291, P<0.0001), shorter operative duration (r=0.3233, P=0.0207) and longer follow up (r=-0.3358, P=0.0160) were related with better final BCVA, while independent predictive factors were better baseline BCVA [partial R-square (PR2)=0.5316, P<0.0001], shorter symptoms duration (PR2=0.0609, P=0.0101), longer follow up duration (PR2=0.0278, P=0.0477) and shorter operative duration (PR2=0.0338, P=0.0350). Patients with vision improvement took up 49.02% (25/51). Univariate and multivariate analyses both revealed predictive factors for better vision improvement were better baseline vision [odds ratio (OR) =50.369, P=0.0041] and longer follow up duration (OR=1.144, P=0

  8. Construct validity of functional capacity tests in healthy workers

    PubMed Central

    2013-01-01

    Background Functional Capacity (FC) is a multidimensional construct within the activity domain of the International Classification of Functioning, Disability and Health framework (ICF). Functional capacity evaluations (FCEs) are assessments of work-related FC. The extent to which these work-related FC tests are associated to bio-, psycho-, or social factors is unknown. The aims of this study were to test relationships between FC tests and other ICF factors in a sample of healthy workers, and to determine the amount of statistical variance in FC tests that can be explained by these factors. Methods A cross sectional study. The sample was comprised of 403 healthy workers who completed material handling FC tests (lifting low, overhead lifting, and carrying) and static work FC tests (overhead working and standing forward bend). The explainable variables were; six muscle strength tests; aerobic capacity test; and questionnaires regarding personal factors (age, gender, body height, body weight, and education), psychological factors (mental health, vitality, and general health perceptions), and social factors (perception of work, physical workloads, sport-, leisure time-, and work-index). A priori construct validity hypotheses were formulated and analyzed by means of correlation coefficients and regression analyses. Results Moderate correlations were detected between material handling FC tests and muscle strength, gender, body weight, and body height. As for static work FC tests; overhead working correlated fair with aerobic capacity and handgrip strength, and low with the sport-index and perception of work. For standing forward bend FC test, all hypotheses were rejected. The regression model revealed that 61% to 62% of material handling FC tests were explained by physical factors. Five to 15% of static work FC tests were explained by physical and social factors. Conclusions The current study revealed that, in a sample of healthy workers, material handling FC tests were

  9. IDENTIFICATION AND CHARACTERIZATION OF DISEASE USING PULMONARY FUNCTION TESTS

    EPA Science Inventory

    Abstract
    Pulmonary function testing is used routinely in human medicine to objectively define functional deficits in individuals with respiratory disease. Despite the fact that respiratory disease is a common problem in veterinary medicine, evaluation of the small animal pa...

  10. An application of characteristic function in order to predict reliability and lifetime of aeronautical hardware

    NASA Astrophysics Data System (ADS)

    Żurek, Józef; Kaleta, Ryszard; Zieja, Mariusz

    2016-06-01

    The forecasting of reliability and life of aeronautical hardware requires recognition of many and various destructive processes that deteriorate the health/maintenance status thereof. The aging of technical components of aircraft as an armament system proves of outstanding significance to reliability and safety of the whole system. The aging process is usually induced by many and various factors, just to mention mechanical, biological, climatic, or chemical ones. The aging is an irreversible process and considerably affects (i.e. reduces) reliability and lifetime of aeronautical equipment. Application of the characteristic function of the aging process is suggested to predict reliability and lifetime of aeronautical hardware. An increment in values of diagnostic parameters is introduced to formulate then, using the characteristic function and after some rearrangements, the partial differential equation. An analytical dependence for the characteristic function of the aging process is a solution to this equation. With the inverse transformation applied, the density function of the aging of aeronautical hardware is found. Having found the density function, one can determine the aeronautical equipment's reliability and lifetime. The in-service collected or the life tests delivered data are used to attain this goal. Coefficients in this relationship are found using the likelihood function.

  11. Dynamic testing of learning potential in adults with cognitive impairments: A systematic review of methodology and predictive value.

    PubMed

    Boosman, Hileen; Bovend'Eerdt, Thamar J H; Visser-Meily, Johanna M A; Nijboer, Tanja C W; van Heugten, Caroline M

    2016-09-01

    Dynamic testing includes procedures that examine the effects of brief training on test performance where pre- to post-training change reflects patients' learning potential. The objective of this systematic review was to provide clinicians and researchers insight into the concept and methodology of dynamic testing and to explore its predictive validity in adult patients with cognitive impairments. The following electronic databases were searched: PubMed, PsychINFO, and Embase/Medline. Of 1141 potentially relevant articles, 24 studies met the inclusion criteria. The mean methodological quality score was 4.6 of 8. Eleven different dynamic tests were used. The majority of studies used dynamic versions of the Wisconsin Card Sorting Test. The training mostly consisted of a combination of performance feedback, reinforcement, expanded instruction, or strategy training. Learning potential was quantified using numerical (post-test score, difference score, gain score, regression residuals) and categorical (groups) indices. In five of six longitudinal studies, learning potential significantly predicted rehabilitation outcome. Three of four studies supported the added value of dynamic testing over conventional testing in predicting rehabilitation outcome. This review provides preliminary support that dynamic tests can provide a valuable addition to conventional tests to assess patients' abilities. Although promising, there was a large variability in methods used for dynamic testing and, therefore, it remains unclear which dynamic testing methods are most appropriate for patients with cognitive impairments. More research is warranted to further evaluate and refine dynamic testing methodology and to further elucidate its predictive validity concerning rehabilitation outcomes relative to other cognitive and functional status indices.

  12. Transfer function tests of the Joy longwall shearer

    NASA Technical Reports Server (NTRS)

    Fisher, P. H., Jr.

    1978-01-01

    A series of operational tests was performed on the Joy longwall shearer located at the Bureau of Mines in Bructon, Pennsylvania. The purpose of these tests was to determine the transfer function and operational characteristics of the system. These characteristics will be used to generate a simulation model of the longwall shearer used in the development of the closed-loop vertical control system.

  13. Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration

    PubMed Central

    Xiong, Jianghui; Rayner, Simon; Luo, Kunyi; Li, Yinghui; Chen, Shanguang

    2006-01-01

    Background The automation of many common molecular biology techniques has resulted in the accumulation of vast quantities of experimental data. One of the major challenges now facing researchers is how to process this data to yield useful information about a biological system (e.g. knowledge of genes and their products, and the biological roles of proteins, their molecular functions, localizations and interaction networks). We present a technique called Global Mapping of Unknown Proteins (GMUP) which uses the Gene Ontology Index to relate diverse sources of experimental data by creation of an abstraction layer of evidence data. This abstraction layer is used as input to a neural network which, once trained, can be used to predict function from the evidence data of unannotated proteins. The method allows us to include almost any experimental data set related to protein function, which incorporates the Gene Ontology, to our evidence data in order to seek relationships between the different sets. Results We have demonstrated the capabilities of this method in two ways. We first collected various experimental datasets associated with yeast (Saccharomyces cerevisiae) and applied the technique to a set of previously annotated open reading frames (ORFs). These ORFs were divided into training and test sets and were used to examine the accuracy of the predictions made by our method. Then we applied GMUP to previously un-annotated ORFs and made 1980, 836 and 1969 predictions corresponding to the GO Biological Process, Molecular Function and Cellular Component sub-categories respectively. We found that GMUP was particularly successful at predicting ORFs with functions associated with the ribonucleoprotein complex, protein metabolism and transportation. Conclusion This study presents a global and generic gene knowledge discovery approach based on evidence integration of various genome-scale data. It can be used to provide insight as to how certain biological processes are

  14. [Interpretation and use of routine pulmonary function tests: Spirometry, static lung volumes, lung diffusion, arterial blood gas, methacholine challenge test and 6-minute walk test].

    PubMed

    Bokov, P; Delclaux, C

    2016-02-01

    Resting pulmonary function tests (PFT) include the assessment of ventilatory capacity: spirometry (forced expiratory flows and mobilisable volumes) and static volume assessment, notably using body plethysmography. Spirometry allows the potential definition of obstructive defect, while static volume assessment allows the potential definition of restrictive defect (decrease in total lung capacity) and thoracic hyperinflation (increase in static volumes). It must be kept in mind that this evaluation is incomplete and that an assessment of ventilatory demand is often warranted, especially when facing dyspnoea: evaluation of arterial blood gas (searching for respiratory insufficiency) and measurement of the transfer coefficient of the lung, allowing with the measurement of alveolar volume to calculate the diffusing capacity of the lung for CO (DLCO: assessment of alveolar-capillary wall and capillary blood volume). All these pulmonary function tests have been the subject of an Americano-European Task force (standardisation of lung function testing) published in 2005, and translated in French in 2007. Interpretative strategies for lung function tests have been recommended, which define abnormal lung function tests using the 5th and 95th percentiles of predicted values (lower and upper limits of normal values). Thus, these recommendations need to be implemented in all pulmonary function test units. A methacholine challenge test will only be performed in the presence of an intermediate pre-test probability for asthma (diagnostic uncertainty), which is an infrequent setting. The most convenient exertional test is the 6-minute walk test that allows the assessment of walking performance, the search for arterial desaturation and the quantification of dyspnoea complaint.

  15. Evaluation of screening tests for predicting older driver performance and safety assessed by an on-road test.

    PubMed

    Wood, Joanne M; Horswill, Mark S; Lacherez, Philippe F; Anstey, Kaarin J

    2013-01-01

    A number of tests and test batteries are available for the prediction of older driver safety, but many of these have not been validated against standardized driving outcome measures. The aim of this study was to evaluate a series of previously described screening tests in terms of their ability to predict the potential for safe and unsafe driving. Participants included 79 community-dwelling older drivers (M=72.16 years, SD=5.46; range 65-88 years; 57 males and 22 females) who completed a previously validated multi-disciplinary driving assessment, a hazard perception test, a hazard change detection test and a battery of vision and cognitive tests. Participants also completed a standardized on-road driving assessment. The multi-disciplinary test battery had the highest predictive ability with a sensitivity of 80% and a specificity of 73%, followed by the hazard perception test which demonstrated a sensitivity of 75% and a specificity of 61%. These findings suggest that a relatively simple and practical battery of tests from a range of domains has the capacity to predict safe and unsafe driving in older adults.

  16. Radial basis function network learns ceramic processing and predicts related strength and density

    NASA Technical Reports Server (NTRS)

    Cios, Krzysztof J.; Baaklini, George Y.; Vary, Alex; Tjia, Robert E.

    1993-01-01

    Radial basis function (RBF) neural networks were trained using the data from 273 Si3N4 modulus of rupture (MOR) bars which were tested at room temperature and 135 MOR bars which were tested at 1370 C. Milling time, sintering time, and sintering gas pressure were the processing parameters used as the input features. Flexural strength and density were the outputs by which the RBF networks were assessed. The 'nodes-at-data-points' method was used to set the hidden layer centers and output layer training used the gradient descent method. The RBF network predicted strength with an average error of less than 12 percent and density with an average error of less than 2 percent. Further, the RBF network demonstrated a potential for optimizing and accelerating the development and processing of ceramic materials.

  17. Testing Predictions of Continental Insulation using Oceanic Crustal Thicknesses

    NASA Astrophysics Data System (ADS)

    Hoggard, Mark; Shorttle, Oliver; White, Nicky

    2016-04-01

    The thermal blanketing effect of continental crust has been predicted to lead to elevated temperatures within the upper mantle beneath supercontinents. Initial break-up is associated with increased magmatism and the generation of flood basalts. Continued rifting and sea-floor spreading lead to a steady reduction of this thermal anomaly. Recently, evidence in support of this behaviour has come from the major element geochemistry of mid-ocean ridge basalts, which suggest excess rifting temperatures of ˜ 150 °C that decay over ˜ 100 Ma. We have collated a global inventory of ˜ 1000 seismic reflection profiles and ˜ 500 wide-angle refraction experiments from the oceanic realm. Data are predominantly located along passive margins, but there are also multiple surveys in the centres of the major oceanic basins. Oceanic crustal thickness has been mapped, taking care to avoid areas of secondary magmatic thickening near seamounts or later thinning such as across transform faults. These crustal thicknesses are a proxy for mantle potential temperature at the time of melt formation beneath a mid-ocean ridge system, allowing us to quantify the amplitude and duration of thermal anomalies generated beneath supercontinents. The Jurassic break-up of the Central Atlantic and the Cretaceous rifting that formed the South Atlantic Ocean are both associated with excess temperatures of ˜ 50 °C that have e-folding times of ˜ 50 Ma. In addition to this background trend, excess temperatures reach > 150 °C around the region of the Rio Grande Rise, associated with the present-day Tristan hotspot. The e-folding time of this more local event is ˜ 10 Ma, which mirrors results obtained for the North Atlantic Ocean south of Iceland. In contrast, crustal thicknesses from the Pacific Ocean reveal approximately constant potential temperature through time. This observation is in agreement with predictions, as the western Pacific was formed by rifting of an oceanic plate. In summary

  18. Executive Function Predicts Artificial Language Learning in Children and Adults

    ERIC Educational Resources Information Center

    Kapa, Leah Lynn

    2013-01-01

    Prior research has established an executive function advantage among bilinguals as compared to monolingual peers. These non-linguistic cognitive advantages are largely assumed to result from the experience of managing two linguistic systems. However, the possibility remains that the relationship between bilingualism and executive function is…

  19. Predictive Capability of Anorectal Physiologic Tests for Unfavorable Outcomes Following Biofeedback Therapy in Dyssynergic Defecation

    PubMed Central

    Shin, Jae Kook; Kim, Eun Sook; Yoon, Jin Young; Lee, Jin Ha; Jeon, Soung Min; Bok, Hyun Jung; Park, Jae Jun; Moon, Chang Mo; Hong, Sung Pil; Lee, Yong Chan; Kim, Won Ho

    2010-01-01

    The purpose of this study is to evaluate the predictive capability of anorectal physiologic tests for unfavorable outcomes prior to the initiation of biofeedback therapy in patients with dyssynergic defecation. We analyzed a total of 80 consecutive patients who received biofeedback therapy for chronic idiopathic functional constipation with dyssynergic defecation. After classifying the patients into two groups (responders and non-responders), univariate and multivariate analyses were performed to determine the predictors associated with the responsiveness to biofeedback therapy. Of the 80 patients, 63 (78.7%) responded to biofeedback therapy and 17 (21.3%) did not. On univariate analysis, the inability to evacuate an intrarectal balloon (P=0.028), higher rectal volume for first, urgent, and maximal sensation (P=0.023, P=0.008, P=0.007, respectively), and increased anorectal angle during squeeze (P=0.020) were associated with poor outcomes. On multivariate analysis, the inability to evacuate an intrarectal balloon (P=0.018) and increased anorectal angle during squeeze (P=0.029) were both found to be independently associated with a lack of response to biofeedback therapy. Our data show that the two anorectal physiologic test factors are associated with poor response to biofeedback therapy for patients with dyssynergic defecation. These findings may assist physicians in predicting the responsiveness to therapy for this patient population. PMID:20592899

  20. PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

    PubMed Central

    Phan, Hang T. T.; Sternberg, Michael J. E.

    2012-01-01

    Motivation: Analysis of protein–protein interaction networks (PPINs) at the system level has become increasingly important in understanding biological processes. Comparison of the interactomes of different species not only provides a better understanding of species evolution but also helps with detecting conserved functional components and in function prediction. Method and Results: Here we report a PPIN alignment method, called PINALOG, which combines information from protein sequence, function and network topology. Alignment of human and yeast PPINs reveals several conserved subnetworks between them that participate in similar biological processes, notably the proteasome and transcription related processes. PINALOG has been tested for its power in protein complex prediction as well as function prediction. Comparison with PSI-BLAST in predicting protein function in the twilight zone also shows that PINALOG is valuable in predicting protein function. Availability and implementation: The PINALOG web-server is freely available from http://www.sbg.bio.ic.ac.uk/~pinalog. The PINALOG program and associated data are available from the Download section of the web-server. Contact: m.sternberg@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22419782

  1. TRANSP Tests Of TGLF and Predictions For ITER

    SciTech Connect

    none,; Budny, Robert; Yuan, Xingqiu

    2014-02-26

    Gyro kinetic simulations of turbulence capture some of the features observed in transport, fluctuations, and correlations measured in tokamak plasmas. These codes calculations are CPU intensive, and are not practical for incorporation in present time-dependant transport codes, so reduced models based on these gyro kinetic codes are being used. An example is the TGLF model [1] which is a quasilinear gyrofluid model calibrated to nonlinear results from the GYRO code [2]. Recently TGLF has been incorporated into TRANSP. Analysis of experimental data using TRANSP with such models provides fundamental understanding of turbulent transport. Predictions of ITER performance with various plasma scenarios using such models are useful for optimizing design and for exposing issues that can be addressed in present experiments and theory. For instance, which combinations of heating, torquing, and current drive are optimal. Another application is for nuclear licensing (e.g. system integrity, neutron rates). Others are generating inputs for design of diagnostic systems and for theoretical studies. An example of the later is Alfv´en Eigenmode and AE-induced loss of fast ions. The beam ion distribution can either enhance or reduce the alpha pressure drive of the AE instability. The AE instability can cause dangerous amounts of fast ion losses, as was seen in TFTR.

  2. Testing Theories That Predict Time Variation of Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Landau, Susana J.; Vucetich, Hector

    2002-05-01

    We consider astronomical and local bounds on the time variation of fundamental constants to test some generic Kaluza-Klein-like models and some particular cases of Beckenstein theory. Bounds on the free parameters of the different theories are obtained. Furthermore, we find that none of the proposed models is able to explain recent results (as from Webb and coworkers in 1999 and 2001) claiming an observed variation of the fine-structure constant from quasar absorption systems at redshifts 0.5

  3. The Autonomic System Functional State Predicts Responsiveness in Disorder of Consciousness.

    PubMed

    Riganello, Francesco; Cortese, Maria D; Dolce, Giuliano; Lucca, Lucia F; Sannita, Walter G

    2015-07-15

    Diagnosis and early prognosis of the vegetative state/unresponsive wakefulness syndrome (VS/UWS) and its differentiation from the minimally-conscious state still rest on the clinical observation of responsiveness. The incidence of established clinical indicators of responsiveness also has proven variable in the single subject and is correlated to measures of heart rate variability (HRV) describing the sympathetic/parasympathetic balance. We tested responsiveness when the HRV descriptors nuLF and peakLF were or were not in the ranges with highest incidence of response based on findings from previous studies (10.0-70.0 and 0.05-0.11 Hz, respectively). Testing was blind by The Coma Recovery Scale-revised in the two conditions and in two experimental sessions with a one-week interval. The incidence of responses was not randomly distributed in the "response" and "no-response" conditions (McNemar test; p < 0.0001). The observed incidence in the "response" condition (visual: 55.1%; auditory: 51.5%) was higher than predicted statistically (32.1%) or described in previous clinical studies; responses were only occasional in the "no-response" condition (visual, 15.9%; auditory, 13.4%). Models validated the predictability with high accuracy. The current clinical criteria for diagnosis and prognosis based on neurological signs should be reconsidered, including variability over time and the autonomic system functional state, which could also qualify per se as an independent indicator for diagnosis and prognosis.

  4. Tiltrotor Aeroacoustic Code (TRAC) Prediction Assessment and Initial Comparisons with Tram Test Data

    NASA Technical Reports Server (NTRS)

    Burley, Casey L.; Brooks, Thomas F.; Charles, Bruce D.; McCluer, Megan

    1999-01-01

    A prediction sensitivity assessment to inputs and blade modeling is presented for the TiltRotor Aeroacoustic Code (TRAC). For this study, the non-CFD prediction system option in TRAC is used. Here, the comprehensive rotorcraft code, CAMRAD.Mod1, coupled with the high-resolution sectional loads code HIRES, predicts unsteady blade loads to be used in the noise prediction code WOPWOP. The sensitivity of the predicted blade motions, blade airloads, wake geometry, and acoustics is examined with respect to rotor rpm, blade twist and chord, and to blade dynamic modeling. To accomplish this assessment, an interim input-deck for the TRAM test model and an input-deck for a reference test model are utilized in both rigid and elastic modes. Both of these test models are regarded as near scale models of the V-22 proprotor (tiltrotor). With basic TRAC sensitivities established, initial TRAC predictions are compared to results of an extensive test of an isolated model proprotor. The test was that of the TiltRotor Aeroacoustic Model (TRAM) conducted in the Duits-Nederlandse Windtunnel (DNW). Predictions are compared to measured noise for the proprotor operating over an extensive range of conditions. The variation of predictions demonstrates the great care that must be taken in defining the blade motion. However, even with this variability, the predictions using the different blade modeling successfully capture (bracket) the levels and trends of the noise for conditions ranging from descent to ascent.

  5. Better prediction of functional effects for sequence variants

    PubMed Central

    2015-01-01

    Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classifier that improves over the state-of-the-art in distinguishing between effect and neutral variants. Our method's improved performance results from screening many potentially relevant protein features and from refining our development data sets. Cross-validated on >100k experimentally annotated variants, SNAP2 significantly outperformed other methods, attaining a two-state accuracy (effect/neutral) of 83%. SNAP2 also outperformed combinations of other methods. Performance increased for human variants but much more so for other organisms. Our method's carefully calibrated reliability index informs selection of variants for experimental follow up, with the most strongly predicted half of all effect variants predicted at over 96% accuracy. As expected, the evolutionary information from automatically generated multiple sequence alignments gave the strongest signal for the prediction. However, we also optimized our new method to perform surprisingly well even without alignments. This feature reduces prediction runtime by over two orders of magnitude, enables cross-genome comparisons, and renders our new method as the best solution for the 10-20% of sequence orphans. SNAP2 is available at: https://rostlab.org/services/snap2web Definitions used Delta, input feature that results from computing the difference feature scores for native amino acid and feature scores for variant amino acid; nsSNP, non-synoymous SNP; PMD, Protein Mutant Database; SNAP, Screening for non-acceptable polymorphisms; SNP, single nucleotide polymorphism; variant, any amino acid changing sequence variant. PMID:26110438

  6. Predictive Quantum Chemistry: A Step Toward ``Chemistry Without Test Tubes''

    NASA Astrophysics Data System (ADS)

    Perera, Ajith

    2007-12-01

    The merits of the claims made in two recent papers entitled "First generation of pentazole (HN5, pentazolic acid), the final azole, and a zinc pentazolate salt in solution: A new N-dearylation of 1-(p-methoxyphenyl) pyrazoles, a 2-(p-methoxyphenyl) tetrazole and application of the methodology to 1-(p-methoxyphenyl) pentazole" (R. N. Butler, J. C. Stephan and L. A. Burke, J. Chem. Commun. 2003, 1016-1017) and "First generation of the pentazolate anion is solution is far from over" (T. Schroer, R. Haiges, S. Schneider and K. O. Christe, Chem. Commun. 2005, 1607-1609) are verified by predictive quality theoretical methods. Knowing whether the CF3OH in HF solution undergoes protonation to form CF3[OH2]+ is critical to the success of the recently proposed synthetic route to form the prototype perfluorinated alcohol, CF3OH. Chirstie and co-workers first considered the 13C and 19F shielding constants to distinguish CF3OH and CF3[OH2]+, but it turns out that they both have similar chemical shifts. Furthermore, they noted that the computed 13C chemical shifts differ by 11 ppm from the measured ones and claimed that "These findings presented a dilemma because either experimental or the calculated shifts has to be seriously flawed and, therefore chemical shifts alone it was impossible to decide whether CF3OH in liquid HF is protonated or not". Instead of chemical shifts, they propose to use 13C-19F NMR spin-spin coupling constants and argue that the observed 20 Hz difference of 1J(13C-19F) to the increase in the covalent character upon protonation. The reported discrepancy in computed and measured chemical shifts is reexamined and the spin-spin coupling constants results are verified by the predicative-level calculations.

  7. Pharmacogenetics and Predictive Testing of Drug Hypersensitivity Reactions

    PubMed Central

    Böhm, Ruwen; Cascorbi, Ingolf

    2016-01-01

    Adverse drug reactions adverse drug reaction (ADR) occur in approximately 17% of patients. Avoiding ADR is thus mandatory from both an ethical and an economic point of view. Whereas, pharmacogenetics changes of the pharmacokinetics may contribute to the explanation of some type A reactions, strong relationships of genetic markers has also been shown for drug hypersensitivity belonging to type B reactions. We present the classifications of ADR, discuss genetic influences and focus on delayed-onset hypersensitivity reactions, i.e., drug-induced liver injury, drug-induced agranulocytosis, and severe cutaneous ADR. A guidance how to read and interpret the contingency table is provided as well as an algorithm whether and how a test for a pharmacogenetic biomarker should be conducted.

  8. A test of cirrus ice crystal scattering phase functions

    NASA Astrophysics Data System (ADS)

    Field, P. R.; Baran, A. J.; Kaye, P. H.; Hirst, E.; Greenaway, R.

    2003-07-01

    In-situ ice crystal scattering has been measured in cirrus cloud with the Small Ice Detector laser scattering probe. Using light scattered from single particles (maximum dimension ~<100 μm) at 4-10° and 20-40° we have tested ice crystal scattering phase functions for spheres, hexagonal columns, hexagonal plates, polycrystals an aggregate of columns and an analytic function. We find that phase functions that lack a pronounced 22° halo are the best representatives for the example data presented here. Spherical ice particle phase functions do not satisfy the measurements.

  9. A weighted generalized score statistic for comparison of predictive values of diagnostic tests.

    PubMed

    Kosinski, Andrzej S

    2013-03-15

    Positive and negative predictive values are important measures of a medical diagnostic test performance. We consider testing equality of two positive or two negative predictive values within a paired design in which all patients receive two diagnostic tests. The existing statistical tests for testing equality of predictive values are either Wald tests based on the multinomial distribution or the empirical Wald and generalized score tests within the generalized estimating equations (GEE) framework. As presented in the literature, these test statistics have considerably complex formulas without clear intuitive insight. We propose their re-formulations that are mathematically equivalent but algebraically simple and intuitive. As is clearly seen with a new re-formulation we presented, the generalized score statistic does not always reduce to the commonly used score statistic in the independent samples case. To alleviate this, we introduce a weighted generalized score (WGS) test statistic that incorporates empirical covariance matrix with newly proposed weights. This statistic is simple to compute, always reduces to the score statistic in the independent samples situation, and preserves type I error better than the other statistics as demonstrated by simulations. Thus, we believe that the proposed WGS statistic is the preferred statistic for testing equality of two predictive values and for corresponding sample size computations. The new formulas of the Wald statistics may be useful for easy computation of confidence intervals for difference of predictive values. The introduced concepts have potential to lead to development of the WGS test statistic in a general GEE setting.

  10. Landslide velocity prediction using a rainfall to displacements transfer function. La Barmasse case study (Valais, Switzerland).

    NASA Astrophysics Data System (ADS)

    Abellán, Antonio; Michoud, Clément; Jaboyedoff, Michel; Baillifard, François; Demierre, Jonathan; Carrea, Dario

    2013-04-01

    We present a model for ground displacements prediction using a transfer function. Model was mainly tested at the Barmasse rockslide (Valais, Switzerland) which is an active structurally-controlled instability formed by intensively deformed and metamorphosed mica schists. The kinematics of the slide, which currently threatens roads and inhabitants of the Bal de Bagnes Valley, is characterized by a continuous displacement with variable rates of displacements. Indeed, the velocity is strongly affected by external forces: a sharp increase in landslide velocity is observed with a short delay after every snow melting period and after each rainfall pulse. The instability is currently monitored by different remote sensing and in situ techniques (Terrestrial LiDAR, GB Radar and extensometers). In order to predict ground displacements, we developed a new model composed by two different parts: (a) calculation of the Effective Rainfall (Peff) and (b) modelling of the landslide velocity. First of all, Peff was obtained using Thornthwaite (1946) method, which estimates the water that infiltrates into the terrain as a function of the total precipitation, Real Evapo-Transpiration (ETR) and water recharge. Afterwards, the rates of displacement were modelled through a stochastic transfer function which links the Peff (input) with daily displacements (output). Model computes the displacement rates at each time lapse (e.g. one day) as a convolution of the above mentioned transfer function times daily effective rainfall during a certain time lapse (50 days in our case). The transfer function has two components: first component account for the sudden increase of landslide velocities after each rainfall pulse and second component account for the progressive decay. The variables of these functions were optimized in Matlab in order to minimize the error between the real and the modelled velocities. The model performance was assessed for two different response functions (following either

  11. Cognitive Declines Precede and Predict Functional Declines in Aging and Alzheimer’s Disease

    PubMed Central

    Zahodne, Laura B.; Manly, Jennifer J.; MacKay-Brandt, Anna; Stern, Yaakov

    2013-01-01

    Objective To investigate the temporal ordering of cognitive and functional declines separately in older adults with or without Alzheimer’s disease (AD). Design and Setting A community-based longitudinal study of aging and dementia in Northern Manhattan (Washington Heights/Hamilton Heights Inwood Columbia Aging Project) and a multicenter, clinic-based longitudinal study of prevalent AD at Columbia University Medical Center, Johns Hopkins School of Medicine, Massachusetts General Hospital, and the Hôpital de la Salpêtrière in Paris, France (the Predictors Study). Participants 3,443 initially non-demented older adults (612 with eventual incident dementia) and 517 patients with AD. Main Outcome Measures Cognitive measures included the modified Mini-Mental State Exam and composite scores of memory and language derived from a standardized neuropsychological battery. Function was measured with the Blessed Dementia Rating Scale, completed by the participant (in the sample of non-demented older adults) or an informant (in the sample of prevalent AD patients). Data were analyzed with autoregressive cross-lagged panel analysis. Results Cognitive scores more consistently predicted subsequent functional abilities than vice versa in non-demented older adults, participants with eventual incident dementia, and patients with prevalent AD. Conclusions Cognitive declines appear to precede and cause functional declines prior to and following dementia diagnosis. Standardized neuropsychological tests are valid predictors of later functional changes in both non-demented and demented older adults. PMID:24023894

  12. Development of a Pharmacogenetic Predictive Test in asthma: proof of concept

    PubMed Central

    Wu, Ann Chen; Himes, Blanca E.; Lasky-Su, Jessica; Litonjua, Augusto; Li, Lingling; Lange, Christoph; Lima, John; Irvin, Charles G.; Weiss, Scott T.

    2013-01-01

    Objective To assess the feasibility of developing a Combined Clinical and Pharmacogenetic Predictive Test, comprised of multiple single nucleotide polymorphisms (SNPs) that is associated with poor bronchodilator response (BDR). Methods We genotyped SNPs that tagged the whole genome of the parents and children in the Childhood Asthma Management Program (CAMP) and implemented an algorithm using a family-based association test that ranked SNPs by statistical power. The top eight SNPs that were associated with BDR comprised the Pharmacogenetic Predictive Test. The Clinical Predictive Test was comprised of baseline forced expiratory volume in 1 s (FEV1). We evaluated these predictive tests and a Combined Clinical and Pharmacogenetic Predictive Test in three distinct populations: the children of the CAMP trial and two additional clinical trial populations of asthma. Our outcome measure was poor BDR, defined as BDR of less than 20th percentile in each population. BDR was calculated as the percent difference between the prebronchodilator and postbronchodilator (two puffs of albuterol at 180 μg/puff) FEV1 value. To assess the predictive ability of the test, the corresponding area under the receiver operating characteristic curves (AUROCs) were calculated for each population. Results The AUROC values for the Clinical Predictive Test alone were not significantly different from 0.50, the AUROC of a random classifier. Our Combined Clinical and Pharmacogenetic Predictive Test comprised of genetic polymorphisms in addition to FEV1 predicted poor BDR with an AUROC of 0.65 in the CAMP children (n= 422) and 0.60 (n= 475) and 0.63 (n= 235) in the two independent populations. Both the Combined Clinical and Pharmacogenetic Predictive Test and the Pharmacogenetic Predictive Test were significantly more accurate than the Clinical Predictive Test (AUROC between 0.44 and 0.55) in each of the populations. Conclusion Our finding that genetic polymorphisms with a clinical trait are

  13. Percutaneous Nerve Evaluation Test Versus Staged Test Trials for Sacral Neuromodulation: Sensitivity, Specificity, and Predictive Values of Each Technique

    PubMed Central

    Hassouna, Magdy

    2016-01-01

    Purpose InterStim device is an U.S. Food and Drug Administration approved minimal invasive therapy for sacral neuromodulation for lower urinary tract dysfunction. Before InterStim implantation, a trial with the appropriate screening tests is required to determine patient therapy eligibility. There are two different techniques for patient screening: percutaneous nerve evaluation (PNE) test and staged test. Few studies have reported success and failure rates for each technique. However, test sensitivity and predictive values of either test have not been studied. The aim of our study was to determine the sensitivity and specificity of each test and to establish a decision algorithm for the most appropriate testing method to be used as a screening test. Methods This cross-sectional study was conducted from August 2009 to February 2012 and included patients with lower urinary tract dysfunction who participated in the stimulation test trial. Patients underwent PNE as the first stimulation test, while those who encountered technical difficulty during PNE or electrode migration underwent staged testing. Results A total of 213 patients, including 172 female and 41 male subjects, underwent PNE. The patients’ diagnoses included refractory overactive bladder (47.9%), nonobstructive urinary retention (29.6%), and frequency urgency syndrome (22.1%). A total of 202 patients were screened with PNE and 10 patients with staged testing. Overall sensitivity of PNE was 87.3%, and it was 90% for staged test. PNE specificity was 98.5% as compared to 92.9% for staged test. Positive and negative predictive values for PNE were 99% and 82.1% and for staged test were 90% and 92.9%, respectively. Conclusions PNE test has high specificity and positive predictive value. We recommend PNE, a simple office-based, less expensive procedure as the first option for screening. PMID:27706006

  14. Testing an application of a biotic ligand model to predict acute toxicity of metal mixtures to rainbow trout.

    PubMed

    Iwasaki, Yuichi; Kamo, Masashi; Naito, Wataru

    2015-04-01

    The authors tested the applicability of a previously developed biotic ligand model (BLM) to predict acute toxicity of single metals and metal mixtures (cadmium, lead, and zinc) to rainbow trout fry (Oncorhynchus mykiss) from a single available dataset. The BLM used in the present study hypothesizes that metals inhibit an essential cation (calcium) and organisms die as a result of its deficiency, leading to an assumption that the proportion of metal-binding ligand (f) is responsible for the toxic effects of metals on the survival of rainbow trout. The f value is a function of free-ion concentrations of metals computed by a chemical speciation model, and the function has affinity constants as model parameters. First, the survival effects of single metals were statistically modeled separately (i.e., f-survival relationship) by using the generalized linear mixed model with binomial distribution. The modeled responses of survival rates to f overlapped reasonably irrespective of metals tested, supporting the theoretical prediction from the BLM that f-survival relationships are comparable regardless of metal species. The authors thus developed the generalized linear mixed model based on all data pooled across the single-metal tests. The best-fitted model well predicted the survival responses observed in mixture tests (r = 0.97), providing support for the applicability of the BLM to predict effects of metal mixtures.

  15. An automated miniaturized Haploscope for testing binocular visual function

    NASA Technical Reports Server (NTRS)

    Decker, T. A.; Williams, R. E.; Kuether, C. L.; Wyman-Cornsweet, D.

    1976-01-01

    A computer-controlled binocular vision testing device has been developed as one part of a system designed for NASA to test the vision of astronauts during spaceflight. The device, called the Mark III Haploscope, utilizes semi-automated psychophysical test procedures to measure visual acuity, stereopsis, phorias, fixation disparity and accommodation/convergence relationships. All tests are self-administered, yield quantitative data and may be used repeatedly without subject memorization. Future applications of this programmable, compact device include its use as a clinical instrument to perform routine eye examinations or vision screening, and as a research tool to examine the effects of environment or work-cycle upon visual function.

  16. Testing for cognitive function in animals in a regulatory context.

    PubMed

    Bushnell, Philip J

    2015-01-01

    Superior cognitive functions have allowed the human species to proliferate in a world of incredible biological diversity. Threats to these essential capacities cannot be ignored, and a strategy is needed to evaluate the hazard posed by exposure to chemical and other agents. Because people exposed to chemicals often complain about confusion and forgetfulness, it is commonly thought that cognitive functions should be sensitive indicators of adverse consequences of chemical exposure. For these reasons, complex tests of cognitive function have been developed and deployed in experimental animal laboratories for decades. However, the results of these tests are rarely used as points of departure for chemical risk assessments. Due to their high cost in time, animals, and equipment, the efficacy and utility of these tests need to be evaluated in relation to cheaper and faster whole-animal screening methods. This review examines evidence for the assertions that cognitive functions represent uniquely sensitive indicators of chemical exposure, and that animal models of these functions are necessary to detect and quantify the neurotoxicity of chemicals. Studies conducted since the early 1980s to compare these approaches to assess the neurotoxicity of chemicals are reviewed for both adult and perinatal exposures in experimental rodents. Forty-one studies of 35 chemicals were found that directly compared acute effects using complex tests (i.e., tests that require training animals) with acute effects using screening tests (i.e., tests that do not require training animals) in adult rodents. Complex tests detected effects of three substances (bitertanol, iso-amyl nitrite, and Pfiesteria toxin) that had no effect on screening tests; for an additional five chemicals (carbaryl, deltamethrin, methyl mercury, tetraethyl tin, and Isopar-C), complex tests identified effects at lower doses than did screening tests. Fewer comparable cases were found for developmental exposures: screening and

  17. Amylase-creatinine clearance ratio. A simple test to predict gentamicin nephrotoxicity.

    PubMed

    Aderka, D; Tene, M; Graff, E; Levo, Y

    1988-05-01

    The initial target of aminoglycoside nephrotoxicity is the proximal tubule. Yet, no simple test is available to predict such toxicity. Taking advantage of the fact that amylase is filtered in the glomerulus and reabsorbed by the proximal tubules, we prospectively examined in 23 patients if changes in renal amylase creatinine clearance ratio (ACCR) can predict gentamicin nephrotoxicity. Eighteen of these patients had an initial creatinine clearance (rCcr) above 30 mL/min. Eleven of them (group A) had an ACCR above 3.5% (control 3% +/- 1.03%) and all exhibited an average reduction of 32.2% +/- 11.6% in rCcr following one week of gentamicin therapy. In contrast, only one of seven patients (group B) with an initial ACCR below 3.5% had a reduction, albeit transient, in rCcr. During gentamicin therapy, group A patients had a further increase in ACCR which was proportional to the reduction observed in rCcr (r = -.54). Our preliminary data suggest that ACCR may prove a simple and possibly a reliable predictor of kidney function deterioration during gentamicin therapy in patients with rCcr above 30 mL/min: patients with pretherapy ACCR above 3.5% may exhibit a deterioration in the creatinine clearance during the first week of therapy. For patients with pretherapy renal failure (rCcr less than 30 mL/min) the creatinine levels (but not the ACCR) seem to retain their significance in predicting and monitoring further renal function deterioration during aminoglycoside therapy.

  18. Amylase-creatinine clearance ratio. A simple test to predict gentamicin nephrotoxicity.

    PubMed

    Aderka, D; Tene, M; Graff, E; Levo, Y

    1988-05-01

    The initial target of aminoglycoside nephrotoxicity is the proximal tubule. Yet, no simple test is available to predict such toxicity. Taking advantage of the fact that amylase is filtered in the glomerulus and reabsorbed by the proximal tubules, we prospectively examined in 23 patients if changes in renal amylase creatinine clearance ratio (ACCR) can predict gentamicin nephrotoxicity. Eighteen of these patients had an initial creatinine clearance (rCcr) above 30 mL/min. Eleven of them (group A) had an ACCR above 3.5% (control 3% +/- 1.03%) and all exhibited an average reduction of 32.2% +/- 11.6% in rCcr following one week of gentamicin therapy. In contrast, only one of seven patients (group B) with an initial ACCR below 3.5% had a reduction, albeit transient, in rCcr. During gentamicin therapy, group A patients had a further increase in ACCR which was proportional to the reduction observed in rCcr (r = -.54). Our preliminary data suggest that ACCR may prove a simple and possibly a reliable predictor of kidney function deterioration during gentamicin therapy in patients with rCcr above 30 mL/min: patients with pretherapy ACCR above 3.5% may exhibit a deterioration in the creatinine clearance during the first week of therapy. For patients with pretherapy renal failure (rCcr less than 30 mL/min) the creatinine levels (but not the ACCR) seem to retain their significance in predicting and monitoring further renal function deterioration during aminoglycoside therapy. PMID:2452611

  19. Predictability Effects on Durations of Content and Function Words in Conversational English

    SciTech Connect

    Bell, Alan; Brenier, Jason; Gregory, Michelle L.; girand, cynthia; Jurafsky, Daniel

    2009-01-01

    Content and function word duration are affected differently by their frequency and predictability. Regression analyses of conversational speech show that content words are shorter when they are more frequent, but function words are not. Repeated content words are shorter, but function words are not. Furthermore, function words have shorter pronunciations, after controlling for frequency and predictability. both content and function words are strongly affected by predictability from the word following them, and only very frequent function words show sensitivity to predictability from the preceding word. The results support the view that content and function words are accessed by different production mechanisms. We argue that words’ form differences due to frequency or repetition stem from their faster or slower lexical access, mediated by a general mechanism that coordinates the pace of higher-level planning and the execution of the articulatory plan.

  20. FIFE data analysis: Testing BIOME-BGC predictions for grasslands

    NASA Technical Reports Server (NTRS)

    Hunt, E. Raymond, Jr.

    1994-01-01

    The First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE) was conducted in a 15 km by 15 km research area located 8 km south of Manhattan, Kansas. The site consists primarily of native tallgrass prairie mixed with gallery oak forests and croplands. The objectives of FIFE are to better understand the role of biology in controlling the interactions between the land and the atmosphere, and to determine the value of remotely sensed data for estimating climatological parameters. The goals of FIFE are twofold: the upscale integration of models, and algorithm development for satellite remote sensing. The specific objectives of the field campaigns carried out in 1987 and 1989 were the simultaneous acquisition of satellite, atmospheric, and surface data; and the understanding of the processes controlling surface energy and mass exchange. Collected data were used to study the dynamics of various ecosystem processes (photosynthesis, evaporation and transpiration, autotrophic and heterotrophic respiration, etc.). Modelling terrestrial ecosystems at scales larger than that of a homogeneous plot led to the development of simple, generalized models of biogeochemical cycles that can be accurately applied to different biomes through the use of remotely sensed data. A model was developed called BIOME-BGC (for BioGeochemical Cycles) from a coniferous forest ecosystem model, FOREST-BGC, where a biome is considered a combination of a life forms in a specified climate. A predominately C4-photosynthetic grassland is probably the most different from a coniferous forest possible, hence the FIFE site was an excellent study area for testing BIOME-BGC. The transition from an essentially one-dimensional calculation to three-dimensional, landscape scale simulations requires the introduction of such factors as meteorology, climatology, and geomorphology. By using remotely sensed geographic information data for important model inputs, process

  1. A Computerized Test of Self-Control Predicts Classroom Behavior

    PubMed Central

    Hoerger, Marguerite L; Mace, F. Charles

    2006-01-01

    We assessed choices on a computerized test of self-control (CTSC) for a group of children with features of attention deficit hyperactivity disorder (ADHD) and a group of controls. Thirty boys participated in the study. Fifteen of the children had been rated by their parents as hyperactive and inattentive, and 15 were age- and gender-matched controls in the same classroom. The children were observed in the classroom for three consecutive mornings, and data were collected on their activity levels and attention. The CTSC consisted of two tasks. In the delay condition, children chose to receive three rewards after a delay of 60 s or one reward immediately. In the task-difficulty condition, the children chose to complete a difficult math problem and receive three rewards or complete an easier problem for one reward. The children with ADHD features made more impulsive choices than their peers during both conditions, and these choices correlated with measures of their activity and attention in the classroom. PMID:16813037

  2. What Predicts Changes in Useful Field of View Test Performance?

    PubMed Central

    Lunsman, Melissa; Edwards, Jerri D.; Andel, Ross; Small, Brent J.; Ball, Karlene K.; Roenker, Daniel L.

    2015-01-01

    The Useful Field of View Test (UFOV1) has been used to examine age-related changes in visual processing and cognition and as an indicator of everyday performance outcomes, particularly driving, for over 20 years. How UFOV performance changes with age and what may impact such changes have not previously been investigated longitudinally. Predictors of change in UFOV performance over a five-year period among control-group participants (n = 690) from the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) study were examined. Random effects models were estimated with four-subtest total UFOV as the outcome and baseline age, education, gender, race, visual acuity, depressive symptoms, mental status, and self-rated health, as well as attrition, as predictors. UFOV performance generally followed a curvilinear pattern, improving and then declining over time. Only increased age was consistently related to greater declines in UFOV performance over time. UFOV and WAIS-R Digit Symbol Substitution (DSS), a standard measure of cognitive speed, had similar trajectories of change. The implications of these results are discussed. PMID:19140660

  3. Pulmonary Function Testing After Stereotactic Body Radiotherapy to the Lung

    SciTech Connect

    Bishawi, Muath; Kim, Bong; Moore, William H.; Bilfinger, Thomas V.

    2012-01-01

    Purpose: Surgical resection remains the standard of care for operable early-stage non-small-cell lung cancer (NSCLC). However, some patients are not fit for surgery because of comorbidites such as chronic obstructive pulmonary disease (COPD) and other medical conditions. We aimed to evaluate pulmonary function and tumor volume before and after stereotactic body radiotherapy (SBRT) for patients with and without COPD in early-stage lung cancer. Methods and Materials: A review of prospectively collected data of Stage I and II lung cancers, all treated with SBRT, was performed. The total SBRT treatment was 60 Gy administered in three 20 Gy fractions. The patients were analyzed based on their COPD status, using their pretreatment pulmonary function test cutoffs as established by the American Thoracic Society guidelines (forced expiratory volume [FEV]% {<=}50% predicted, FEV%/forced vital capacity [FVC]% {<=}70%). Changes in tumor volume were also assessed by computed tomography. Results: Of a total of 30 patients with Stage I and II lung cancer, there were 7 patients in the COPD group (4 men, 3 women), and 23 in t he No-COPD group (9 men, 14 women). At a mean follow-up time of 4 months, for the COPD and No-COPD patients, pretreatment and posttreatment FEV% was similar: 39 {+-} 5 vs. 40 {+-} 9 (p = 0.4) and 77 {+-} 0.5 vs. 73 {+-} 24 (p = 0.9), respectively. The diffusing capacity of the lungs for carbon monoxide (DL{sub CO}) did significantly increase for the No-COPD group after SBRT treatment: 60 {+-} 24 vs. 69 {+-} 22 (p = 0.022); however, DL{sub CO} was unchanged for the COPD group: 49 {+-} 13 vs. 50 {+-} 14 (p = 0.8). Although pretreatment tumor volume was comparable for both groups, tumor volume significantly shrank in the No-COPD group from 19 {+-} 24 to 9 {+-} 16 (p < 0.001), and there was a trend in the COPD patients from 12 {+-} 9 to 6 {+-} 5 (p = 0.06). Conclusion: SBRT did not seem to have an effect on FEV{sub 1} and FVC, but it shrank tumor volume and

  4. Unique sequences and predicted functions of myosins in Tetrahymena thermophila.

    PubMed

    Sugita, Maki; Iwataki, Yoshinori; Nakano, Kentaro; Numata, Osamu

    2011-07-01

    Myosins are eukaryotic actin-dependent molecular motors that play important roles in many cellular events. The function of each myosin is determined by a variety of functional domains in its tail region. In some major model organisms, the functions and properties of myosins have been investigated based on their amino acid sequences. However, in protists, myosins have been little studied beyond the level of genome sequences. We therefore investigated the mRNA expression levels and amino acid sequences of 13 myosin genes in the ciliate Tetrahymena thermophila. This study is an overview of myosins in T. thermophila, which has no typical myosins, such as class I, II, or V myosins. We showed that all 13 myosins were expressed in vegetative cells. Furthermore, these myosins could be divided into 3 subclasses based on four functional domains in their tail regions. Subclass 1 comprised of 8 myosins has both MyTH4 and FERM domains, and has a potential to function in vesicle transport or anchoring between membrane and actin filaments. Subclass 2 comprised of 4 myosins has RCC1 (regulator of chromosome condensation 1) domains, which are found only in some protists, and may have unconventional features. Subclass 3 is comprised of one myosin, which has a long coiled-coil domain like class II myosin. In addition, phylogenetic analysis on the basis of motor domains showed that T. thermophila myosins are separated into two clusters: one consists of subclasses 1 and 2, and the other consists of subclass 3.

  5. Considerations on the Use of 3-D Geophysical Models to Predict Test Ban Monitoring Observables

    SciTech Connect

    Harris, D B; Zucca, J J; McCallen, D B; Pasyanos, M E; Flanagan, M P; Myers, S C; Walter, W R; Rodgers, A J; Harben, P E

    2007-07-09

    The use of 3-D geophysical models to predict nuclear test ban monitoring observables (phase travel times, amplitudes, dispersion, etc.) is widely anticipated to provide improvements in the basic seismic monitoring functions of detection, association, location, discrimination and yield estimation. A number of questions arise when contemplating a transition from 1-D, 2-D and 2.5-D models to constructing and using 3-D models, among them: (1) Can a 3-D geophysical model or a collection of 3-D models provide measurably improved predictions of seismic monitoring observables over existing 1-D models, or 2-D and 2 1/2-D models currently under development? (2) Is a single model that can predict all observables achievable, or must separate models be devised for each observable? How should joint inversion of disparate observable data be performed, if required? (3) What are the options for model representation? Are multi-resolution models essential? How does representation affect the accuracy and speed of observable predictions? (4) How should model uncertainty be estimated, represented and how should it be used? Are stochastic models desirable? (5) What data types should be used to construct the models? What quality control regime should be established? (6) How will 3-D models be used in operations? Will significant improvements in the basic monitoring functions result from the use of 3-D models? Will the calculation of observables through 3-D models be fast enough for real-time use or must a strategy of pre-computation be employed? (7) What are the theoretical limits to 3-D model development (resolution, uncertainty) and performance in predicting monitoring observables? How closely can those limits be approached with projected data availability, station distribution and inverse methods? (8) What priorities should be placed on the acquisition of event ground truth information, deployment of new stations, development of new inverse techniques, exploitation of large

  6. Numerical prediction of basalt response for near-surface test facility heater tests No. 1 and No. 2

    SciTech Connect

    Hocking, G.; Williams, J.R.; Boonlualohr, P.; Mathews, I.; Mustoe, G.

    1980-11-01

    This report details the numerical predictions undertaken by Dames and Moore for Rockwell Hanford Operations' Basalt Waste Isolation Project. Predictions are made for the temperatures, stresses, strains and displacements in the basalt around Full-Scale Heater Tests No. 1 and No. 2 at the Near-Surface Test Facility using the finite element code DAMSWEL. The rock around the main heaters was modeled using an axisymmetric idealization in which deformational properties were transversely isotropic with a bilinear stress/strain relationship which was independent of temperature. The selection of the input parameters represents an engineering assessment of their values based on the results of laboratory tests and in situ measurements. The predictive modeling analysis, using the best information available as of April 1980, was completed prior to test startup. Additional information on geology, geological characterization, rock-mass characterization, laboratory properties, and field properties of basalt is being acquired on a regular basis as part of the overall Near-Surface Test Facility test program. An assessment of the effect of additions to the data base upon the predictive modeling and test analysis shall be made on a periodic basis.

  7. Executive function on the Psychology Experiment Building Language tests

    PubMed Central

    Li, Victoria; Eiwaz, Massarra A.; Kobel, Yuliyana V.; Benice, Ted S.; Chu, Alex M.; Olsen, Reid H. J.; Rice, Douglas Z.; Gray, Hilary M.; Mueller, Shane T.

    2013-01-01

    The measurement of executive function has a long history in clinical and experimental neuropsychology. The goal of the present report was to determine the profile of behavior across the lifespan on four computerized measures of executive function contained in the recently developed Psychology Experiment Building Language (PEBL) test battery http://pebl.sourceforge.net/ and evaluate whether this pattern is comparable to data previously obtained with the non-PEBL versions of these tests. Participants (N = 1,223; ages, 5–89 years) completed the PEBL Trail Making Test (pTMT), the Wisconsin Card Sort Test (pWCST; Berg, Journal of General Psychology, 39, 15–22, 1948; Grant & Berg, Journal of Experimental Psychology, 38, 404–411, 1948), the Tower of London (pToL), or a time estimation task (Time-Wall). Age-related effects were found over all four tests, especially as age increased from young childhood through adulthood. For several tests and measures (including pToL and pTMT), age-related slowing was found as age increased in adulthood. Together, these findings indicate that the PEBL tests provide valid and versatile new research tools for measuring executive functions. PMID:21534005

  8. Functional prediction: identification of protein orthologs and paralogs.

    PubMed Central

    Chen, R.; Jeong, S. S.

    2000-01-01

    Orthologs typically retain the same function in the course of evolution. Using beta-decarboxylating dehydrogenase family as a model, we demonstrate that orthologs can be confidently identified. The strategy is based on our recent findings that substitutions of only a few amino acid residues in these enzymes are sufficient to exchange substrate and coenzyme specificities. Hence, the few major specificity determinants can serve as reliable markers for determining orthologous or paralogous relationships. The power of this approach has been demonstrated by correcting similarity-based functional misassignment and discovering new genes and related pathways, and should be broadly applicable to other enzyme families. PMID:11206056

  9. Testing earthquake prediction algorithms: Statistically significant advance prediction of the largest earthquakes in the Circum-Pacific, 1992-1997

    USGS Publications Warehouse

    Kossobokov, V.G.; Romashkova, L.L.; Keilis-Borok, V. I.; Healy, J.H.

    1999-01-01

    Algorithms M8 and MSc (i.e., the Mendocino Scenario) were used in a real-time intermediate-term research prediction of the strongest earthquakes in the Circum-Pacific seismic belt. Predictions are made by M8 first. Then, the areas of alarm are reduced by MSc at the cost that some earthquakes are missed in the second approximation of prediction. In 1992-1997, five earthquakes of magnitude 8 and above occurred in the test area: all of them were predicted by M8 and MSc identified correctly the locations of four of them. The space-time volume of the alarms is 36% and 18%, correspondingly, when estimated with a normalized product measure of empirical distribution of epicenters and uniform time. The statistical significance of the achieved results is beyond 99% both for M8 and MSc. For magnitude 7.5 + , 10 out of 19 earthquakes were predicted by M8 in 40% and five were predicted by M8-MSc in 13% of the total volume considered. This implies a significance level of 81% for M8 and 92% for M8-MSc. The lower significance levels might result from a global change in seismic regime in 1993-1996, when the rate of the largest events has doubled and all of them become exclusively normal or reversed faults. The predictions are fully reproducible; the algorithms M8 and MSc in complete formal definitions were published before we started our experiment [Keilis-Borok, V.I., Kossobokov, V.G., 1990. Premonitory activation of seismic flow: Algorithm M8, Phys. Earth and Planet. Inter. 61, 73-83; Kossobokov, V.G., Keilis-Borok, V.I., Smith, S.W., 1990. Localization of intermediate-term earthquake prediction, J. Geophys. Res., 95, 19763-19772; Healy, J.H., Kossobokov, V.G., Dewey, J.W., 1992. A test to evaluate the earthquake prediction algorithm, M8. U.S. Geol. Surv. OFR 92-401]. M8 is available from the IASPEI Software Library [Healy, J.H., Keilis-Borok, V.I., Lee, W.H.K. (Eds.), 1997. Algorithms for Earthquake Statistics and Prediction, Vol. 6. IASPEI Software Library]. ?? 1999 Elsevier

  10. Validity of the Optometry Admission Test in Predicting Performance in Schools and Colleges of Optometry.

    ERIC Educational Resources Information Center

    Kramer, Gene A.; Johnston, JoElle

    1997-01-01

    A study examined the relationship between Optometry Admission Test scores and pre-optometry or undergraduate grade point average (GPA) with first and second year performance in optometry schools. The test's predictive validity was limited but significant, and comparable to those reported for other admission tests. In addition, the scores…

  11. Submaximal Treadmill Exercise Test to Predict VO[subscript 2]max in Fit Adults

    ERIC Educational Resources Information Center

    Vehrs, Pat R.; George, James D.; Fellingham, Gilbert W.; Plowman, Sharon A.; Dustman-Allen, Kymberli

    2007-01-01

    This study was designed to develop a single-stage submaximal treadmill jogging (TMJ) test to predict VO[subscript 2]max in fit adults. Participants (N = 400; men = 250 and women = 150), ages 18 to 40 years, successfully completed a maximal graded exercise test (GXT) at 1 of 3 laboratories to determine VO[subscript 2]max. The TMJ test was completed…

  12. Experience Tables, Predictive Validity Studies, and Validation of Placement Tables for the MDTP Placement Tests.

    ERIC Educational Resources Information Center

    College of the Canyons, Valencia, CA. Office of Institutional Development.

    California's College of the Canyons has used the four Mathematics Diagnostic Testing Project (MDTP) tests to assess students' abilities in basic and college math since spring 1989. These four reports dated June 1993, July 1993, May 1994, and June 1994 examine the predictive validity of the MDTP tests and the cut scores used to place students. The…

  13. Predictive Properties of the Gesell School Readiness Screening Test within Samples from Two Treatment Contexts.

    ERIC Educational Resources Information Center

    Banerji, Madhabi

    The predictive properties of the Gesell School Readiness Screening Test (GSRT) were examined, taking into account the stated purposes of the test and the context of test use. Two samples were used: (1) a control sample of 55 students (21 males and 34 females) whose GSRT scores were not used for placement or tracking; and (2) a treatment sample of…

  14. Measuring individuals' response quality in self-administered psychological tests: an introduction to Gendre's functional method.

    PubMed

    Dupuis, Marc; Meier, Emanuele; Capel, Roland; Gendre, Francis

    2015-01-01

    The functional method is a new test theory using a new scoring method that assumes complexity in test structure, and thus takes into account every correlation between factors and items. The main specificity of the functional method is to model test scores by multiple regression instead of estimating them by using simplistic sums of points. In order to proceed, the functional method requires the creation of hyperspherical measurement space, in which item responses are expressed by their correlation with orthogonal factors. This method has three main qualities. First, measures are expressed in the absolute metric of correlations; therefore, items, scales and persons are expressed in the same measurement space using the same single metric. Second, factors are systematically orthogonal and without errors, which is optimal in order to predict other outcomes. Such predictions can be performed to estimate how one would answer to other tests, or even to model one's response strategy if it was perfectly coherent. Third, the functional method provides measures of individuals' response validity (i.e., control indices). Herein, we propose a standard procedure in order to identify whether test results are interpretable and to exclude invalid results caused by various response biases based on control indices.

  15. Simple functional performance tests and mortality in COPD

    PubMed Central

    Puhan, Milo A.; Siebeling, Lara; Zoller, Marco; Muggensturm, Patrick; ter Riet, Gerben

    2013-01-01

    Exercise tests are important to characterise chronic obstructive pulmonary disease patients and predict their prognosis, but are often not available outside of rehabilitation or research settings. Our aim was to assess the predictive performance of the sit-to-stand and handgrip strength tests. The prospective cohort study in Dutch and Swiss primary care settings included a broad spectrum of patients (n=409) with Global Initiative for Chronic Obstructive Lung Disease stages II to IV. To assess the association of the tests with outcomes, we used Cox proportional hazards (mortality), negative binomial (centrally adjudicated exacerbations) and mixed linear regression models (longitudinal health-related quality of life) while adjusting for age, sex and severity of disease. The sit-to-stand test was strongly (adjusted hazard ratio per five more repetitions of 0.58, 95% CI 0.40–0.85; p=0.004) and the handgrip strength test moderately strongly (0.84, 95% CI 0.72–1.00; p=0.04) associated with mortality. Both tests were also significantly associated with health-related quality of life but not with exacerbations. The sit-to-stand test alone was a stronger predictor of 2-year mortality (area under curve 0.78) than body mass index (0.52), forced expiratory volume in 1 s (0.61), dyspnoea (0.63) and handgrip strength (0.62). The sit-to-stand test may close an important gap in the evaluation of exercise capacity and prognosis of chronic obstructive pulmonary disease patients across practice settings. PMID:23520321

  16. Prediction of Functional Outcome in Individuals at Clinical High Risk for Psychosis

    PubMed Central

    Carrión, Ricardo E.; McLaughlin, Danielle; Goldberg, Terry E.; Auther, Andrea M.; Olsen, Ruth H.; Olvet, Doreen M.; Correll, Christoph U.; Cornblatt, Barbara A.

    2014-01-01

    Importance A major public health concern associated with schizophrenia and psychotic disorders is the long-term disability that involves impaired cognition, lack of social support, and an inability to function independently in the community. A critical goal of early detection and intervention studies in psychosis is therefore to understand the factors leading to this often profound impairment. Objective To develop a predictive model of functional (social and role) outcome in a clinical high-risk sample for psychosis. Design Prospective, naturalistic, longitudinal 3- to 5-year follow-up study. Setting The Recognition and Prevention Program in New York, a research clinic located in the Zucker Hillside Hospital in New York. Participants One hundred one treatment-seeking patients at clinical high risk for psychosis. Ninety-two (91%) were followed up prospectively for a mean (SD) of 3 (1.6) years. Intervention Neurocognitive and clinical assessment. Main Outcomes and Measures The primary outcome variables were social and role functioning at the last follow-up visit. Results Poor social outcome was predicted by reduced processing speed (odds ratio [OR], 1.38; 95% CI, 1.050-1.823; P = .02), impaired social functioning at baseline (OR, 1.85; 95% CI, 1.258-2.732; P = .002), and total disorganized symptoms (OR, 5.06; 95% CI, 1.548-16.527; P = .007). Reduced performance on tests for verbal memory (OR, 1.74; 95% CI, 1.169-2.594; P = .006), role functioning at baseline (OR, 1.34; 95% CI, 1.053-1.711; P = .02), and motor disturbances (OR, 1.77; 95% CI, 1.060-2.969; P = .03) predicted role outcome. The areas under the curve for the social and role prediction models were 0.824 (95% CI, 0.736-0.913; P < .001) and 0.77 (95% CI, 0.68-0.87; P < .001), respectively, demonstrating a high discriminative ability. In addition, poor functional outcomes were not entirely dependent on the development of psychosis, because 40.3% and 45.5% of nonconverters at clinical high risk had poor social

  17. An empirical test of a diffusion model: predicting clouded apollo movements in a novel environment.

    PubMed

    Ovaskainen, Otso; Luoto, Miska; Ikonen, Iiro; Rekola, Hanna; Meyke, Evgeniy; Kuussaari, Mikko

    2008-05-01

    Functional connectivity is a fundamental concept in conservation biology because it sets the level of migration and gene flow among local populations. However, functional connectivity is difficult to measure, largely because it is hard to acquire and analyze movement data from heterogeneous landscapes. Here we apply a Bayesian state-space framework to parameterize a diffusion-based movement model using capture-recapture data on the endangered clouded apollo butterfly. We test whether the model is able to disentangle the inherent movement behavior of the species from landscape structure and sampling artifacts, which is a necessity if the model is to be used to examine how movements depend on landscape structure. We show that this is the case by demonstrating that the model, parameterized with data from a reference landscape, correctly predicts movements in a structurally different landscape. In particular, the model helps to explain why a movement corridor that was constructed as a management measure failed to increase movement among local populations. We illustrate how the parameterized model can be used to derive biologically relevant measures of functional connectivity, thus linking movement data with models of spatial population dynamics.

  18. Borderline Personality Traits and Disorder: Predicting Prospective Patient Functioning

    ERIC Educational Resources Information Center

    Hopwood, Christopher J.; Zanarini, Mary C.

    2010-01-01

    Objective: Decisions about the composition of personality assessment in the "Diagnostic and Statistical Manual of Mental Disorders" (5th ed.; DSM-V) will be heavily influenced by the clinical utility of candidate constructs. In this study, we addressed 1 aspect of clinical utility by testing the incremental validity of 5-factor model (FFM)…

  19. Behavioral, Brain Imaging and Genomic Measures to Predict Functional Outcomes Post - Bed Rest and Spaceflight

    NASA Technical Reports Server (NTRS)

    Mulavara, A. P.; DeDios, Y. E.; Gadd, N. E.; Caldwell, E. E.; Batson, C. D.; Goel, R.; Seidler, R. D.; Oddsson, L.; Zanello, S.; Clarke, T.; Peters, B.; Cohen, H. S.; Reschke, M.; Wood, S.; Bloomberg, J. J.

    2016-01-01

    Astronauts experience sensorimotor disturbances during their initial exposure to microgravity and during the re-adaptation phase following a return to an Earth-gravitational environment. These alterations may disrupt crewmembers' ability to perform mission critical functional tasks requiring ambulation, manual control and gaze stability. Interestingly, astronauts who return from spaceflight show substantial differences in their abilities to readapt to a gravitational environment. The ability to predict the manner and degree to which individual astronauts would be affected would improve the effectiveness of countermeasure training programs designed to enhance sensorimotor adaptability. For such an approach to succeed, we must develop predictive measures of sensorimotor adaptability that will allow us to foresee, before actual spaceflight, which crewmembers are likely to experience the greatest challenges to their adaptive capacities. The goals of this project are to identify and characterize this set of predictive measures. Our approach includes: 1) behavioral tests to assess sensory bias and adaptability quantified using both strategic and plastic-adaptive responses; 2) imaging to determine individual brain morphological and functional features, using structural magnetic resonance imaging (MRI), diffusion tensor imaging, resting state functional connectivity MRI, and sensorimotor adaptation task-related functional brain activation; and 3) assessment of genotypic markers of genetic polymorphisms in the catechol-O-methyl transferase, dopamine receptor D2, and brain-derived neurotrophic factor genes and genetic polymorphisms of alpha2-adrenergic receptors that play a role in the neural pathways underlying sensorimotor adaptation. We anticipate that these predictive measures will be significantly correlated with individual differences in sensorimotor adaptability after long-duration spaceflight and exposure to an analog bed rest environment. We will be conducting a

  20. GROUND-WATER MODEL TESTING: SYSTEMATIC EVALUATION AND TESTING OF CODE FUNCTIONALITY AND PERFORMANCE

    EPA Science Inventory

    Effective use of ground-water simulation codes as management decision tools requires the establishment of their functionality, performance characteristics, and applicability to the problem at hand. This is accomplished through application of a systematic code-testing protocol and...

  1. Outcomes of Anatomical versus Functional Testing for Coronary Artery Disease

    PubMed Central

    Douglas, Pamela S.; Hoffmann, Udo; Patel, Manesh R.; Mark, Daniel B.; Al-Khalidi, Hussein R.; Cavanaugh, Brendan; Cole, Jason; Dolor, Rowena J.; Fordyce, Christopher B.; Huang, Megan; Khan, Muhammad Akram; Kosinski, Andrzej S.; Krucoff, Mitchell W.; Malhotra, Vinay; Picard, Michael H.; Udelson, James E.; Velazquez, Eric J.; Yow, Eric; Cooper, Lawton S.; Lee, Kerry L.

    2015-01-01

    BACKGROUND Many patients have symptoms suggestive of coronary artery disease (CAD) and are often evaluated with the use of diagnostic testing, although there are limited data from randomized trials to guide care. METHODS We randomly assigned 10,003 symptomatic patients to a strategy of initial anatomical testing with the use of coronary computed tomographic angiography (CTA) or to functional testing (exercise electrocardiography, nuclear stress testing, or stress echocardiography). The composite primary end point was death, myocardial infarction, hospitalization for unstable angina, or major procedural complication. Secondary end points included invasive cardiac catheterization that did not show obstructive CAD and radiation exposure. RESULTS The mean age of the patients was 60.8±8.3 years, 52.7% were women, and 87.7% had chest pain or dyspnea on exertion. The mean pretest likelihood of obstructive CAD was 53.3±21.4%. Over a median follow-up period of 25 months, a primary end-point event occurred in 164 of 4996 patients in the CTA group (3.3%) and in 151 of 5007 (3.0%) in the functional-testing group (adjusted hazard ratio, 1.04; 95% confidence interval, 0.83 to 1.29; P = 0.75). CTA was associated with fewer catheterizations showing no obstructive CAD than was functional testing (3.4% vs. 4.3%, P = 0.02), although more patients in the CTA group underwent catheterization within 90 days after randomization (12.2% vs. 8.1%). The median cumulative radiation exposure per patient was lower in the CTA group than in the functional-testing group (10.0 mSv vs. 11.3 mSv), but 32.6% of the patients in the functional-testing group had no exposure, so the overall exposure was higher in the CTA group (mean, 12.0 mSv vs. 10.1 mSv; P<0.001). CONCLUSIONS In symptomatic patients with suspected CAD who required noninvasive testing, a strategy of initial CTA, as compared with functional testing, did not improve clinical outcomes over a median follow-up of 2 years. (Funded by the

  2. Low yield of unselected testing in patients with acutely abnormal liver function tests

    PubMed Central

    Chadwick, Andrew

    2015-01-01

    Objectives To audit the diagnostic yield and cost implications of the use of a ‘liver screen’ for inpatients with abnormal liver function tests. Design We performed a retrospective audit of inpatients with abnormal liver function tests. We analysed all investigations ordered including biochemistry, immunology, virology and radiology. The final diagnosis was ascertained in each case, and the diagnostic yield and cost per positive diagnosis for each investigation were calculated. Setting St Thomas’ NHS Trust. Participants All inpatients investigated for abnormal liver function tests over a 12-month period. Main outcome measures We calculated the percentage of courses due to each diagnosis, the yield of each investigation and the cost per positive diagnosis for each investigation. Results A total of 308 patients were included, and a final diagnosis was made in 224 patients (73%) on the basis of both clinical data and investigations. There was considerable heterogeneity in the tests included in an acute liver screen. History and ultrasound yielded the most diagnoses (40% and 30%, respectively). The yield of autoimmune and metabolic screens was minimal. Conclusions Our results demonstrate the low yield of unselected testing in patients with abnormal liver function tests. A thorough history, ultrasound and testing for blood-borne viruses are the cornerstones of diagnosis. Specialist input should be sought before further testing. Prospective studies to evaluate the yield and cost-effectiveness of different testing strategies are needed. PMID:26770816

  3. Public interest in predictive genetic testing, including direct-to-consumer testing, for susceptibility to major depression: preliminary findings

    PubMed Central

    Wilde, Alex; Meiser, Bettina; Mitchell, Philip B; Schofield, Peter R

    2010-01-01

    The past decade has seen rapid advances in the identification of associations between candidate genes and a range of common multifactorial disorders. This paper evaluates public attitudes towards the complexity of genetic risk prediction in psychiatry involving susceptibility genes, uncertain penetrance and gene–environment interactions on which successful molecular-based mental health interventions will depend. A qualitative approach was taken to enable the exploration of the views of the public. Four structured focus groups were conducted with a total of 36 participants. The majority of participants indicated interest in having a genetic test for susceptibility to major depression, if it was available. Having a family history of mental illness was cited as a major reason. After discussion of perceived positive and negative implications of predictive genetic testing, nine of 24 participants initially interested in having such a test changed their mind. Fear of genetic discrimination and privacy issues predominantly influenced change of attitude. All participants still interested in having a predictive genetic test for risk for depression reported they would only do so through trusted medical professionals. Participants were unanimously against direct-to-consumer genetic testing marketed through the Internet, although some would consider it if there was suitable protection against discrimination. The study highlights the importance of general practitioner and public education about psychiatric genetics, and the availability of appropriate treatment and support services prior to implementation of future predictive genetic testing services. PMID:19690586

  4. Public interest in predictive genetic testing, including direct-to-consumer testing, for susceptibility to major depression: preliminary findings.

    PubMed

    Wilde, Alex; Meiser, Bettina; Mitchell, Philip B; Schofield, Peter R

    2010-01-01

    The past decade has seen rapid advances in the identification of associations between candidate genes and a range of common multifactorial disorders. This paper evaluates public attitudes towards the complexity of genetic risk prediction in psychiatry involving susceptibility genes, uncertain penetrance and gene-environment interactions on which successful molecular-based mental health interventions will depend. A qualitative approach was taken to enable the exploration of the views of the public. Four structured focus groups were conducted with a total of 36 participants. The majority of participants indicated interest in having a genetic test for susceptibility to major depression, if it was available. Having a family history of mental illness was cited as a major reason. After discussion of perceived positive and negative implications of predictive genetic testing, nine of 24 participants initially interested in having such a test changed their mind. Fear of genetic discrimination and privacy issues predominantly influenced change of attitude. All participants still interested in having a predictive genetic test for risk for depression reported they would only do so through trusted medical professionals. Participants were unanimously against direct-to-consumer genetic testing marketed through the Internet, although some would consider it if there was suitable protection against discrimination. The study highlights the importance of general practitioner and public education about psychiatric genetics, and the availability of appropriate treatment and support services prior to implementation of future predictive genetic testing services.

  5. Initiating moderate to heavy alcohol use predicts changes in neuropsychological functioning for adolescent girls and boys.

    PubMed

    Squeglia, Lindsay M; Spadoni, Andrea D; Infante, M Alejandra; Myers, Mark G; Tapert, Susan F

    2009-12-01

    This study prospectively examines the influence of alcohol on neuropsychological functioning in boys and girls characterized prior to initiating drinking (N = 76, ages 12-14). Adolescents who transitioned into heavy (n = 25; 11 girls, 14 boys) or moderate (n = 11; 2 girls, 9 boys) drinking were compared with matched controls who remained nonusers throughout the approximately 3-year follow-up period (N = 40; 16 girls, 24 boys). For girls, more past year drinking days predicted a greater reduction in visuospatial task performance from baseline to follow-up, above and beyond performance on equivalent measures at baseline (R2Delta = 10%, p < .05), particularly on tests of visuospatial memory (R2Delta = 8%, p < .05). For boys, a tendency was seen for more past year hangover symptoms to predict worsened sustained attention (R2Delta = 7%, p < .05). These preliminary longitudinal findings suggest that initiating moderately heavy alcohol use and incurring hangover during adolescence may adversely influence neurocognitive functioning. Neurocognitive deficits linked to heavy drinking during this critical developmental period may lead to direct and indirect changes in neuromaturational course, with effects that would extend into adulthood.

  6. Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD.

    PubMed

    Aidas, Kęstutis; Lanevskij, Kiril; Kubilius, Rytis; Juška, Liutauras; Petkevičius, Daumantas; Japertas, Pranas

    2015-11-01

    Aqueous pK(a) of selected primary benzenesulfonamides are predicted in a systematic manner using density functional theory methods and the SMD solvent model together with direct and proton exchange thermodynamic cycles. Some test calculations were also performed using high-level composite CBS-QB3 approach. The direct scheme generally does not yield a satisfactory agreement between calculated and measured acidities due to a severe overestimation of the Gibbs free energy changes of the gas-phase deprotonation reaction by the used exchange-correlation functionals. The relative pK(a) values calculated using proton exchange method compare to experimental data very well in both qualitative and quantitative terms, with a mean absolute error of about 0.4 pK(a) units. To achieve this accuracy, we find it mandatory to perform geometry optimization of the neutral and anionic species in the gas and solution phases separately, because different conformations are stabilized in these two cases. We have attempted to evaluate the effect of the conformer-averaged free energies in the pK(a) predictions, and the general conclusion is that this procedure is highly too costly as compared with the very small improvement we have gained.

  7. Pre-Test Analysis Predictions for the Shell Buckling Knockdown Factor Checkout Tests - TA01 and TA02

    NASA Technical Reports Server (NTRS)

    Thornburgh, Robert P.; Hilburger, Mark W.

    2011-01-01

    This report summarizes the pre-test analysis predictions for the SBKF-P2-CYL-TA01 and SBKF-P2-CYL-TA02 shell buckling tests conducted at the Marshall Space Flight Center (MSFC) in support of the Shell Buckling Knockdown Factor (SBKF) Project, NASA Engineering and Safety Center (NESC) Assessment. The test article (TA) is an 8-foot-diameter aluminum-lithium (Al-Li) orthogrid cylindrical shell with similar design features as that of the proposed Ares-I and Ares-V barrel structures. In support of the testing effort, detailed structural analyses were conducted and the results were used to monitor the behavior of the TA during the testing. A summary of predicted results for each of the five load sequences is presented herein.

  8. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.

    PubMed

    Cheng, Gong; Qian, Bin; Samudrala, Ram; Baker, David

    2005-01-01

    The prediction of functional sites in newly solved protein structures is a challenge for computational structural biology. Most methods for approaching this problem use evolutionary conservation as the primary indicator of the location of functional sites. However, sequence conservation reflects not only evolutionary selection at functional sites to maintain protein function, but also selection throughout the protein to maintain the stability of the folded state. To disentangle sequence conservation due to protein functional constraints from sequence conservation due to protein structural constraints, we use all atom computational protein design methodology to predict sequence profiles expected under solely structural constraints, and to compute the free energy difference between the naturally occurring amino acid and the lowest free energy amino acid at each position. We show that functional sites are more likely than non-functional sites to have computed sequence profiles which differ significantly from the naturally occurring sequence profiles and to have residues with sub-optimal free energies, and that incorporation of these two measures improves sequence based prediction of protein functional sites. The combined sequence and structure based functional site prediction method has been implemented in a publicly available web server.

  9. A global remote sensing mission to detect and predict plant functional biodiversity change

    NASA Astrophysics Data System (ADS)

    Cavender-Bares, J.; Jetz, W.; Pavlick, R.; Schimel, D.; Gamon, J. A.; Hobbie, S. E.; Townsend, P. A.

    2015-12-01

    Global biodiversity is one of the most crucial and least-observed dimensions of the earth system and increasingly important for anticipating changes to both the climate system and ecosystem services. Parallel developments in biodiversity science and remote sensing show that new satellite observations could directly provide global monitoring of one key dimension of global biodiversity, plant functional trait diversity. Remote sensing has already proven a pivotal aid to address the biodiversity data gap. Data on plant productivity, phenology, land-cover and other environmental parameters from MODIS and Landsat satellites currently serve as highly effective covariates for spatiotemporal biodiversity models. The growing functional trait paradigm in ecology, supported by the development of a global plant trait database that includes information for more than one-third of the global flora, highlights the importance of detecting functional diversity globally. Functional traits such as nutrient concentrations, characteristic growth forms and wood density drive both, how organisms respond to environmental change and the effects of organisms on ecosystems. Additionally, the ever more complete tree of life for plants, which presents a link to the shared evolutionary history of plant traits within lineages, coupled with advances in macroevolutionary models and data gap filling techniques, allows predictions of traits that cannot be directly observed. Using experimental manipulations of plant functional and phylogenetic diversity, our team is testing the extent to which we can link above and belowground measurements of biodiversity to remotely sensed optical diversity using hyperspectral data. These efforts will provide the means to fruitfully harness functional diversity data from space from the envisioned Global Biodiversity Observatory (GBO) mission. In turn, remotely sensed hyperspectral data from GBO will allow fundamental breakthroughs and resolve one of the most

  10. Predictive validity of the Biomedical Admissions Test: an evaluation and case study.

    PubMed

    McManus, I C; Ferguson, Eamonn; Wakeford, Richard; Powis, David; James, David

    2011-01-01

    There has been an increase in the use of pre-admission selection tests for medicine. Such tests need to show good psychometric properties. Here, we use a paper by Emery and Bell [2009. The predictive validity of the Biomedical Admissions Test for pre-clinical examination performance. Med Educ 43:557-564] as a case study to evaluate and comment on the reporting of psychometric data in the field of medical student selection (and the comments apply to many papers in the field). We highlight pitfalls when reliability data are not presented, how simple zero-order associations can lead to inaccurate conclusions about the predictive validity of a test, and how biases need to be explored and reported. We show with BMAT that it is the knowledge part of the test which does all the predictive work. We show that without evidence of incremental validity it is difficult to assess the value of any selection tests for medicine.

  11. Strainrange partitioning life predictions of the long time metal properties council creep-fatigue tests

    NASA Technical Reports Server (NTRS)

    Saltsman, J. F.; Halford, G. R.

    1979-01-01

    The method of strainrange partitioning is used to predict the cyclic lives of the Metal Properties Council's long time creep-fatigue interspersion tests of several steel alloys. Comparisons are made with predictions based upon the time- and cycle-fraction approach. The method of strainrange partitioning is shown to give consistently more accurate predictions of cyclic life than is given by the time- and cycle-fraction approach.

  12. Strainrange partitioning life predictions of the long time Metal Properties Council creep-fatigue tests

    NASA Technical Reports Server (NTRS)

    Saltsman, J. F.; Halford, G. R.

    1979-01-01

    The method of Strainrange Partitioning is used to predict the cyclic lives of the Metal Properties Council's long time creep-fatigue interspersion tests of several steel alloys. Comparisons are made with predictions based upon the Time- and Cycle-Fraction approach. The method of Strainrange Partitioning is shown to give consistently more accurate predictions of cyclic life than is given by the Time- and Cycle-Fraction approach.

  13. Genomic islands predict functional adaptation in marine actinobacteria

    SciTech Connect

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric; Moore, Bradley; Jensen, Paul

    2009-04-01

    Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

  14. Adolescents' functional numeracy is predicted by their school entry number system knowledge.

    PubMed

    Geary, David C; Hoard, Mary K; Nugent, Lara; Bailey, Drew H

    2013-01-01

    One in five adults in the United States is functionally innumerate; they do not possess the mathematical competencies needed for many modern jobs. We administered functional numeracy measures used in studies of young adults' employability and wages to 180 thirteen-year-olds. The adolescents began the study in kindergarten and participated in multiple assessments of intelligence, working memory, mathematical cognition, achievement, and in-class attentive behavior. Their number system knowledge at the beginning of first grade was defined by measures that assessed knowledge of the systematic relations among Arabic numerals and skill at using this knowledge to solve arithmetic problems. Early number system knowledge predicted functional numeracy more than six years later (ß = 0.195, p = .0014) controlling for intelligence, working memory, in-class attentive behavior, mathematical achievement, demographic and other factors, but skill at using counting procedures to solve arithmetic problems did not. In all, we identified specific beginning of schooling numerical knowledge that contributes to individual differences in adolescents' functional numeracy and demonstrated that performance on mathematical achievement tests underestimates the importance of this early knowledge.

  15. Use of contiguity on the chromosome to predict functional coupling.

    SciTech Connect

    Overbeek, R.; Fonstein, M.; Souza, D'Souza, M.; Pusch, G. D.; Maltsev, N.; Mathematics and Computer Science; Univ. of Chicago

    1999-01-01

    The availability of a growing number of completely sequenced genomes opens new opportunities for understanding of complex biological systems. Success of genome-based biology will, to a large extent, depend on the development of new approaches and tools for efficient comparative analysis of the genomes and their organization. We have developed a technique for detecting possible functional coupling between genes based on detection of potential operons. The approach involves computation of 'pairs of close bidirectional best hits', which are pairs of genes that apparently occur within operons in multiple genomes. Using these pairs, one can compose evidence (based on the number of distinct genomes and the phylogenetic distance between the orthologous pairs) that a pair of genes is potentially functionally coupled. The technique has revealed a surprisingly rich and apparently accurate set of functionally coupled genes. The approach depends on the use of a relatively large number of genomes, and the amount of detected coupling grows dramatically as the number of genomes increases.

  16. EPA'S TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

    EPA Science Inventory

    EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals that likely represent the greatest hazard to human ...

  17. EPA's Toxcast ™ Program for Predicting Hazard and Priortizing Toxicity Testing of Environemntal Chemicals (T)

    EPA Science Inventory

    EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals that likely represent the greatest hazard to human ...

  18. EPAS TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS(S).

    EPA Science Inventory

    EPAs National Center for Computational Toxicology is developing methods that apply computational chemistry, high-throughput screening (HTS) and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

  19. Routes to Reading and Spelling: Testing the Predictions of Dual-Route Theory

    ERIC Educational Resources Information Center

    Sheriston, Lee; Critten, Sarah; Jones, Emily

    2016-01-01

    Dual-route theory, which emphasizes the importance of lexical and nonlexical routes, makes specific predictions about the kinds of strategies that young students might adopt when attempting to correctly read and spell regular and irregular words. The current study tests these predictions by assessing strategy choice on regular, irregular, and…

  20. Predicting Item Difficulty in a Reading Comprehension Test with an Artificial Neural Network.

    ERIC Educational Resources Information Center

    Perkins, Kyle; And Others

    1995-01-01

    This article reports the results of using a three-layer back propagation artificial neural network to predict item difficulty in a reading comprehension test. Three classes of variables were examined: text structure, propositional analysis, and cognitive demand. Results demonstrate that the networks can consistently predict item difficulty. (JL)

  1. The Prediction of Item Parameters Based on Classical Test Theory and Latent Trait Theory

    ERIC Educational Resources Information Center

    Anil, Duygu

    2008-01-01

    In this study, the prediction power of the item characteristics based on the experts' predictions on conditions try-out practices cannot be applied was examined for item characteristics computed depending on classical test theory and two-parameters logistic model of latent trait theory. The study was carried out on 9914 randomly selected students…

  2. Initial Comparison of Single Cylinder Stirling Engine Computer Model Predictions with Test Results

    NASA Technical Reports Server (NTRS)

    Tew, R. C., Jr.; Thieme, L. G.; Miao, D.

    1979-01-01

    A Stirling engine digital computer model developed at NASA Lewis Research Center was configured to predict the performance of the GPU-3 single-cylinder rhombic drive engine. Revisions to the basic equations and assumptions are discussed. Model predictions with the early results of the Lewis Research Center GPU-3 tests are compared.

  3. The Development of Similarity: Testing the Prediction of a Computational Model of Metaphor Comprehension

    ERIC Educational Resources Information Center

    Purser, Harry R. M.; Thomas, Michael S. C.; Snoxall, Sarah; Mareschal, Denis

    2009-01-01

    An empirical study is presented that tests a novel prediction generated by the Metaphor-by-Pattern-Completion (MPC) connectionist model of metaphor comprehension (Thomas & Mareschal, 2001). The MPC model predicts a developmental progression in the way that children process metaphors, from a preference for basic-level metaphors to a preference for…

  4. Evaluation of early airway disease in smokers: cost effectiveness of pulmonary function testing.

    PubMed

    Loss, R W; Hall, W J; Speers, D M

    1979-01-01

    We studied 73 young adults who were presently cigarette smokers to evaluate whether the identification of abnormalities in pulmonary function tests had a detectable influence on modification of smoking habits. Utilizing rate schedules for these tests presently applicable in Rochester, New York, we determined the potential cost to these subjects and community relative to the number of subjects who stopped smoking as a result of test findings. Subjects were evaluated by questionnaire and function testing including spirometry, flow-volume curves, body plethysmography and single breath nitrogen washout test (SBN2). Functional abnormalities were present in 75% of subjects screened. The SBN2 test was most sensitive, identifying 97% of subjects with any abnormality. The presence of common respiratory symptoms was found to be highly predictive of test abnormalities. Subjects were informed of results and counseled. At six-month follow-up, 7% of subjects with abnormal test results had stopped smoking. Utilizing even our most cost-effective test, the SBN2, it would cost +1,392 for each "benefit" defined as one subject not smoking for six months. Application of these screening techniques is unlikely to be effective in altering smoking habits in the absence of continued physician support.

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

    PubMed

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

    2015-07-01

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

  6. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.

    PubMed

    Zhang, Chao; Joshi, Trupti; Lin, Guan Ning; Xu, Dong

    2008-01-01

    Characterising gene function is one of the major challenging tasks in the post-genomic era. Various approaches have been developed to integrate multiple sources of high-throughput data to predict gene function. Most of those approaches are just used for research purpose and have not been implemented as publicly available tools. Even for those implemented applications, almost all of them are still web-based 'prediction servers' that have to be managed by specialists. This paper introduces a systematic method for integrating various sources of high-throughput data to predict gene function and analyse our prediction results and evaluates its performances based on the competition for mouse gene function prediction (MouseFunc). A stand-alone Java-based software package 'GeneFAS' is freely available at http://digbio. missouri.eduigenefas.

  7. Negative HPV screening test predicts low cervical cancer risk better than negative Pap test

    Cancer.gov

    Based on a study that included more than 1 million women, investigators at NCI have determined that a negative test for HPV infection compared to a negative Pap test provides greater safety, or assurance, against future risk of cervical cancer.

  8. Predicting the Reliability of Brittle Material Structures Subjected to Transient Proof Test and Service Loading

    NASA Astrophysics Data System (ADS)

    Nemeth, Noel N.; Jadaan, Osama M.; Palfi, Tamas; Baker, Eric H.

    Brittle materials today are being used, or considered, for a wide variety of high tech applications that operate in harsh environments, including static and rotating turbine parts, thermal protection systems, dental prosthetics, fuel cells, oxygen transport membranes, radomes, and MEMS. Designing brittle material components to sustain repeated load without fracturing while using the minimum amount of material requires the use of a probabilistic design methodology. The NASA CARES/Life 1 (Ceramic Analysis and Reliability Evaluation of Structure/Life) code provides a general-purpose analysis tool that predicts the probability of failure of a ceramic component as a function of its time in service. This capability includes predicting the time-dependent failure probability of ceramic components against catastrophic rupture when subjected to transient thermomechanical loads (including cyclic loads). The developed methodology allows for changes in material response that can occur with temperature or time (i.e. changing fatigue and Weibull parameters with temperature or time). For this article an overview of the transient reliability methodology and how this methodology is extended to account for proof testing is described. The CARES/Life code has been modified to have the ability to interface with commercially available finite element analysis (FEA) codes executed for transient load histories. Examples are provided to demonstrate the features of the methodology as implemented in the CARES/Life program.

  9. The impact of information order on intentions to undergo predictive genetic testing: an experimental study.

    PubMed

    Morrison, Val; Henderson, Bethan J; Taylor, Caroline; A'Ch Dafydd, Nonn; Unwin, Abbie

    2010-10-01

    As predictive genetic testing availability increases so does our need to understand factors associated with test uptake. This study tests whether the order positive and negative information about genetic testing for breast cancer is presented in affects intention to take a genetic test. Eighty-four women were randomly allocated into three groups: (1) positive then negative information; (2) negative then positive information; and (3) a control group. A significant effect was found in relation to perceived risk, attitudes towards genetic testing, perceived disadvantages of testing and intention. Our findings point to a primacy effect, whereby information presented first has the greatest effect.

  10. Novel semantic similarity measure improves an integrative approach to predicting gene functional associations

    PubMed Central

    2013-01-01

    Background Elucidation of the direct/indirect protein interactions and gene associations is required to fully understand the workings of the cell. This can be achieved through the use of both low- and high-throughput biological experiments and in silico methods. We present GAP (Gene functional Association Predictor), an integrative method for predicting and characterizing gene functional associations. GAP integrates different biological features using a novel taxonomy-based semantic similarity measure in predicting and prioritizing high-quality putative gene associations. The proposed similarity measure increases information gain from the available gene annotations. The annotation information is incorporated from several public pathway databases, Gene Ontology annotations as well as drug and disease associations from the scientific literature. Results We evaluated GAP by comparing its prediction performance with several other well-known functional interaction prediction tools over a comprehensive dataset of known direct and indirect interactions, and observed significantly better prediction performance. We also selected a small set of GAP’s highly-scored novel predicted pairs (i.e., currently not found in any known database or dataset), and by manually searching the literature for experimental evidence accessible in the public domain, we confirmed different categories of predicted functional associations with available evidence of interaction. We also provided extra supporting evidence for subset of the predicted functionally-associated pairs using an expert curated database of genes associated to autism spectrum disorders. Conclusions GAP’s predictedfunctional interactome” contains ≈1M highly-scored predicted functional associations out of which about 90% are novel (i.e., not experimentally validated). GAP’s novel predictions connect disconnected components and singletons to the main connected component of the known interactome. It can, therefore, be

  11. Use of Practice Tests in the Prediction of GED Test Scores.

    ERIC Educational Resources Information Center

    Herring, Warren

    1999-01-01

    Analyzes the relationship between success on the two new practice-test forms (EE and FF) developed by Steck-Vaughn and success on the General Educational Development (GED) test. Success with practice-form EE correlated with GED test scores; form FF failed to correlate. (JOW)

  12. [Eosin Y-water test for sperm function examination].

    PubMed

    Zha, Shu-wei; Lü, Nian-qing; Xu, Hao-qin

    2015-06-01

    Based on the principles of the in vitro staining technique, hypotonic swelling test, and water test, the Eosin Y-water test method was developed to simultaneous