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Sample records for function tests predict

  1. Prediction of functional aerobic capacity without exercise testing

    NASA Technical Reports Server (NTRS)

    Jackson, A. S.; Blair, S. N.; Mahar, M. T.; Wier, L. T.; Ross, R. M.; Stuteville, J. E.

    1990-01-01

    The purpose of this study was to develop functional aerobic capacity prediction models without using exercise tests (N-Ex) and to compare the accuracy with Astrand single-stage submaximal prediction methods. The data of 2,009 subjects (9.7% female) were randomly divided into validation (N = 1,543) and cross-validation (N = 466) samples. The validation sample was used to develop two N-Ex models to estimate VO2peak. Gender, age, body composition, and self-report activity were used to develop two N-Ex prediction models. One model estimated percent fat from skinfolds (N-Ex %fat) and the other used body mass index (N-Ex BMI) to represent body composition. The multiple correlations for the developed models were R = 0.81 (SE = 5.3 ml.kg-1.min-1) and R = 0.78 (SE = 5.6 ml.kg-1.min-1). This accuracy was confirmed when applied to the cross-validation sample. The N-Ex models were more accurate than what was obtained from VO2peak estimated from the Astrand prediction models. The SEs of the Astrand models ranged from 5.5-9.7 ml.kg-1.min-1. The N-Ex models were cross-validated on 59 men on hypertensive medication and 71 men who were found to have a positive exercise ECG. The SEs of the N-Ex models ranged from 4.6-5.4 ml.kg-1.min-1 with these subjects.(ABSTRACT TRUNCATED AT 250 WORDS).

  2. High-throughput functional testing of ENCODE segmentation predictions

    PubMed Central

    Kwasnieski, Jamie C.; Fiore, Christopher; Chaudhari, Hemangi G.

    2014-01-01

    The histone modification state of genomic regions is hypothesized to reflect the regulatory activity of the underlying genomic DNA. Based on this hypothesis, the ENCODE Project Consortium measured the status of multiple histone modifications across the genome in several cell types and used these data to segment the genome into regions with different predicted regulatory activities. We measured the cis-regulatory activity of more than 2000 of these predictions in the K562 leukemia cell line. We tested genomic segments predicted to be Enhancers, Weak Enhancers, or Repressed elements in K562 cells, along with other sequences predicted to be Enhancers specific to the H1 human embryonic stem cell line (H1-hESC). Both Enhancer and Weak Enhancer sequences in K562 cells were more active than negative controls, although surprisingly, Weak Enhancer segmentations drove expression higher than did Enhancer segmentations. Lower levels of the covalent histone modifications H3K36me3 and H3K27ac, thought to mark active enhancers and transcribed gene bodies, associate with higher expression and partly explain the higher activity of Weak Enhancers over Enhancer predictions. While DNase I hypersensitivity (HS) is a good predictor of active sequences in our assay, transcription factor (TF) binding models need to be included in order to accurately identify highly expressed sequences. Overall, our results show that a significant fraction (∼26%) of the ENCODE enhancer predictions have regulatory activity, suggesting that histone modification states can reflect the cis-regulatory activity of sequences in the genome, but that specific sequence preferences, such as TF-binding sites, are the causal determinants of cis-regulatory activity. PMID:25035418

  3. Sensitivity and specificity of the functional hallux limitus test to predict foot function.

    PubMed

    Payne, Craig; Chuter, Vivienne; Miller, Kathryn

    2002-05-01

    Functional hallux limitus is an underrecognized entity that generally does not produce symptoms but can result in a variety of compensatory mechanisms that can produce symptoms. Clinically, hallux limitus can be determined by assessing the range of motion available at the first metatarsophalangeal joint while the first ray is prevented from plantarflexing. The aim of this study was to determine the sensitivity and specificity of this clinical test to predict abnormal excessive midtarsal joint function during gait. A total of 86 feet were examined for functional hallux limitus and abnormal pronation of the midtarsal joint during late midstance. The test had a sensitivity of 0.72 and a specificity of 0.66, suggesting that clinicians should consider functional hallux limitus when there is late midstance pronation of the midtarsal joint during gait. PMID:12015407

  4. Predictive Testing

    MedlinePlus

    ... Primary care providers Specialists Getting covered Research Basic science research Research in people ... screening Diagnostic testing Direct-to-consumer genetic testing Newborn screening Pharmacogenomic testing ...

  5. Cognitive Functioning Predicts Driver Safety On Road-Tests 1 and 2 Years Later

    PubMed Central

    Aksan, Nazan; Anderson, Steven W.; Dawson, Jeffrey D.; Johnson, Amy M.; Uc, Ergun Y.; Rizzo, Matthew

    2011-01-01

    BACKGROUND Our ability to predict aging related declines in driving performance from off-road assessments have clinical practice and social policy implications. OBJECTIVES 1) To describe longitudinal changes in mean-level and evaluate rank-order stability in potential predictors of driving safety (visual sensory, motor, visual attention, and cognitive functioning) and safety errors during an 18-mile on-road-drive-test among older adults. 2) To evaluate the relative predictive power of earlier visual sensory, motor, visual attention, and cognitive functioning on future safety errors controlling for earlier driving capacity. DESIGN A three-year longitudinal observational study; SETTING A large teaching hospital in the Mid-West; PARTICIPANTS 111 neurologically normal older adults (60 to 89 years at baseline); MEASUREMENTS Safety errors based on video review of a standard 18-mile on-road driving test served as the outcome measure. Comprehensive battery of tests on the predictor side included visual sensory functioning, motor functioning, cognitive functioning, and a measure of Useful Field of View. RESULTS Longitudinal changes in mean-levels of safety errors and cognitive functioning were small from year-to-year. Relative rank-order stability between consecutive assessments was moderate in overall safety errors, it was moderate to strong in visual attention and cognitive functioning. While prospective bivariate correlations ranged from fair to moderate between safety errors and predictors, only functioning in the cognitive domain predicted future driver performance one and two-years later in multivariate analyses. CONCLUSION Normative aging related declines in driver performance as assessed by on-road tests emerge slowly. The findings clearly demonstrated that even in the presence conservative controls, such as previous driving ability, age, visual sensory and motor functioning, cognitive functioning predicted future driving performance on-road one and two-years later

  6. 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

  7. 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

  8. 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.

  9. Can a Clinical Test of Reaction Time Predict a Functional Head-Protective Response?

    PubMed Central

    ECKNER, JAMES T.; LIPPS, DAVID B.; KIM, HOGENE; RICHARDSON, JAMES K.; ASHTON-MILLER, JAMES A.

    2015-01-01

    Purpose Reaction time is commonly prolonged after a sport-related concussion. Besides being a marker for injury, a rapid reaction time is necessary for protective maneuvers that can reduce the frequency and severity of additional head impacts. The purpose of this study was to determine whether a clinical test of simple visuomotor reaction time predicted the time taken to raise the hands to protect the head from a rapidly approaching ball. Methods Twenty-six healthy adult participants recruited from campus and community recreation and exercise facilities completed two experimental protocols during a single session: a manual visuomotor simple reaction time test (RTclin) and a sport-related head-protective response (RTsprt). RTclin measured the time required to catch a thin vertically oriented device on its release by the tester and was calculated from the distance the device fell before being arrested. RTsprt measured the time required to raise the hands from waist level to block a foam tennis ball fired toward the subject’s face from an air cannon and was determined using an optoelectronic camera system. A correlation coefficient was calculated between RTclin and RTsprt, with linear regression used to assess for effect modification by other covariates. Results A strong positive correlation was found between RTclin and RTsprt (r = 0.725, P < 0.001) independent of age, gender, height, or weight. Conclusions RTclin is predictive of a functional sport-related head-protective response. To our knowledge, this is the first demonstration of a clinical test predicting the ability to protect the head in a simulated sport environment. This correlation with a functional head-protective response is a relevant consideration for the potential use of RTclin as part of a multifaceted concussion assessment program. PMID:20689458

  10. Link functions in multi-locus genetic models: implications for testing, prediction, and interpretation.

    PubMed

    Clayton, David

    2012-05-01

    "Complex" diseases are, by definition, influenced by multiple causes, both genetic and environmental, and statistical work on the joint action of multiple risk factors has, for more than 40 years, been dominated by the generalized linear model (GLM). In genetics, models for dichotomous traits have traditionally been approached via the model of an underlying, normally distributed, liability. This corresponds to the GLM with binomial errors and a probit link function. Elsewhere in epidemiology, however, the logistic regression model, a GLM with logit link function, has been the tool of choice, largely because of its convenient properties in case-control studies. The choice of link function has usually been dictated by mathematical convenience, but it has some important implications in (a) the choice of association test statistic in the presence of existing strong risk factors, (b) the ability to predict disease from genotype given its heritability, and (c) the definition, and interpretation of epistasis (or epistacy). These issues are reviewed, and a new association test proposed. PMID:22508388

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

    PubMed Central

    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. 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

  13. Usefulness of platelet function tests to predict bleeding with antithrombotic medications.

    PubMed

    Gorog, Diana A; Otsui, Kazunori; Inoue, Nobutaka

    2015-01-01

    The pharmacological inhibition of platelets has always been regarded as a double-edged sword: the challenge of balancing the antithrombotic effect against the bleeding risk. Potent antiplatelet agents and novel oral anticoagulants, sometimes in combination, are increasingly used in the treatment of cardiovascular disease and for thromboprophylaxis in atrial fibrillation. Although such treatment has reduced the risk of thrombotic events, the potential for major bleeding has increased, and a technique to identify those at increased bleeding risk is greatly needed. Platelet function tests (PFTs), most frequently VerifyNow and also the vasodilator-stimulated phosphoprotein -phosphorylation assay, have been used to identify low on-treatment platelet reactivity, to identify individuals who may be at increased bleeding risk. Such results predict nuisance bleeding, but many individuals have low on-treatment platelet reactivity and yet do not exhibit major or even minor bleeding. Although PFTs may be useful in assessing populations, they do not allow identification of individual patients at risk of bleeding on either antiplatelet or novel oral anticoagulant therapy, nor do they allow the tailoring of such therapy to optimize the risk:benefit ratio. Thrombin plays a cardinal role in both arterial thrombus formation and hemostasis, yet most PFTs fail to assess the contribution of thrombin, because they employ anticoagulated blood. Techniques such as the calibrated automated thrombogram and the point-of-care global thrombosis test, performed on native blood, which measure endogenous thrombin potential, seem to show the most promise for profiling bleeding risk, as tests that most physiologically assess the effects of medications on thrombin. PMID:25839991

  14. The utility of pulmonary function testing in predicting outcomes following liver transplantation.

    PubMed

    Kia, Leila; Cuttica, Michael J; Yang, Amy; Donnan, Erica N; Whitsett, Maureen; Singhvi, Ajay; Lemmer, Alexander; Levitsky, Josh

    2016-06-01

    Although pulmonary function tests (PFTs) are routinely performed in patients during the evaluation period before liver transplantation (LT), their utility in predicting post-LT mortality and morbidity outcomes is not known. The aim of this study was to determine the impact of obstructive and/or restrictive lung disease on post-LT outcomes. We conducted a retrospective analysis of patients who had pre-LT PFTs and underwent a subsequent LT (2007-2013). We used statistical analyses to determine independent associations between PFT parameters and outcomes (graft/patient survival, time on ventilator, and hospital/intensive care unit [ICU] length of stay [LOS]). A total of 415 LT recipients with available PFT data were included: 65% of patients had normal PFTs; 8% had obstructive lung disease; and 27% had restrictive lung disease. There was no difference in patient and graft survival between patients with normal, obstructive, and restrictive lung disease. However, restrictive lung disease was associated with longer post-LT time on ventilator and both ICU and hospital LOS (P < 0.05). More specific PFT parameters (diffusing capacity of the lungs for carbon monoxide, total lung capacity, and residual volume) were all significant predictors of ventilator time and both ICU and hospital LOS (P < 0.05). Although pre-LT PFT parameters may not predict post-LT mortality, restrictive abnormalities correlate with prolonged post-LT ventilation and LOS. Efforts to identify and minimize the impact of restrictive abnormalities on PFTs might improve such outcomes. Liver Transplantation 22 805-811 2016 AASLD. PMID:26929108

  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. 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

  17. 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

  18. Testing earthquake predictions

    NASA Astrophysics Data System (ADS)

    Luen, Brad; Stark, Philip B.

    2008-01-01

    Statistical tests of earthquake predictions require a null hypothesis to model occasional chance successes. To define and quantify 'chance success' is knotty. Some null hypotheses ascribe chance to the Earth: Seismicity is modeled as random. The null distribution of the number of successful predictions - or any other test statistic - is taken to be its distribution when the fixed set of predictions is applied to random seismicity. Such tests tacitly assume that the predictions do not depend on the observed seismicity. Conditioning on the predictions in this way sets a low hurdle for statistical significance. Consider this scheme: When an earthquake of magnitude 5.5 or greater occurs anywhere in the world, predict that an earthquake at least as large will occur within 21 days and within an epicentral distance of 50 km. We apply this rule to the Harvard centroid-moment-tensor (CMT) catalog for 2000-2004 to generate a set of predictions. The null hypothesis is that earthquake times are exchangeable conditional on their magnitudes and locations and on the predictions - a common "nonparametric" assumption in the literature. We generate random seismicity by permuting the times of events in the CMT catalog. We consider an event successfully predicted only if (i) it is predicted and (ii) there is no larger event within 50 km in the previous 21 days. The P-value for the observed success rate is <0.001: The method successfully predicts about 5% of earthquakes, far better than 'chance' because the predictor exploits the clustering of earthquakes - occasional foreshocks - which the null hypothesis lacks. Rather than condition on the predictions and use a stochastic model for seismicity, it is preferable to treat the observed seismicity as fixed, and to compare the success rate of the predictions to the success rate of simple-minded predictions like those just described. If the proffered predictions do no better than a simple scheme, they have little value.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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. PMID:24565332

  4. 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. ...

  5. 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.

  6. Assessment of trait anxiety and prediction of changes in state anxiety using functional brain imaging: A test-retest study.

    PubMed

    Tian, Xue; Wei, Dongtao; Du, Xue; Wang, Kangcheng; Yang, Junyi; Liu, Wei; Meng, Jie; Liu, Huijuan; Liu, Guangyuan; Qiu, Jiang

    2016-06-01

    Anxiety is a multidimensional construct that includes stable trait anxiety and momentary state anxiety, which have a combined effect on our mental and physical well-being. However, the relationship between intrinsic brain activity and the feeling of anxiety, particularly trait and state anxiety, remain unclear. In this study, we used resting-state functional magnetic resonance imaging (fMRI) (amplitude of low-frequency fluctuations (ALFF) and regional homogeneity (ReHo)) to determine the effects of intrinsic brain activity on stable inter-individual trait anxiety and intra-individual state anxiety variability in a cross-sectional and test-retest study. We found that at both time points, the trait anxiety score was significantly associated with intrinsic brain activity (both the ALFF and ReHo) in the right ventral medial prefrontal cortex (vmPFC) and ALFF of the dorsal anterior cingulate cortex/anterior midcingulate cortex (dACC/aMCC). More importantly, the change in intrinsic brain activity in the right insula was predictive of intra-individual state anxiety variability over a 9-month interval. The test-retest nature of this study's design could provide an opportunity to distinguish between the intrinsic brain activity associated with state and trait anxiety. These results could deepen our understanding of anxiety from a neuroscientific perspective. PMID:27001499

  7. Psychological functioning before predictive testing for Huntington's disease: the role of the parental disease, risk perception, and subjective proximity of the disease

    PubMed Central

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

    1999-01-01

    BACKGROUND—Psychometric testing of participants in predictive DNA testing for Huntington's disease (HD) has shown that 15% of the subjects at risk for HD had at least mild depression or a high score for general anxiety or both in the pre-test period. The main aim of the study was the delineation of variables associated with pre-test distress of applicants for predictive testing for HD. Based on theoretical considerations, four specific hypotheses were tested regarding the role of (1) the test participant's age at the (perceived) parental onset of HD, (2) the affected parent's sex, (3) the perception of the risk for HD, and (4) the subjective proximity of the disease. Secondly, these four variables were used in multiple regression analyses to select the best predictors of pre- and post-test psychological functioning (one year after the test). Increasing the understanding of pre- and post-test distress is important for developing better counselling and support strategies for test applicants.
METHODS—Data were collected by means of clinical interviews and psychometric questionnaires during the pre- and post-test (one year after the test) counselling sessions for predictive testing for HD.
RESULTS—We found significant associations of the participant's age at the parental onset, the subjective proximity of the disease onset, and the perceived risk with pre-test psychometric measures of psychological functioning. Multiple regression analyses showed that the best predictors of pre-test functioning were the perceived proximity of the disease onset and its interaction with risk perception. Regarding post-test functioning, none of the proposed variables had a unique contribution beyond that accounted for by pre-test psychological functioning.
CONCLUSIONS—Test participants who are close to the perceived age of onset of HD and who have a pessimistic risk perception should be given special attention during pre-test counselling because of their possible negative

  8. 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 ...

  9. 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.

  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. 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

  12. Extraocular muscle function testing

    MedlinePlus

    Extraocular muscle function testing examines the function of the eye muscles. A health care provider observes the movement of ... evaluate weakness or other problem in the extraocular muscles. These problems may result in double vision or ...

  13. 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.

  14. 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

  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. 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

  18. Sperm function test.

    PubMed

    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. Comparing the Predictive Value of Task Performance and Task-Specific Sensitivity During Physical Function Testing Among People With Knee Osteoarthritis.

    PubMed

    Wideman, Timothy H; Edwards, Robert R; Finan, Patrick H; Haythornthwaite, Jennifer A; Smith, Michael T

    2016-05-01

    Study Design Cross-sectional cohort. Background Knee osteoarthritis (OA) is a leading cause of pain and mobility restriction. Past research has advocated the use of brief, functional tasks to evaluate these restrictions, such as the six-minute-walk test and the timed up-and-go test. Typically, only task performance (ie, walking distance, completion time) is used to inform clinical practice. Recent research, however, suggests that individual variance in how people feel while completing these tasks (ie, task sensitivity) might also have important clinical value. Objective To compare the predictive value of task performance and task-specific sensitivity in determining OA-related physical function (measured by the Western Ontario and McMaster Universities Osteoarthritis Index) and pain-related interference (measured by the Multidimensional Pain Inventory). Methods One hundred eight participants with chronic knee OA completed the six-minute-walk test and the timed up-and-go test, and reported levels of discomfort and affective response (mood) associated with each test. Results In separate regression models, both task performance and task-specific sensitivity predicted OA-related physical function and pain-related interference. A final regression model including all significant predictors showed that task-specific sensitivity (specifically, post-six-minute-walk discomfort) emerged as a unique predictor of both outcomes. Conclusion These findings highlight the value of a novel clinical assessment strategy for patients with knee OA. While clinicians commonly focus on how patients perform on standardized functional tasks, these results highlight the value of also considering levels of posttask sensitivity. Measures of task-specific sensitivity relate to Maitland's concept of pain irritability, which may be a useful framework for future research on sensitizing factors and pain-related disability. J Orthop Sports Phys Ther 2016;46(5):346-356. Epub 21 Mar 2016. doi:10

  20. 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

  1. Prediction of liver disease in patients whose liver function tests have been checked in primary care: model development and validation using population-based observational cohorts

    PubMed Central

    McLernon, David J; Donnan, Peter T; Sullivan, Frank M; Roderick, Paul; Rosenberg, William M; Ryder, Steve D; Dillon, John F

    2014-01-01

    Objective To derive and validate a clinical prediction model to estimate the risk of liver disease diagnosis following liver function tests (LFTs) and to convert the model to a simplified scoring tool for use in primary care. Design Population-based observational cohort study of patients in Tayside Scotland identified as having their LFTs performed in primary care and followed for 2 years. Biochemistry data were linked to secondary care, prescriptions and mortality data to ascertain baseline characteristics of the derivation cohort. A separate validation cohort was obtained from 19 general practices across the rest of Scotland to externally validate the final model. Setting Primary care, Tayside, Scotland. Participants Derivation cohort: LFT results from 310 511 patients. After exclusions (including: patients under 16 years, patients having initial LFTs measured in secondary care, bilirubin >35 μmol/L, liver complications within 6 weeks and history of a liver condition), the derivation cohort contained 95 977 patients with no clinically apparent liver condition. Validation cohort: after exclusions, this cohort contained 11 653 patients. Primary and secondary outcome measures Diagnosis of a liver condition within 2 years. Results From the derivation cohort (n=95 977), 481 (0.5%) were diagnosed with a liver disease. The model showed good discrimination (C-statistic=0.78). Given the low prevalence of liver disease, the negative predictive values were high. Positive predictive values were low but rose to 20–30% for high-risk patients. Conclusions This study successfully developed and validated a clinical prediction model and subsequent scoring tool, the Algorithm for Liver Function Investigations (ALFI), which can predict liver disease risk in patients with no clinically obvious liver disease who had their initial LFTs taken in primary care. ALFI can help general practitioners focus referral on a small subset of patients with higher predicted risk

  2. Pretest Predictions for Ventilation Tests

    SciTech Connect

    Y. Sun; H. Yang; H.N. Kalia

    2007-01-17

    The objective of this calculation is to predict the temperatures of the ventilating air, waste package surface, concrete pipe walls, and insulation that will be developed during the ventilation tests involving various test conditions. The results will be used as input to the following three areas: (1) Decisions regarding testing set-up and performance. (2) Assessing how best to scale the test phenomena measured. (3) Validating numerical approach for modeling continuous ventilation. The scope of the calculation is to identify the physical mechanisms and parameters related to thermal response in the ventilation tests, and develop and describe numerical methods that can be used to calculate the effects of continuous ventilation. Sensitivity studies to assess the impact of variation of linear power densities (linear heat loads) and ventilation air flow rates are included. The calculation is limited to thermal effect only.

  3. Testing the self-consistency of the excursion set approach to predicting the dark matter halo mass function.

    PubMed

    Achitouv, I; Rasera, Y; Sheth, R K; Corasaniti, P S

    2013-12-01

    The excursion set approach provides a framework for predicting how the abundance of dark matter halos depends on the initial conditions. A key ingredient of this formalism is the specification of a critical overdensity threshold (barrier) which protohalos must exceed if they are to form virialized halos at a later time. However, to make its predictions, the excursion set approach explicitly averages over all positions in the initial field, rather than the special ones around which halos form, so it is not clear that the barrier has physical motivation or meaning. In this Letter we show that once the statistical assumptions which underlie the excursion set approach are considered a drifting diffusing barrier model does provide a good self-consistent description both of halo abundance as well as of the initial overdensities of the protohalo patches. PMID:24476252

  4. 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.

  5. Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

    PubMed Central

    2009-01-01

    Background Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both. Results Here, we present and demonstrate a theory to split the knowledge-based potentials in scoring terms biologically meaningful and to combine them in new scores to predict near-native structures. Our strategy allows circumventing the problem of defining the reference state. In this approach we give the proof for a simple and linear application that can be further improved by optimizing the combination of Zscores. Using the simplest composite score () we obtained predictions similar to state-of-the-art methods. Besides, our approach has the advantage of identifying the most relevant terms involved in the stability of the protein structure. Finally, we also use the composite Zscores to assess the conformation of models and to detect local errors. Conclusion We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations. PMID:19917096

  6. [Endothelial function test].

    PubMed

    Tomiyama, Hirofumi

    2015-11-01

    Endothelial dysfunction is thought to have pivotal roles for the development of hypertension, initiation/progression of hypertensive organ damages, and prognosis. In clinical setting, flow-mediated vasodilatation (FMD) of brachial artery is used as a marker of endothelial function. However, well-trained sonographer is needed to conduct FMD measurement, and therefore, FMD has not been fully standardized (i.e., the reference value of FMD has not been established). Even so, FMD predicts future cardiovascular events. Lifestyle modifications (i.e., smoking cessation, exercise, or weight loss) and antihypertensive medication provide beneficial effects on endothelial function. Thus, FMD have a potential as a useful surrogate marker for the management of hypertension. PMID:26619655

  7. 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.

  8. 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…

  9. Adrenal function testing.

    PubMed

    Dluhy, R G

    1978-12-01

    Glucocorticoid stimulation and suppression tests are essential to the definitive diagnosis of diseases of the hypothalamic-pituitary-adrenal axis, because they document abnormal physiologic control of hormonal secretion. Similarly, diseases of the renin-angiotensin-aldosterone axis are diagnosed by mineralocorticoid stimulation and suppression testing. [Ed. Note: See Moore TJ, Williams GH: Adrenal causes of hypertension, in this issue.] Unlike tests of glucocorticoid function, testing of the renin-angiotension-aldosterone system is more complicated, because knowledge of posture and dietary sodium are necessary to interpret the results. However, measurement of the tropic hormone renin and plasma levels of aldosterone can be accurately made, allowing precise definition of this system. Errors are most commonly encountered when dynamic tests of cortisol output are performed in patients taking medications that may interfere with the assays or with the metabolism of the administered compounds, such as dexamethasone or metyrapone. Abnormal, spurious values may also be obtained in some individuals who do not have adrenocortical hyperfunction if they are very obese or if testing is performed in a setting of clinical stress. Careful attention to these pitfalls will avoid errors and allow the clinician to arrive at the correct diagnosis. PMID:216524

  10. 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

  11. 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

  12. 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

  13. Quantitative Liver Function Tests Improve the Prediction of Clinical Outcomes in Chronic Hepatitis C: Results from the HALT-C Trial

    PubMed Central

    Everson, Gregory T.; Shiffman, Mitchell L.; Hoefs, John C.; Morgan, Timothy R.; Sterling, Richard K.; Wagner, David A.; Lauriski, Shannon; Curto, Teresa M.; Stoddard, Anne; Wright, Elizabeth C.

    2011-01-01

    Risk for future clinical outcomes is proportional to the severity of liver disease in patients with chronic hepatitis C. We measured disease severity by quantitative liver function tests (QLFTs) to determine cutoffs for QLFTs that identified patients who were at low and high risk for a clinical outcome. Two hundred twenty seven participants in the Hepatitis C Antiviral Long-Term Treatment Against Cirrhosis (HALT-C) Trial underwent baseline QLFTs and were followed for a median of 5.5 years for clinical outcomes. QLFTs were repeated in 196 patients at month 24 and in 165 patients at month 48. Caffeine elimination rate (k), antipyrine (AP) clearance (Cl), MEGX concentration, methionine breath test (MBT), galactose elimination capacity (GEC), dual cholate (CA) clearances and shunt, and perfused hepatic mass (PHM) and liver and spleen volumes (SPECT) were measured. Baseline QLFTs were significantly worse (p=0.0017 to <0.0001) and spleen volumes larger (p<0.0001) in the 54 patients who subsequently experienced clinical outcomes. QLFT cutoffs that characterized patients as “low” and “high risk” for clinical outcome yielded hazard ratios ranging from 2.21 (95%CI 1.29–3.78) for GEC to 6.52 (95%CI 3.63–11.71) for CA Cloral. QLFTs independently predicted outcome in models with Ishak fibrosis score, platelet count, and standard laboratory tests. In serial studies, patients with “high risk” results for CA Cloral or PHM had a nearly 15-fold increase in risk for clinical outcome. Less than 5% of patients with “low risk” QLFTs experienced a clinical outcome. Conclusion QLFTs independently predict risk for future clinical outcomes. By improving risk assessment, QLFTs could enhance noninvasive monitoring, counseling, and management of patients with chronic hepatitis C. PMID:22030902

  14. 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…

  15. Predicting hand function after hemidisconnection.

    PubMed

    Küpper, Hanna; Kudernatsch, Manfred; Pieper, Tom; Groeschel, Samuel; Tournier, Jacques-Donald; Raffelt, David; Winkler, Peter; Holthausen, Hans; Staudt, Martin

    2016-09-01

    Hemidisconnections (i.e. hemispherectomies or hemispherotomies) invariably lead to contralateral hemiparesis. Many patients with a pre-existing hemiparesis, however, experience no deterioration in motor functions, and some can still grasp with their paretic hand after hemidisconnection. The scope of our study was to predict this phenomenon. Hypothesizing that preserved contralateral grasping ability after hemidisconnection can only occur in patients controlling their paretic hands via ipsilateral corticospinal projections already in the preoperative situation, we analysed the asymmetries of the brainstem (by manual magnetic resonance imaging volumetry) and of the structural connectivity of the corticospinal tracts within the brainstem (by magnetic resonance imaging diffusion tractography), assuming that marked hypoplasia or Wallerian degeneration on the lesioned side in patients who can grasp with their paretic hands indicate ipsilateral control. One hundred and two patients who underwent hemidisconnections between 0.8 and 36 years of age were included. Before the operation, contralateral hand function was normal in 3/102 patients, 47/102 patients showed hemiparetic grasping ability and 52/102 patients could not grasp with their paretic hands. After hemidisconnection, 20/102 patients showed a preserved grasping ability, and 5/102 patients began to grasp with their paretic hands only after the operation. All these 25 patients suffered from pre- or perinatal brain lesions. Thirty of 102 patients lost their grasping ability. This group included all seven patients with a post-neonatally acquired or progressive brain lesion who could grasp before the operation, and also all three patients with a preoperatively normal hand function. The remaining 52/102 patients were unable to grasp pre- and postoperatively. On magnetic resonance imaging, the patients with preserved grasping showed significantly more asymmetric brainstem volumes than the patients who lost their grasping

  16. Structural model of ρ1 GABAC receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function

    PubMed Central

    Adamian, Larisa; Gussin, Hélène A; Tseng, Yan Yuan; Muni, Niraj J; Feng, Feng; Qian, Haohua; Pepperberg, David R; Liang, Jie

    2009-01-01

    The homopentameric ρ1 GABAC receptor is a ligand-gated ion channel with a binding pocket for γ-aminobutyric acid (GABA) at the interfaces of N-terminal extracellular domains. We combined evolutionary analysis, structural modeling, and experimental testing to study determinants of GABAC receptor assembly and channel gating. We estimated the posterior probability of selection pressure at amino acid residue sites measured as ω-values and built a comparative structural model, which identified several polar residues under strong selection pressure at the subunit interfaces that may form intersubunit hydrogen bonds or salt bridges. At three selected sites (R111, T151, and E55), mutations disrupting intersubunit interactions had strong effects on receptor folding, assembly, and function. We next examined the role of a predicted intersubunit salt bridge for residue pair R158–D204. The mutant R158D, where the positively charged residue is replaced by a negatively charged aspartate, yielded a partially degraded receptor and lacked membrane surface expression. The membrane surface expression was rescued by the double mutant R158D–D204R, where positive and negative charges are switched, although the mutant receptor was inactive. The single mutants R158A, D204R, and D204A exhibited diminished activities and altered kinetic profiles with fast recovery kinetics, suggesting that R158–D204 salt bridge perhaps stabilizes the open state of the GABAC receptor. Our results emphasize the functional importance of highly conserved polar residues at the protein–protein interfaces in GABAC ρ1 receptors and demonstrate how the integration of computational and experimental approaches can aid discovery of functionally important interactions. PMID:19768800

  17. Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS).

    PubMed

    Zhu, Chengsong; Li, Xianran; Yu, Jianming

    2011-08-01

    High-density array-based genome-wide association studies (GWAS) are complemented by exome sequencing and whole-genome resequencing-based association studies. Here we present a composite resequencing-based genome-wide association study (CR-GWAS) strategy that systematically exploits collective biological information and analytical tools for a robust analysis. We showcased the utility of this strategy by using Arabidopsis (Arabidopsis thaliana) resequencing data. Bioinformatic predictions of biological function alteration at each locus were integrated into the process of association testing of both common and rare variants for complex traits with a suite of statistics. Significant signals were then filtered with a priori candidate loci generated from genome database and gene network models to obtain a posteriori candidate loci. A probabilistic gene network (AraNet) that interrogates network neighborhoods of genes was then used to expand the filtering power to examine the significant testing signals. Using this strategy, we confirmed the known true positives and identified several new promising associations. Promising genes (AP1, FCA, FRI, FLC, FLM, SPL5, FY, and DCL2) were shown to control for flowering time through either common variants or rare variants within a diverse set of Arabidopsis accessions. Although many of these candidate genes were cloned earlier with mutational studies, identifying their allele variation contribution to overall phenotypic variation among diverse natural accessions is critical. Our rare allele testing established a greater number of connections than previous analyses in which this issue was not addressed. More importantly, our results demonstrated the potential of integrating various biological, statistical, and bioinformatic tools into complex trait dissection. PMID:22384334

  18. Graph pyramids for protein function prediction

    PubMed Central

    2015-01-01

    Background Uncovering the hidden organizational characteristics and regularities among biological sequences is the key issue for detailed understanding of an underlying biological phenomenon. Thus pattern recognition from nucleic acid sequences is an important affair for protein function prediction. As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification. But conventional classification approaches mostly rely on the global features by considering only strong protein similarity matches. This leads to significant loss of prediction accuracy. Methods Here we construct the Protein-Protein Similarity (PPS) network, which captures the subtle properties of protein families. The proposed method considers the local as well as the global features, by examining the interactions among 'weakly interacting proteins' in the PPS network and by using hierarchical graph analysis via the graph pyramid. Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels. Results Experimental results on benchmark data sets show that the proposed hierarchical voting algorithm using graph pyramid helps to improve computational efficiency as well the protein classification accuracy. Quantitatively, among 14,086 test sequences, on an average the proposed method misclassified only 21.1 sequences whereas baseline BLAST score based global feature matching method misclassified 362.9 sequences. With each correctly classified test sequence, the fast incremental learning ability of the proposed method further enhances the training model. Thus it has achieved more than 96% protein classification accuracy using only 20% per class training data. PMID:26044522

  19. 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)

  20. 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…

  1. [Time course of changes in gustatory function test results and subjective symptoms, and predictive factors for response in patients with taste disorder receiving 24-week zinc replacement treatment].

    PubMed

    Sakagami, Masafumi; Kurono, Yuichi; Inokuchi, Akira; Takeda, Noriaki; Aiba, Tsunemasa; Nin, Tomomi; Ikeda, Minoru

    2014-08-01

    In a taste disorder, an agreement between patients' complaints and gustatory function test results is not necessarily found both at the initial hospital visit and during the course of treatment; therefore, it is difficult to assess treatment responses and review treatment strategies based on the assessed treatment responses. The present study investigated the time course of changes in disc gustometry results and subjective symptom scores measured at 4-week intervals in 44 patients with a taste disorder who were considered eligible for zinc replacement treatment and who received polaprezinc at a dose of 150 mg/day (equivalent to a 34 mg/day dose of zinc) for up to 24 weeks. The study also examined the potential differences in treatment outcomes according to the predictive factors for response such as patient background and assessed disc gustometry results during the course of treatment. Results indicated that disc gustometry results and subjective symptom scores showed different time courses of changes. The response rate as measured by disc gustometry was 47.7% at week 12 of treatment, and showed a subsequent slow increase to 56.8% at week 24. On the other hand, subjective symptom scores showed a time-proportional improvement up to week 24. Among the patients included in the present study, a clear difference was found according to the presence or absence of an improving trend as determined by disc gustometry at week 12 of treatment, although there were no differences in ultimate treatment responses, including categories of taste disorder, according to patient background. Patients showing a trend toward improvement had significantly better treatment responses in terms of both ultimate response rates and subjective symptom scores, whereas patients showing no trend toward improvement were less likely to respond to the subsequent 12-week continued treatment. PMID:25255648

  2. 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 ...

  3. Thyroid function tests

    MedlinePlus

    ... free T4 (the main thyroid hormone in your blood) TSH (the hormone from the pituitary gland that stimulates the thyroid to produce T4) T3 (also included sometimes) Other thyroid tests include: T3 resin uptake Thyroid scan

  4. 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 ...

  5. 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. ...

  6. 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

  7. Predicting Death from Behavioral Test Performance

    ERIC Educational Resources Information Center

    Botwinick, Jack; And Others

    1978-01-01

    This study described several brief behavioral measures which, with further validation, could be useful in predicting the deaths of older adults within a five-year period following testing. Such tests can be used in routine biomedical examinations, alerting the physician to possible problems in the future. (Author)

  8. 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

  9. Rumination prospectively predicts executive functioning impairments in adolescents

    PubMed Central

    Connolly, Samantha L.; Wagner, Clara A.; Shapero, Benjamin G.; Pendergast, Laura L.; Abramson, Lyn Y.; Alloy, Lauren B.

    2014-01-01

    Background and objectives The current study tested the resource allocation hypothesis, examining whether baseline rumination or depressive symptom levels prospectively predicted deficits in executive functioning in an adolescent sample. The alternative to this hypothesis was also evaluated by testing whether lower initial levels of executive functioning predicted increases in rumination or depressive symptoms at follow-up. Methods A community sample of 200 adolescents (ages 12–13) completed measures of depressive symptoms, rumination, and executive functioning at baseline and at a follow-up session approximately 15 months later. Results Adolescents with higher levels of baseline rumination displayed decreases in selective attention and attentional switching at follow-up. Rumination did not predict changes in working memory or sustained and divided attention. Depressive symptoms were not found to predict significant changes in executive functioning scores at follow-up. Baseline executive functioning was not associated with change in rumination or depression over time. Conclusions Findings partially support the resource allocation hypothesis that engaging in ruminative thoughts consumes cognitive resources that would otherwise be allocated towards difficult tests of executive functioning. Support was not found for the alternative hypothesis that lower levels of initial executive functioning would predict increased rumination or depressive symptoms at follow-up. Our study is the first to find support for the resource allocation hypothesis using a longitudinal design and an adolescent sample. Findings highlight the potentially detrimental effects of rumination on executive functioning during early adolescence. PMID:23978629

  10. 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.

  11. What Should University Admissions Tests Predict?

    ERIC Educational Resources Information Center

    Stemler, Steven E.

    2012-01-01

    University admissions tests should predict an applicant's ability to succeed in college, but how should this success be defined and measured? The status quo has been to use 1st-year grade point average (FYGPA) as the key indicator of college success, but a review of documents such as university mission statements reveals that universities expect…

  12. Predictive Validity of the Dental Admission Test.

    ERIC Educational Resources Information Center

    Kramer, Gene A.

    1986-01-01

    The relationship of Dental Admission Test (DAT) scales and predental grade point averages with freshman and sophomore dental school performance measures and National Board Dental Examination (NBDE) Part I averages were examined. The results indicated that the DAT scales had limited predictive validity. (Author/MLW)

  13. The Predictive Validity of GRE Aptitude Test.

    ERIC Educational Resources Information Center

    Kaiser, Javaid

    The continued controversy concerning the predictive validity of the Graduate Record Examination (GRE) aptitude test and its influence on selection decisions, including admission and financial aid, has necessitated the establishment of local norms. The sample involved 407 University of Kansas education and computer science students. Information on…

  14. Predictive Service Life Tests for Roofing Membranes

    NASA Astrophysics Data System (ADS)

    Bailey, David M.; Cash, Carl G.; Davies, Arthur G.

    2002-09-01

    The average service life of roofing membranes used in low-slope applications on U.S. Army buildings is estimated to be considerably shorter than the industry-presumed 20-year design life, even when installers carefully adhere to the latest guide specifications. This problem is due in large part to market-driven product development cycles, which do not include time for long-term field testing. To reduce delivery costs, contractors may provide untested, interior membranes in place of ones proven satisfactory in long-term service. Federal procurement regulations require that roofing systems and components be selected according to desired properties and generic type, not brand name. The problem is that a material certified to have satisfactory properties at installation time will not necessarily retain those properties in service. The overall objective of this research is to develop a testing program that can be executed in a matter of weeks to adequately predict a membrane's long-term performance in service. This report details accelerated aging tests of 12 popular membrane materials in the laboratory, and describes outdoor experiment stations set up for long-term exposure tests of those same membranes. The laboratory results will later be correlated with the outdoor test results to develop performance models and predictive service life tests.

  15. 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. PMID:20059365

  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. Springback Prediction on Slit-Ring Test

    SciTech Connect

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

    2005-08-05

    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%.

  18. Tongue Blade Bite Test Predicts Mandible Fractures.

    PubMed

    Neiner, John; Free, Rachael; Caldito, Gloria; Moore-Medlin, Tara; Nathan, Cherie-Ann

    2016-06-01

    The aim of the study is to evaluate the utility of a simple tongue blade bite test in predicting mandible fractures and use this test as an alternative screening tool for further workup. This is a retrospective chart review. An institutional review board approved the retrospective review of patients evaluated by the Department of Otolaryngology at a single institution for facial trauma performed from November 1, 2011, to February 27, 2014. Patients who had a bite test documented were included in the study. CT was performed in all cases and was used as the gold standard to diagnose mandible fractures. Variables analyzed included age, sex, fracture type/location on CT, bite test positivity, and operative intervention. A total of 86 patients met the inclusion criteria and of those 12 were pediatric patients. Majority of the patients were male (80.2%) and adult (86.0%; average age: 34.3 years). Fifty-seven patients had a negative bite test and on CT scans had no mandible fracture. Twenty-three patients had a positive bite test and a CT scan confirmed fracture. The bite test revealed a sensitivity of 88.5% (95% CI: 69.8-97.6%), specificity of 95.0% (95% CI:86.1-99%), positive predictive value [PPV] of 88.5% (95% CI: 69.8-97.6%), and negative predictive value [NPV] of 95.0% (95% CI: 86.1-99.0%). Among pediatric patients, the sensitivity was 100% (95% CI: 29.9-100%), specificity was 88.9% (95% CI: 68.4-100%), PPV was 75.0% (95% CI: 19.4-99.4%), and NPV was 100% (95% CI: 63.1-100%). The tongue blade bite test is a quick inexpensive diagnostic tool for the otolaryngologist with high sensitivity and specificity for predicting mandible fractures. In the pediatric population, where avoidance of unnecessary CT scans is of highest priority, a wider range of data collection should be undertaken to better assess its utility. PMID:27162567

  19. 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.

  20. Pretest Predictions for Phase II Ventilation Tests

    SciTech Connect

    Yiming Sun

    2001-09-19

    The objective of this calculation is to predict the temperatures of the ventilating air, waste package surface, and concrete pipe walls that will be developed during the Phase II ventilation tests involving various test conditions. The results will be used as inputs to validating numerical approach for modeling continuous ventilation, and be used to support the repository subsurface design. The scope of the calculation is to identify the physical mechanisms and parameters related to thermal response in the Phase II ventilation tests, and describe numerical methods that are used to calculate the effects of continuous ventilation. The calculation is limited to thermal effect only. This engineering work activity is conducted in accordance with the ''Technical Work Plan for: Subsurface Performance Testing for License Application (LA) for Fiscal Year 2001'' (CRWMS M&O 2000d). This technical work plan (TWP) includes an AP-2.21Q, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', activity evaluation (CRWMS M&O 2000d, Addendum A) that has determined this activity is subject to the YMP quality assurance (QA) program. The calculation is developed in accordance with the AP-3.12Q procedure, ''Calculations''. Additional background information regarding this activity is contained in the ''Development Plan for Ventilation Pretest Predictive Calculation'' (DP) (CRWMS M&O 2000a).

  1. Optimizing nondecomposable loss functions in structured prediction.

    PubMed

    Ranjbar, Mani; Lan, Tian; Wang, Yang; Robinovitch, Steven N; Li, Ze-Nian; Mori, Greg

    2013-04-01

    We develop an algorithm for structured prediction with nondecomposable performance measures. The algorithm learns parameters of Markov Random Fields (MRFs) and can be applied to multivariate performance measures. Examples include performance measures such as Fβ score (natural language processing), intersection over union (object category segmentation), Precision/Recall at k (search engines), and ROC area (binary classifiers). We attack this optimization problem by approximating the loss function with a piecewise linear function. The loss augmented inference forms a Quadratic Program (QP), which we solve using LP relaxation. We apply this approach to two tasks: object class-specific segmentation and human action retrieval from videos. We show significant improvement over baseline approaches that either use simple loss functions or simple scoring functions on the PASCAL VOC and H3D Segmentation datasets, and a nursing home action recognition dataset. PMID:22868650

  2. Single event phenomena: Testing and prediction

    NASA Technical Reports Server (NTRS)

    Kinnison, James D.

    1992-01-01

    Highly integrated microelectronic devices are often used to increase the performance of satellite systems while reducing the system power dissipation, size, and weight. However, these devices are usually more susceptible to radiation than less integrated devices. In particular, the problem of sensitivity to single event upset and latchup is greatly increased as the integration level is increased. Therefore, a method for accurately evaluating the susceptibility of new devices to single event phenomena is critical to qualifying new components for use in space systems. This evaluation includes testing devices for upset or latchup and extrapolating the results of these tests to the orbital environment. Current methods for testing devices for single event effects are reviewed, and methods for upset rate prediction, including a new technique based on Monte Carlo simulation, are presented.

  3. 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.

  4. Predicting edge seal performance from accelerated testing

    NASA Astrophysics Data System (ADS)

    Hardikar, Kedar; Vitkavage, Dan; Saproo, Ajay; Krajewski, Todd

    2014-10-01

    Degradation in performance of a PV module attributable to moisture ingress has received significant attention in PV reliability research. Assessment of field performance of PV modules against moisture ingress through product-level testing in temperature-humidity control chambers poses challenges. Development of a meaningful acceleration factor model is challenging due to different rates of degradation of components embedded in a PV module, when exposed to moisture. Test results are typically a convolution of moisture barrier performance of the edge seal and degradation of laminated components when exposed to moisture. It is desirable to have an alternate method by which moisture barrier performance of the edge seal in its end product form can be assessed in any given field conditions, independent of particular cell design. In this work, a relatively inexpensive test technique was developed to test the edge seal in its end product form in a manner that is decoupled from other components of the PV module. A theoretical framework was developed to assess moisture barrier performance of edge seal with desiccants subjected to different conditions. This framework enables the analysis of test results from accelerated tests and prediction of the field performance of the edge seal. Results from this study lead to the conclusion that the edge seal on certain Miasole glass-glass modules studied is effective for the most aggressive weather conditions examined, beyond the intended service.

  5. Biochemical functional predictions for protein structures of unknown or uncertain function

    PubMed Central

    Mills, Caitlyn L.; Beuning, Penny J.; Ondrechen, Mary Jo

    2015-01-01

    With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations. PMID:25848497

  6. Abnormality on Liver Function Test

    PubMed Central

    2013-01-01

    Children with abnormal liver function can often be seen in outpatient clinics or inpatients wards. Most of them have respiratory disease, or gastroenteritis by virus infection, accompanying fever. Occasionally, hepatitis by the viruses causing systemic infection may occur, and screening tests are required. In patients with jaundice, the tests for differential diagnosis and appropriate treatment are important. In the case of a child with hepatitis B virus infection vertically from a hepatitis B surface antigen positive mother, the importance of the recognition of immune clearance can't be overstressed, for the decision of time to begin treatment. Early diagnosis changes the fate of a child with Wilson disease. So, screening test for the disease should not be omitted. Non-alcoholic fatty liver disease, which is mainly discovered in obese children, is a new strong candidate triggering abnormal liver function. Muscular dystrophy is a representative disease mimicking liver dysfunction. Although muscular dystrophy is a progressive disorder, and early diagnosis can't change the fate of patients, it will be better to avoid parent's blame for delayed diagnosis. PMID:24511518

  7. [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

  8. 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

  9. Flight-Test Evaluation of Flutter-Prediction Methods

    NASA Technical Reports Server (NTRS)

    Lind, RIck; Brenner, Marty

    2003-01-01

    The flight-test community routinely spends considerable time and money to determine a range of flight conditions, called a flight envelope, within which an aircraft is safe to fly. The cost of determining a flight envelope could be greatly reduced if there were a method of safely and accurately predicting the speed associated with the onset of an instability called flutter. Several methods have been developed with the goal of predicting flutter speeds to improve the efficiency of flight testing. These methods include (1) data-based methods, in which one relies entirely on information obtained from the flight tests and (2) model-based approaches, in which one relies on a combination of flight data and theoretical models. The data-driven methods include one based on extrapolation of damping trends, one that involves an envelope function, one that involves the Zimmerman-Weissenburger flutter margin, and one that involves a discrete-time auto-regressive model. An example of a model-based approach is that of the flutterometer. These methods have all been shown to be theoretically valid and have been demonstrated on simple test cases; however, until now, they have not been thoroughly evaluated in flight tests. An experimental apparatus called the Aerostructures Test Wing (ATW) was developed to test these prediction methods.

  10. 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?

  11. 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.…

  12. Executive functions predict conceptual learning of science.

    PubMed

    Rhodes, Sinéad M; Booth, Josephine N; Palmer, Lorna Elise; Blythe, Richard A; Delibegovic, Mirela; Wheate, Nial J

    2016-06-01

    We examined the relationship between executive functions and both factual and conceptual learning of science, specifically chemistry, in early adolescence. Sixty-three pupils in their second year of secondary school (aged 12-13 years) participated. Pupils completed tasks of working memory (Spatial Working Memory), inhibition (Stop-Signal), attention set-shifting (ID/ED), and planning (Stockings of Cambridge), from the CANTAB. They also participated in a chemistry teaching session, practical, and assessment on the topic of acids and alkalis designed specifically for this study. Executive function data were related to (1) the chemistry assessment which included aspects of factual and conceptual learning and (2) a recent school science exam. Correlational analyses between executive functions and both the chemistry assessment and science grades revealed that science achievements were significantly correlated with working memory. Linear regression analysis revealed that visuospatial working memory ability was predictive of chemistry performance. Interestingly, this relationship was observed solely in relation to the conceptual learning condition of the assessment highlighting the role of executive functions in understanding and applying knowledge about what is learned within science teaching. PMID:26751597

  13. Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

    PubMed Central

    Hwang, Sohyun; Rhee, Seung Y; Marcotte, Edward M; Lee, Insuk

    2012-01-01

    AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests. PMID:21886106

  14. Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression

    PubMed Central

    Lehtinen, Sonja; Lees, Jon; Bähler, Jürg; Shawe-Taylor, John; Orengo, Christine

    2015-01-01

    With the growing availability of large-scale biological datasets, automated methods of extracting functionally meaningful information from this data are becoming increasingly important. Data relating to functional association between genes or proteins, such as co-expression or functional association, is often represented in terms of gene or protein networks. Several methods of predicting gene function from these networks have been proposed. However, evaluating the relative performance of these algorithms may not be trivial: concerns have been raised over biases in different benchmarking methods and datasets, particularly relating to non-independence of functional association data and test data. In this paper we propose a new network-based gene function prediction algorithm using a commute-time kernel and partial least squares regression (Compass). We compare Compass to GeneMANIA, a leading network-based prediction algorithm, using a number of different benchmarks, and find that Compass outperforms GeneMANIA on these benchmarks. We also explicitly explore problems associated with the non-independence of functional association data and test data. We find that a benchmark based on the Gene Ontology database, which, directly or indirectly, incorporates information from other databases, may considerably overestimate the performance of algorithms exploiting functional association data for prediction. PMID:26288239

  15. 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...

  16. 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...

  17. 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...

  18. 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.

  19. 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.

  20. 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. PMID:23184588

  1. 14 CFR 35.40 - Functional test.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... the endurance test (§ 35.39) must be used in the functional tests and must be driven by a representative engine on a test stand or on an airplane. The propeller must complete these tests without evidence of failure or malfunction. This test may be combined with the endurance test for accumulation...

  2. 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

  3. Track/train dynamics test procedure transfer function test

    NASA Technical Reports Server (NTRS)

    Vigil, R. A.

    1975-01-01

    A transfer function vibration test was made on an 80 ton open hopper freight car in an effort to obtain validation data on the car's nonlinear elastic model. Test configuration, handling, test facilities, test operations, and data acquisition/reduction activities necessary to meet the conditions of test requirements are given.

  4. 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 ...

  5. 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 ...

  6. 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 ...

  7. Habitual fat intake predicts memory function in younger women

    PubMed Central

    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

  8. Text Mining Improves Prediction of Protein Functional Sites

    PubMed Central

    Cohn, Judith D.; Ravikumar, Komandur E.

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

  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. HEALTH SIGNIFICANCE OF PULMONARY FUNCTION TESTS

    EPA Science Inventory

    As the sensitivity and precision of functional tests improves, we become increasingly able to measure responses to pollutant exposures with little, if any, demonstrable health significance. Proper interpretation of such functional responses generally requires an ability to evalua...

  11. 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

  12. Neuropsychological tests for predicting cognitive decline in older adults

    PubMed Central

    Baerresen, Kimberly M; Miller, Karen J; Hanson, Eric R; Miller, Justin S; Dye, Richelin V; Hartman, Richard E; Vermeersch, David; Small, Gary W

    2015-01-01

    Summary Aim To determine neuropsychological tests likely to predict cognitive decline. Methods A sample of nonconverters (n = 106) was compared with those who declined in cognitive status (n = 24). Significant univariate logistic regression prediction models were used to create multivariate logistic regression models to predict decline based on initial neuropsychological testing. Results Rey–Osterrieth Complex Figure Test (RCFT) Retention predicted conversion to mild cognitive impairment (MCI) while baseline Buschke Delay predicted conversion to Alzheimer’s disease (AD). Due to group sample size differences, additional analyses were conducted using a subsample of demographically matched nonconverters. Analyses indicated RCFT Retention predicted conversion to MCI and AD, and Buschke Delay predicted conversion to AD. Conclusion Results suggest RCFT Retention and Buschke Delay may be useful in predicting cognitive decline. PMID:26107318

  13. 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 ...

  14. 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...

  15. 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 ...

  16. 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

  17. Predicted vibrational spectra from anharmonic potential functions

    SciTech Connect

    Dunn, K.M.

    1986-01-01

    The dissertation develops a procedure for predicting vibrational spectra of polyatomic molecules from a combination of theoretical and experimental information. Ab initio quantum chemical calculations provide anharmonic force constants including cubics and diagonal quartics. A variational procedure analogous to configuration interaction is then used to compute eigenvalues of the pure vibrational Hamiltonian. The diagonal quadratic force constants are then adjusted until the calculated fundamental frequencies agree with experiment. The resulting theoretical-experimental force field may then be used to predict the energies of vibrationally excited states. The method is applied to three molecules: hydrogen cyanide, ammonia, and methyl fluoride. For hydrogen cyanide, the dissertation presents predicted energies for all of the vibrationally excited states with up to four quanta of excitation distributed among the four modes. The root-mean-square error is 8.7 cm{sup {minus}1} for the states below 11,000 cm{sup {minus}1}. The force constants for ammonia are adjusted to reproduce the fundamental frequencies of ND{sub 3}. The force constants then predict the energies of states below 7000 cm{sup {minus}1} with an rms error of 5.8 cm{sup {minus}1} for ND{sub 3} and 16.7 cm{sup {minus}1} for NH{sub 3}. Finally, the adjusted force constants for methyl fluoride predict the energies of states below 4100 cm{sup {minus}1} with an rms error of 4.3 cm{sup {minus}1}. These force constants are also used to predict the CH stretching overtone region of CH{sub 3}F and the first, second and third overtone regions of CD{sub 2}FH for which experimental information is not available.

  18. ELEFUNT. Tests of Fortran Elementary Functions

    SciTech Connect

    Cody, W.J.

    1980-03-14

    ELEFUNT is an aggressive test of one or more of the elementary function subroutines generally supplied with the support library accompanying a FORTRAN compiler. Functions tested are ALOG/ALOG10, ASIN/ACOS, ATAN, EXP, POWER, SIN/COS, SINH/COSH, SQRT, TAN/COTAN, and TANH.

  19. Simple topological properties predict functional misannotations in a metabolic network

    PubMed Central

    Liberal, Rodrigo; Pinney, John W.

    2013-01-01

    Motivation: Misannotation in sequence databases is an important obstacle for automated tools for gene function annotation, which rely extensively on comparison with sequences with known function. To improve current annotations and prevent future propagation of errors, sequence-independent tools are, therefore, needed to assist in the identification of misannotated gene products. In the case of enzymatic functions, each functional assignment implies the existence of a reaction within the organism’s metabolic network; a first approximation to a genome-scale metabolic model can be obtained directly from an automated genome annotation. Any obvious problems in the network, such as dead end or disconnected reactions, can, therefore, be strong indications of misannotation. Results: We demonstrate that a machine-learning approach using only network topological features can successfully predict the validity of enzyme annotations. The predictions are tested at three different levels. A random forest using topological features of the metabolic network and trained on curated sets of correct and incorrect enzyme assignments was found to have an accuracy of up to 86% in 5-fold cross-validation experiments. Further cross-validation against unseen enzyme superfamilies indicates that this classifier can successfully extrapolate beyond the classes of enzyme present in the training data. The random forest model was applied to several automated genome annotations, achieving an accuracy of in most cases when validated against recent genome-scale metabolic models. We also observe that when applied to draft metabolic networks for multiple species, a clear negative correlation is observed between predicted annotation quality and phylogenetic distance to the major model organism for biochemistry (Escherichia coli for prokaryotes and Homo sapiens for eukaryotes). Contact: j.pinney@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  20. 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.

  1. The inhomogeneous distribution of liver function: possible impact on the prediction of post-operative remnant liver function

    PubMed Central

    Nilsson, Henrik; Karlgren, Silja; Blomqvist, Lennart; Jonas, Eduard

    2015-01-01

    Background Previous studies have shown that liver function is inhomogeneously distributed in diseased livers, and this uneven distribution cannot be compensated for if a global liver function test is used for the prediction of post-operative remnant liver function. Dynamic Gd-EOB-DTPA-enhanced magnetic resonance imaging (MRI) can assess segmental liver function, thus offering the possibility to overcome this problem. Methods In 10 patients with liver cirrhosis and 10 normal volunteers, the contribution of individual liver segments to total liver function and volume was calculated using dynamic Gd-EOB-DTPA-enhanced MRI. Remnant liver function predictions using a segmental method and global assessment were compared for a simulated left hemihepatectomy. For the prediction based on segmental functional MRI assessment, the estimated function of the remnant liver segments was added. Results Global liver function assessment overestimated the remnant liver function in 9 out of 10 patients by as much as 9.3% [median −3.5% (−9.3–3.5%)]. In the normal volunteers there was a slight underestimation of remnant function in 9 out of 10 cases [median 1.07% (−0.7–2.5%)]. Discussion The present study underlines the necessity of a segmental liver function test able to compensate for the non-homogeneous nature of liver function, if the prediction of post-operative remnant liver function is to be improved. PMID:25297934

  2. Network-based prediction of protein function

    PubMed Central

    Sharan, Roded; Ulitsky, Igor; Shamir, Ron

    2007-01-01

    Functional annotation of proteins is a fundamental problem in the post-genomic era. The recent availability of protein interaction networks for many model species has spurred on the development of computational methods for interpreting such data in order to elucidate protein function. In this review, we describe the current computational approaches for the task, including direct methods, which propagate functional information through the network, and module-assisted methods, which infer functional modules within the network and use those for the annotation task. Although a broad variety of interesting approaches has been developed, further progress in the field will depend on systematic evaluation of the methods and their dissemination in the biological community. PMID:17353930

  3. 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

  4. 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. PMID:20476692

  5. 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.

  6. 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.

  7. 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.

  8. Pulmonary function testing: custom programs for manual equipment.

    PubMed

    Petrini, M F

    1984-01-01

    Pulmonary Function Laboratories with manual equipment can expedite calculations and make them more accurate by using a programmable calculator that will compute functions and predictive equations. However, a custom-made set of programs is better than calculator libraries available from the manufacturer. With custom-made programs, calculations remain as the staff is used to receiving them, programs can be stored in the memory and called independently and only those tests used routinely need to be available. PMID:6546910

  9. Predictive testing of eighteen year olds: counseling challenges.

    PubMed

    Gaff, Clara L; Lynch, Elly; Spencer, Lesley

    2006-08-01

    Genetic counseling of teenagers is challenging and complex. The ability to think abstractly, a sense of self and independence from family all develop during adolescence. Predictive genetic testing counseling protocols presuppose that these qualities exist, requiring the at-risk individual to consider the short and long term consequences of testing as well as their motivations. Eighteen year olds are in transition from adolescence to adulthood; eligible for predictive genetic testing, they may not yet be independent of their family or able to articulate their feelings. This paper presents case studies from the authors' clinical practice to illustrate some of the difficulties faced by genetic counselors when 18 year olds request predictive testing for Hereditary Non-Polyposis Colorectal Cancer. By reflecting upon their experiences with these young adults and their families, the authors' intention is to generate discussion about genetic counseling strategies, particularly for predictive genetic testing, that are both age-appropriate and family-sensitive. PMID:16865560

  10. 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.

  11. Combined biological tests for suicide prediction

    PubMed Central

    Coryell, William; Schlesser, Michael

    2007-01-01

    Disturbances in serotonin neuroregulation and in hypothalamic-pituitary-adrenal axis activity are both likely, and possibly independent, factors in the genesis of suicidal behavior. This analysis considers whether clinically accessible measures of these two disturbances have additive value in the estimation of risk for suicide. Seventy-four inpatients with RDC major or schizoaffective depressive disorders entered a prospective follow-up study from 1978–1981, underwent a dexamethasone suppression test (DST) and had fasting serum cholesterol levels available in the medical record. As reported earlier, patients who had had an abnormal DST result were significantly more likely to commit suicide during follow-up. Serum cholesterol concentrations did not differ by DST result and low cholesterol values were associated with subsequent suicide when age and sex were included as covariates. These results indicate that, with the use of age-appropriate thresholds, serum cholesterol concentrations may be combined with DST results to provide a clinically useful estimate of suicide risk. PMID:17289156

  12. 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

  13. Germination and emergence tests for predicting switchgrass field establishment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of switchgrass (Panicum virgatum L.) seed quality tests on field establishment has not been addressed. Our objective was to evaluate the ability of seed quality tests to predict field establishment. Standard Association of Official Seed Analysts (AOSA) tests are based on the percentage of...

  14. Probabilistic Protein Function Prediction from Heterogeneous Genome-Wide Data

    PubMed Central

    Nariai, Naoki; Kolaczyk, Eric D.; Kasif, Simon

    2007-01-01

    Dramatic improvements in high throughput sequencing technologies have led to a staggering growth in the number of predicted genes. However, a large fraction of these newly discovered genes do not have a functional assignment. Fortunately, a variety of novel high-throughput genome-wide functional screening technologies provide important clues that shed light on gene function. The integration of heterogeneous data to predict protein function has been shown to improve the accuracy of automated gene annotation systems. In this paper, we propose and evaluate a probabilistic approach for protein function prediction that integrates protein-protein interaction (PPI) data, gene expression data, protein motif information, mutant phenotype data, and protein localization data. First, functional linkage graphs are constructed from PPI data and gene expression data, in which an edge between nodes (proteins) represents evidence for functional similarity. The assumption here is that graph neighbors are more likely to share protein function, compared to proteins that are not neighbors. The functional linkage graph model is then used in concert with protein domain, mutant phenotype and protein localization data to produce a functional prediction. Our method is applied to the functional prediction of Saccharomyces cerevisiae genes, using Gene Ontology (GO) terms as the basis of our annotation. In a cross validation study we show that the integrated model increases recall by 18%, compared to using PPI data alone at the 50% precision. We also show that the integrated predictor is significantly better than each individual predictor. However, the observed improvement vs. PPI depends on both the new source of data and the functional category to be predicted. Surprisingly, in some contexts integration hurts overall prediction accuracy. Lastly, we provide a comprehensive assignment of putative GO terms to 463 proteins that currently have no assigned function. PMID:17396164

  15. Metabolic Syndrome Biomarkers Predict Lung Function Impairment

    PubMed Central

    Naveed, Bushra; Weiden, Michael D.; Kwon, Sophia; Gracely, Edward J.; Comfort, Ashley L.; Ferrier, Natalia; Kasturiarachchi, Kusali J.; Cohen, Hillel W.; Aldrich, Thomas K.; Rom, William N.; Kelly, Kerry; Prezant, David J.

    2012-01-01

    Rationale: Cross-sectional studies demonstrate an association between metabolic syndrome and impaired lung function. Objectives: To define if metabolic syndrome biomarkers are risk factors for loss of lung function after irritant exposure. Methods: A nested case-control study of Fire Department of New York personnel with normal pre–September 11th FEV1 and who presented for subspecialty pulmonary evaluation before March 10, 2008. We correlated metabolic syndrome biomarkers obtained within 6 months of World Trade Center dust exposure with subsequent FEV1. FEV1 at subspecialty pulmonary evaluation within 6.5 years defined disease status; cases had FEV1 less than lower limit of normal, whereas control subjects had FEV1 greater than or equal to lower limit of normal. Measurements and Main Results: Clinical data and serum sampled at the first monitoring examination within 6 months of September 11, 2001, assessed body mass index, heart rate, serum glucose, triglycerides and high-density lipoprotein (HDL), leptin, pancreatic polypeptide, and amylin. Cases and control subjects had significant differences in HDL less than 40 mg/dl with triglycerides greater than or equal to 150 mg/dl, heart rate greater than or equal to 66 bpm, and leptin greater than or equal to 10,300 pg/ml. Each increased the odds of abnormal FEV1 at pulmonary evaluation by more than twofold, whereas amylin greater than or equal to 116 pg/ml decreased the odds by 84%, in a multibiomarker model adjusting for age, race, body mass index, and World Trade Center arrival time. This model had a sensitivity of 41%, a specificity of 86%, and a receiver operating characteristic area under the curve of 0.77. Conclusions: Abnormal triglycerides and HDL and elevated heart rate and leptin are independent risk factors of greater susceptibility to lung function impairment after September 11, 2001, whereas elevated amylin is protective. Metabolic biomarkers are predictors of lung disease, and may be useful for assessing

  16. PULMONARY FUNCTION TESTING IN SMALL LABORATORY MAMMALS

    EPA Science Inventory

    The lung is the primary organ likely to be exposed by inhalation studies and, therefore, measurement of changes in lung function are of particular interest to the pulmonary physiologist and toxicologist. Tests of pulmonary function have been developed which can be used with small...

  17. Comparison of clinical tests of olfactory function.

    PubMed

    Reden, J; Draf, C; Frank, R A; Hummel, T

    2016-04-01

    To assess olfactory function, various measures are used in clinical routine. In this study, the Sniff Magnitude Test (SMT), a test considering the sniff response to an odor, was applied to patients with olfactory dysfunction (n = 49) and to a control group without subjective olfaction disorder (n = 21). For comparison, the validated "Sniffin' Sticks" test battery, a psychophysical olfactory test consisting of tests for phenyl ethyl alcohol odor threshold, odor discrimination, and odor identification was performed. Analyses indicated that the SMT showed significant differences between patients and controls (p = 0.003). Furthermore, results from the SMT and the "Sniffin' Sticks" correlated significantly (p < 0.001). In conclusion, the SMT appears to be a useful addition to the battery of available clinical tests to assess olfactory function. PMID:26050222

  18. 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

  19. Using search engine technology for protein function prediction.

    PubMed

    Chen, Ziyang; Cai, Zhao; Li, Min; Liu, Binbin

    2011-01-01

    Prediction of protein function is one of the most challenging problems in the post-genomic era. In this paper, we propose a novel algorithm Improved ProteinRank (IPR) for protein function prediction, which is based on the search engine technology and the preferential attachment criteria. In addition, an improved algorithm IPRW is developed from IPR to be used in the weighted protein?protein interaction (PPI) network. The proposed algorithms IPR and IPRW are applied to the PPI network of S.cerevisiae. The experimental results show that both IPR and IPRW outweigh the previous methods for the prediction of protein functions. PMID:21441099

  20. Predicting Test Performance: A Content Valid Approach to Screening Applicants.

    ERIC Educational Resources Information Center

    Pannone, Ronald D.

    1984-01-01

    Examined the validity of a rationally developed biographical questionnaire for predicting content valid test performance for electrician applicants (N=221). Results showed that the utility of the questionnaire in screening applicant populations was both statistically and practically significant. (LLL)

  1. Trends in the Predictive Validity of the Scholastic Aptitude Test.

    ERIC Educational Resources Information Center

    Fincher, Cameron

    Changes in the predictive validity of the Scholastic Aptitude Test (SAT) that have been observed in the University System of Georgia (USGA) over the past two decades were studied. Several analyses were performed using student data from 27 USGA schools to determine the effectiveness of the SAT in predicting freshman grades. National trends…

  2. 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

  3. Evaluation of abnormal liver function tests.

    PubMed

    Agrawal, Swastik; Dhiman, Radha K; Limdi, Jimmy K

    2016-04-01

    Incidentally detected abnormality in liver function tests is a common situation encountered by physicians across all disciplines. Many of these patients do not have primary liver disease as most of the commonly performed markers are not specific for the liver and are affected by myriad factors unrelated to liver disease. Also, many of these tests like liver enzyme levels do not measure the function of the liver, but are markers of liver injury, which is broadly of two types: hepatocellular and cholestatic. A combination of a careful history and clinical examination along with interpretation of pattern of liver test abnormalities can often identify type and aetiology of liver disease, allowing for a targeted investigation approach. Severity of liver injury is best assessed by composite scores like the Model for End Stage Liver Disease rather than any single parameter. In this review, we discuss the interpretation of the routinely performed liver tests along with the indications and utility of quantitative tests. PMID:26842972

  4. Testing prediction methods: Earthquake clustering versus the Poisson model

    USGS Publications Warehouse

    Michael, A.J.

    1997-01-01

    Testing earthquake prediction methods requires statistical techniques that compare observed success to random chance. One technique is to produce simulated earthquake catalogs and measure the relative success of predicting real and simulated earthquakes. The accuracy of these tests depends on the validity of the statistical model used to simulate the earthquakes. This study tests the effect of clustering in the statistical earthquake model on the results. Three simulation models were used to produce significance levels for a VLF earthquake prediction method. As the degree of simulated clustering increases, the statistical significance drops. Hence, the use of a seismicity model with insufficient clustering can lead to overly optimistic results. A successful method must pass the statistical tests with a model that fully replicates the observed clustering. However, a method can be rejected based on tests with a model that contains insufficient clustering. U.S. copyright. Published in 1997 by the American Geophysical Union.

  5. Pulmonary function testing in small laboratory mammals.

    PubMed Central

    O'Neil, J J; Raub, J A

    1984-01-01

    The lung is the primary organ likely to be exposed by inhalation studies and, therefore, measurement of changes in lung function are of particular interest to the pulmonary physiologist and toxicologist. Tests of pulmonary function have been developed which can be used with small animals to measure spirometry (lung volumes), mechanics, distribution of ventilation, gas exchange or control of ventilation. These tests were designed on the basis of similar tests which are used in humans to diagnose and manage patients with lung disease. A major difference is that many of the measurements are performed in anesthetized animals, while human pulmonary function is usually measured in awake cooperating individuals. In addition, the measurement of respiratory events in small animals requires sensitive and rapidly responding equipment, because signals may be small and events can occur quickly. In general, the measurements described provide information on the change in normal lung function which results primarily from structural changes. These tests of pulmonary function can be repetitively and routinely accomplished and the results appear to be highly reproducible. Although some are quite sophisticated, many can be undertaken with relatively inexpensive equipment and provide useful information for toxicological testing. PMID:6434299

  6. Analysing earthquake slip models with the spatial prediction comparison test

    NASA Astrophysics Data System (ADS)

    Zhang, Ling; Mai, P. Martin; Thingbaijam, Kiran K. S.; Razafindrakoto, Hoby N. T.; Genton, Marc G.

    2015-01-01

    Earthquake rupture models inferred from inversions of geophysical and/or geodetic data exhibit remarkable variability due to uncertainties in modelling assumptions, the use of different inversion algorithms, or variations in data selection and data processing. A robust statistical comparison of different rupture models obtained for a single earthquake is needed to quantify the intra-event variability, both for benchmark exercises and for real earthquakes. The same approach may be useful to characterize (dis-)similarities in events that are typically grouped into a common class of events (e.g. moderate-size crustal strike-slip earthquakes or tsunamigenic large subduction earthquakes). For this purpose, we examine the performance of the spatial prediction comparison test (SPCT), a statistical test developed to compare spatial (random) fields by means of a chosen loss function that describes an error relation between a 2-D field (`model') and a reference model. We implement and calibrate the SPCT approach for a suite of synthetic 2-D slip distributions, generated as spatial random fields with various characteristics, and then apply the method to results of a benchmark inversion exercise with known solution. We find the SPCT to be sensitive to different spatial correlations lengths, and different heterogeneity levels of the slip distributions. The SPCT approach proves to be a simple and effective tool for ranking the slip models with respect to a reference model.

  7. 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. PMID:25343279

  8. 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

  9. 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…

  10. PREDICTIVE TEST METHODS: PERMEATION OF POLYMERIC MEMBRANES BY ORGANIC SOLVENTS

    EPA Science Inventory

    As the result of screening elastomeric materials that may be suitable for formulating chemical-protective clothing, a simple test method has been developed that allows the prediction of the permeation of an organic solvent through a polymeric membrane. The test method, based on l...

  11. 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…

  12. 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)

  13. 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

  14. 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.

  15. 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.

  16. Track/train dynamics test report transfer function test. Volume 1: Test

    NASA Technical Reports Server (NTRS)

    Vigil, R. A.

    1975-01-01

    A description is presented of the transfer function test performed on an open hopper freight car loaded with 80 tons of coal. Test data and a post-test update of the requirements document and test procedure are presented. Included are a statement of the test objective, a description of the test configurations, test facilities, test methods, data acquisition/reduction operations, and a chronological test summary. An index to the data for the three test configurations (X, Y, and Z-axis tests) is presented along with test sequence, run number, test reference, and input parameters.

  17. Gene function prediction with knowledge from gene ontology.

    PubMed

    Shen, Ying; Zhang, Lin

    2015-01-01

    Gene function prediction is an important problem in bioinformatics. Due to the inherent noise existing in the gene expression data, the attempt to improve the prediction accuracy resorting to new classification techniques is limited. With the emergence of Gene Ontology (GO), extra knowledge about the gene products can be extracted from GO and facilitates solving the gene function prediction problem. In this paper, we propose a new method which utilises GO information to improve the classifiers' performance in gene function prediction. Specifically, our method learns a distance metric under the supervision of the GO knowledge using the distance learning technique. Compared with the traditional distance metrics, the learned one produces a better performance and consequently classification accuracy can be improved. The effectiveness of our proposed method has been corroborated by the extensive experimental results. PMID:26529907

  18. 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

  19. Empirical sediment transport function predicting seepage erosion undercutting for cohesive bank failure prediction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seepage erosion is an important factor in hillslope instability and failure. However, predicting erosion by subsurface flow or seepage and incorporating its effects into stability models remains a challenge. Limitations exist with all existing seepage erosion sediment transport functions, including ...

  20. INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES

    PubMed Central

    Grant, Marianne A.

    2014-01-01

    Pharmaceutical researchers must evaluate vast numbers of protein sequences and formulate innovative strategies for identifying valid targets and discovering leads against them as a way of accelerating drug discovery. The ever increasing number and diversity of novel protein sequences identified by genomic sequencing projects and the success of worldwide structural genomics initiatives have spurred great interest and impetus in the development of methods for accurate, computationally empowered protein function prediction and active site identification. Previously, in the absence of direct experimental evidence, homology-based protein function annotation remained the gold-standard for in silico analysis and prediction of protein function. However, with the continued exponential expansion of sequence databases, this approach is not always applicable, as fewer query protein sequences demonstrate significant homology to protein gene products of known function. As a result, several non-homology based methods for protein function prediction that are based on sequence features, structure, evolution, biochemical and genetic knowledge have emerged. Herein, we review current bioinformatic programs and approaches for protein function prediction/annotation and discuss their integration into drug discovery initiatives. The development of such methods to annotate protein functional sites and their application to large protein functional families is crucial to successfully utilizing the vast amounts of genomic sequence information available to drug discovery and development processes. PMID:25530654

  1. Preschool Executive Functioning Abilities Predict Early Mathematics Achievement

    ERIC Educational Resources Information Center

    Clark, Caron A. C.; Pritchard, Verena E.; Woodward, Lianne J.

    2010-01-01

    Impairments in executive function have been documented in school-age children with mathematical learning difficulties. However, the utility and specificity of preschool executive function abilities in predicting later mathematical achievement are poorly understood. This study examined linkages between children's developing executive function…

  2. 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…

  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. Variability of routine pulmonary function tests.

    PubMed Central

    Hruby, J; Butler, J

    1975-01-01

    Pulmonary function tests sometimes indicate a progressive deterioration and at other times a 'stepwise' worsening which may be followed by improvement. Interpretation depends on the extent of random or diurnal variations in function. Routing pulmonary function tests (VC, FEV1, FRC, and airway resistance (Raw)) were repeatedly measured in normal subjects, patients with stable irreversible airways obstruction, and patients with stable restrictive disease. In all groups there was a significant (P less than 0.001) diurnal variation in Raw, with high values in the morning, low values at noon, and rising values in the evening. The midday Raw values were about 80% of the highest daily values. The considerable random and diurnal variability seen in all tests is reflected in the range of high and low values (% of mean individual response) in individuals. The largest variation in an individual between measurements taken at two different times was 81% in Raw (range: 40% above to 41% below the mean). There was less variation in FEV1 (29%), FRC (62%), and VC (30%). Thus the finding of a stepwise change in function could reflect its natrual variability. When repeated studies are done to assess progress or the effects of therapy on disease, there are many factors, including the time of day at which the tests are performed, which should be standardized as far as possible. PMID:1198395

  5. A large-scale evaluation of computational protein function prediction

    PubMed Central

    Radivojac, Predrag; Clark, Wyatt T; Ronnen Oron, Tal; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Böhm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-01-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools. PMID:23353650

  6. Protein Structure and Function Prediction Using I-TASSER

    PubMed Central

    Yang, Jianyi; Zhang, Yang

    2016-01-01

    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. PMID:26678386

  7. A large-scale evaluation of computational protein function prediction.

    PubMed

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. PMID:23353650

  8. Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks

    PubMed Central

    Cao, Renzhi; Cheng, Jianlin

    2016-01-01

    Motivations Protein function prediction is an important and challenging problem in bioinformatics and computational biology. Functionally relevant biological information such as protein sequences, gene expression, and protein–protein interactions has been used mostly separately for protein function prediction. One of the major challenges is how to effectively integrate multiple sources of both traditional and new information such as spatial gene–gene interaction networks generated from chromosomal conformation data together to improve protein function prediction. Results In this work, we developed three different probabilistic scores (MIS, SEQ, and NET score) to combine protein sequence, function associations, and protein–protein interaction and spatial gene–gene interaction networks for protein function prediction. The MIS score is mainly generated from homologous proteins found by PSI-BLAST search, and also association rules between Gene Ontology terms, which are learned by mining the Swiss-Prot database. The SEQ score is generated from protein sequences. The NET score is generated from protein–protein interaction and spatial gene–gene interaction networks. These three scores were combined in a new Statistical Multiple Integrative Scoring System (SMISS) to predict protein function. We tested SMISS on the data set of 2011 Critical Assessment of Function Annotation (CAFA). The method performed substantially better than three base-line methods and an advanced method based on protein profile–sequence comparison, profile–profile comparison, and domain co-occurrence networks according to the maximum F-measure. PMID:26370280

  9. Predicting stretcher carriage: Investigating variations in bilateral carry tests.

    PubMed

    Beck, Ben; Middleton, Kane J; Carstairs, Greg L; Billing, Daniel C; Caldwell, Joanne N

    2016-07-01

    Carrying a casualty on a stretcher is a critical task within military and emergency service occupations. This study evaluated the impact of manipulating carry speed and the object type in bilateral carries on the ability to predict performance and reflect the physical and physiological requirements of a unilateral stretcher carry. We demonstrated that three task-related predictive tests; a jerry can carry performed at 4.5 km h(-1)or 5.0 km h(-1) and a kettle-bell carry performed at 5.0 km h(-1) were strongly predictive of the physical and physiological demands of an individual participating as part of a four-person stretcher carry team. Therefore, bilateral predictive assessments have the utility for predicting the suitability of employees to effectively and safely conduct a four-person unilateral stretcher carry. PMID:26995042

  10. Helicopter external noise prediction and correlation with flight test

    NASA Technical Reports Server (NTRS)

    Gupta, B. P.

    1978-01-01

    Mathematical analysis procedures for predicting the main and tail rotor rotational and broadband noise are presented. The aerodynamic and acoustical data from Operational Loads Survey (OLS) flight program are used for validating the analysis and noise prediction methodology. For the long method of rotational noise prediction, the spanwise, chordwise, and azimuthwise airloading is used. In the short method, the airloads are assumed to be concentrated at a single spanwise station and for higher harmonics an airloading harmonic exponent of 2.0 is assumed. For the same flight condition, the predictions from long and short methods of rotational noise prediction are compared with the flight test results. The short method correlates as well or better than the long method.

  11. Revisiting the prediction of protein function at CASP6.

    PubMed

    Pellegrini-Calace, Marialuisa; Soro, Simonetta; Tramontano, Anna

    2006-07-01

    The ability to predict the function of a protein, given its sequence and/or 3D structure, is an essential requirement for exploiting the wealth of data made available by genomics and structural genomics projects and is therefore raising increasing interest in the computational biology community. To foster developments in the area as well as to establish the state of the art of present methods, a function prediction category was tentatively introduced in the 6th edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP) worldwide experiment. The assessment of the performance of the methods was made difficult by at least two factors: (a) the experimentally determined function of the targets was not available at the time of assessment; (b) the experiment is run blindly, preventing verification of whether the convergence of different predictions towards the same functional annotation was due to the similarity of the methods or to a genuine signal detectable by different methodologies. In this work, we collected information about the methods used by the various predictors and revisited the results of the experiment by verifying how often and in which cases a convergent prediction was obtained by methods based on different rationale. We propose a method for classifying the type and redundancy of the methods. We also analyzed the cases in which a function for the target protein has become available. Our results show that predictions derived from a consensus of different methods can reach an accuracy as high as 80%. It follows that some of the predictions submitted to CASP6, once reanalyzed taking into account the type of converging methods, can provide very useful information to researchers interested in the function of the target proteins. PMID:16759228

  12. 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

  13. Creating and evaluating genetic tests predictive of drug response

    PubMed Central

    Weiss, Scott T.; McLeod, Howard L.; Flockhart, David A.; Dolan, M. Eileen; Benowitz, Neal L.; Johnson, Julie A.; Ratain, Mark J.; Giacomini, Kathleen M.

    2009-01-01

    A key goal of pharmacogenetics — the use of genetic variation to elucidate inter-individual variation in drug treatment response — is to aid the development of predictive genetic tests that could maximize drug efficacy and minimize drug toxicity. The completion of the Human Genome Project and the associated HapMap Project, together with advances in technologies for investigating genetic variation, have greatly advanced the potential to develop such tests; however, many challenges remain. With the aim of helping to address some of these challenges, this article discusses the steps that are involved in the development of predictive tests for drug treatment response based on genetic variation, and factors that influence the development and performance of these tests. PMID:18587383

  14. Facilitating family communication about predictive genetic testing: probands' perceptions.

    PubMed

    Gaff, Clara L; Collins, Veronica; Symes, Tiffany; Halliday, Jane

    2005-04-01

    The responsibility of informing relatives that predictive genetic testing is available often falls to the proband. Support is required during this process, however the perceived utility of genetic counseling and other strategies to facilitate communication have not been explored. We investigated the experiences of 12 individuals with hereditary nonpolyposis colorectal cancer (HNPCC) in a semistructured telephone interview. Respondents informed their immediate family about the availability of genetic testing, however many more-distant relatives were not directly informed. Respondents were mostly satisfied with the way they told family members about testing and had mixed views about the usefulness of genetic counseling. Gender differences were observed, with most men expressing a need for guidance or support in communicating to relatives. Letters and booklets were thought to enhance the quality of information but the provision of further aids is unlikely to increase the number of relatives made aware of predictive testing by the proband. PMID:15959644

  15. Reduced Cognitive Function Predicts Functional Decline in Patients with Heart Failure over 12 months

    PubMed Central

    Alosco, Michael L.; Spitznagel, Mary Beth; Cohen, Ronald; Sweet, Lawrence H.; Colbert, Lisa H.; Josephson, Richard; Hughes, Joel; Rosneck, Jim; Gunstad, John

    2016-01-01

    Background Impaired activities of daily living (ADL) are common in heart failure (HF) patients and contribute to the elevated mortality and hospitalization rates in this population. Cognitive impairment is also prevalent in HF, though its ability to predict functional decline over time is unknown. Aims This study examined the longitudinal pattern of activities of daily living in HF persons and whether reduced baseline cognitive status predicts functional decline in this population. Methods 110 persons with HF completed the Lawton-Brody Activities of Daily Living Scale and were administered the Modified Mini-Mental Status Examination (3MS) at baseline and a 12-month follow-up. Three composite scores were derived from the Lawton-Brody, including total, instrumental, and basic ADLs. Results HF patients reported high rates of baseline impairments in instrumental ADLs, including shopping, food preparation, housekeeping duties, laundry, among others. Repeated measures analyses showed significant declines in total and instrumental ADLs from baseline to the 12-month follow-up in HF (p < .05). Hierarchical regression analyses showed that poorer baseline performance on the 3MS predicted worse total ADL performance at 12-months (β = .15, p = .049), including greater dependence in shopping, driving, feeding, and physical ambulation (p < .05 for all). Conclusion The current results show that HF patients report significant functional decline over a 12-month period and brief cognitive tests can identify those patients at highest risk for decline. If replicated, such findings encourage the use of cognitive screening measures to identify HF patients most likely to require assistance with ADL tasks. PMID:23754840

  16. Testing the functional significance of tail streamers

    PubMed Central

    Evans, M. R.; Thomas, A. L. R.

    1997-01-01

    Studies of the evolution of elaborate ornaments have concentrated on their role in increasing attractiveness to mates. The classic examples of such sexually selected structures are the elongated tails of some bird species. Elongated tails can be divided into three categories: graduated tails, pin tails and streamers. There seems to be little debate about whether graduated and pin tails are ornaments; i.e. costly signals used in mate choice. However, in the case of streamers there is considerable discussion about their function. It has been suggested that tail streamers could be (i) entirely naturally selected, (ii) entirely sexually selected, (iii) partly naturally and partly sexually selected. The prime example of a species with tail streamers is the swallow (Hirundo rustica) in which both sexes have tail streamers. In this paper we discuss the aerodynamic consequences of different types of manipulation of the streamer and/or outer tail feather. We make qualitative predictions about the aerodynamic performance of swallows with manipulated tail streamers; these predictions differ depending on whether streamers have a naturally or sexually selected function. We demonstrate that these hypotheses can only be separated if tail streamers are shortened and changes in aerodynamic performance measured during turning flight.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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,…

  2. 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…

  3. 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)

  4. 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

  5. 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

  6. 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

  7. 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. PMID:27235985

  8. Beyond Genotype: Serotonin Transporter Epigenetic Modification Predicts Human Brain Function

    PubMed Central

    Nikolova, Yuliya S.; Koenen, Karestan C.; Galea, Sandro; Wang, Chiou-Miin; Seney, Marianne L.; Sibille, Etienne; Williamson, Douglas E.; Hariri, Ahmad R.

    2014-01-01

    We examined epigenetic regulation in regards to behaviorally and clinically relevant human brain function. Specifically, we found that increased promoter methylation of the serotonin transporter gene predicted increased threat-related amygdala reactivity and decreased mRNA expression in postmortem amygdala tissue. These patterns were independent of functional genetic variation in the same region. Furthermore, the association with amygdala reactivity was replicated in a second cohort and was robust to both sampling methods and age. PMID:25086606

  9. 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

  10. Predicted maximal heart rate for upper body exercise testing.

    PubMed

    Hill, M; Talbot, C; Price, M

    2016-03-01

    Age-predicted maximal heart rate (HRMAX ) equations are commonly used for the purpose of prescribing exercise regimens, as criteria for achieving maximal exertion and for diagnostic exercise testing. Despite the growing popularity of upper body exercise in both healthy and clinical settings, no recommendations are available for exercise modes using the smaller upper body muscle mass. The purpose of this study was to determine how well commonly used age-adjusted prediction equations for HRMAX estimate actual HRMAX for upper body exercise in healthy young and older adults. A total of 30 young (age: 20 ± 2 years, height: 171·9 ± 32·8 cm, mass: 77·7 ± 12·6 kg) and 20 elderly adults (age: 66 ± 6 years, height: 162 ± 8·1 cm, mass: 65·3 ± 12·3 kg) undertook maximal incremental exercise tests on a conventional arm crank ergometer. Age-adjusted maximal heart rate was calculated using prediction equations based on leg exercise and compared with measured HRMAX data for the arms. Maximal HR for arm exercise was significantly overpredicted compared with age-adjusted prediction equations in both young and older adults. Subtracting 10-20 beats min(-1) from conventional prediction equations provides a reasonable estimate of HRMAX for upper body exercise in healthy older and younger adults. PMID:25319169

  11. 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

  12. 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.

  13. Exploring Function Prediction in Protein Interaction Networks via Clustering Methods

    PubMed Central

    Trivodaliev, Kire; Bogojeska, Aleksandra; Kocarev, Ljupco

    2014-01-01

    Complex networks have recently become the focus of research in many fields. Their structure reveals crucial information for the nodes, how they connect and share information. In our work we analyze protein interaction networks as complex networks for their functional modular structure and later use that information in the functional annotation of proteins within the network. We propose several graph representations for the protein interaction network, each having different level of complexity and inclusion of the annotation information within the graph. We aim to explore what the benefits and the drawbacks of these proposed graphs are, when they are used in the function prediction process via clustering methods. For making this cluster based prediction, we adopt well established approaches for cluster detection in complex networks using most recent representative algorithms that have been proven as efficient in the task at hand. The experiments are performed using a purified and reliable Saccharomyces cerevisiae protein interaction network, which is then used to generate the different graph representations. Each of the graph representations is later analysed in combination with each of the clustering algorithms, which have been possibly modified and implemented to fit the specific graph. We evaluate results in regards of biological validity and function prediction performance. Our results indicate that the novel ways of presenting the complex graph improve the prediction process, although the computational complexity should be taken into account when deciding on a particular approach. PMID:24972109

  14. The Prediction of Ego Functioning in Adolescence. Final Report.

    ERIC Educational Resources Information Center

    Taube, Irvin; Vreeland, Rebecca

    The object of this study was to predict ego functioning in college among a group of successful high school graduates. Two hundred and seventy-one graduates of Phillips Exeter Academy who had been admitted to Harvard University during 4 consecutive years were studied. Three types of previously collected data were used: (1) teacher reports on the…

  15. Human transfer functions used to predict system performance parameters

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Automatic, parameter-tracking, model-matching technique compares the responses of a human operator with those of an analog computer model of a human operator to predict and analyze the performance of mechanical or electromechanical systems prior to construction. Transfer functions represent the input-output relation of an operator controlling a closed-loop system.

  16. 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. PMID:26948696

  17. 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.

  18. firestar--advances in the prediction of functionally important residues.

    PubMed

    Lopez, Gonzalo; Maietta, Paolo; Rodriguez, Jose Manuel; Valencia, Alfonso; Tress, Michael L

    2011-07-01

    firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php. PMID:21672959

  19. Prediction of Limit Strains in Limiting Dome Height Formability Test

    NASA Astrophysics Data System (ADS)

    Zadpoor, Amir A.; Sinke, Jos; Benedictus, Rinze

    2007-04-01

    In this paper, the Marciniak-Kunczynski (MK) method is combined with the Storen-Rice analysis in order to improve accuracy of the predicted limit strains in Limiting Dome Height (LDH) test. FEM simulation is carried out by means of a commercial FEM code (ABAQUS) and FEM results are postprocessed by using an improved MK code. It has been shown that while original MK method considerably misspredicts the limit strains, a combination of MK method and Storen-Rice analysis can predict the dome height with a very good accuracy.

  20. 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.

  1. The predictive information obtained by testing multiple software versions

    NASA Technical Reports Server (NTRS)

    Lee, Larry D.

    1987-01-01

    Multiversion programming is a redundancy approach to developing highly reliable software. In applications of this method, two or more versions of a program are developed independently by different programmers and the versions are combined to form a redundant system. One variation of this approach consists of developing a set of n program versions and testing the versions to predict the failure probability of a particular program or a system formed from a subset of the programs. The precision that might be obtained, and also the effect of programmer variability if predictions are made over repetitions of the process of generating different program versions, are examined.

  2. 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…

  3. 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.

  4. Predicting Protein Function via Semantic Integration of Multiple Networks.

    PubMed

    Yu, Guoxian; Fu, Guangyuan; Wang, Jun; Zhu, Hailong

    2016-01-01

    Determining the biological functions of proteins is one of the key challenges in the post-genomic era. The rapidly accumulated large volumes of proteomic and genomic data drives to develop computational models for automatically predicting protein function in large scale. Recent approaches focus on integrating multiple heterogeneous data sources and they often get better results than methods that use single data source alone. In this paper, we investigate how to integrate multiple biological data sources with the biological knowledge, i.e., Gene Ontology (GO), for protein function prediction. We propose a method, called SimNet, to Semantically i ntegrate multiple functional association Networks derived from heterogenous data sources. SimNet firstly utilizes GO annotations of proteins to capture the semantic similarity between proteins and introduces a semantic kernel based on the similarity. Next, SimNet constructs a composite network, obtained as a weighted summation of individual networks, and aligns the network with the kernel to get the weights assigned to individual networks. Then, it applies a network-based classifier on the composite network to predict protein function. Experiment results on heterogenous proteomic data sources of Yeast, Human, Mouse, and Fly show that, SimNet not only achieves better (or comparable) results than other related competitive approaches, but also takes much less time. The Matlab codes of SimNet are available at https://sites.google.com/site/guoxian85/simnet. PMID:26800544

  5. Analysis and Functional Prediction of Reactive Cysteine Residues*

    PubMed Central

    Marino, Stefano M.; Gladyshev, Vadim N.

    2012-01-01

    Cys is much different from other common amino acids in proteins. Being one of the least abundant residues, Cys is often observed in functional sites in proteins. This residue is reactive, polarizable, and redox-active; has high affinity for metals; and is particularly responsive to the local environment. A better understanding of the basic properties of Cys is essential for interpretation of high-throughput data sets and for prediction and classification of functional Cys residues. We provide an overview of approaches used to study Cys residues, from methods for investigation of their basic properties, such as exposure and pKa, to algorithms for functional prediction of different types of Cys in proteins. PMID:22157013

  6. 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

  7. Predictive genetic testing for complex diseases: a public health perspective

    PubMed Central

    Marzuillo, C.; De Vito, C.; D’Andrea, E.; Rosso, A.

    2014-01-01

    From a public health perspective, systematic, evidence-based technology assessments and economic evaluations are needed to guide the incorporation of genomics into clinical and public health practice. However, scientific evidence on the effectiveness of predictive genetic tests is difficult to obtain. This review first highlights the similarities and differences between traditional screening tests and predictive genetic testing for complex diseases and goes on to describe frameworks for the evaluation of genetic testing that have been developed in recent years providing some evidence that currently genetic tests are not used in an appropriate way. Nevertheless, evidence-based recommendations are already available for some genomic applications that can reduce morbidity and mortality and many more are expected to emerge over the next decade. The time is now ripe for the introduction of a range of genetic tests into healthcare practice, but this will require the development of specific health policies, proper public health evaluations, organizational changes within the healthcare systems, capacity building among the healthcare workforce and the education of the public. PMID:24049051

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. Predicting Lifetimes Of CMOS ASIC's From Test Data

    NASA Technical Reports Server (NTRS)

    Buehler, Martin G.; Zamani, Nasser; Zoutendyk, John A.

    1993-01-01

    Concise report discusses recent developments in use of semiempirical mathematical models to predict rates of failure and operating lifetimes of complementary metal oxide/semiconductor (CMOS) application-specific integrated circuits (ASIC's). Each model represents specific mechanism of failure. Once failure mechanisms and models relevant to given ASIC chosen, adjustable parameters in models fitted to life-test data acquired from representative integrated-circuit structures on test coupons fabricated along with ASIC's. Then design parameters of ASIC's incorporated into models, and models yield lifetimes.

  14. Issues concerning the evaluation and regulation of predictive genetic testing.

    PubMed

    Zimmern, R L

    2014-01-01

    This paper is a précis of my keynote address at the Symposium on Predictive Genetic Testing organised by the Robert Koch Institute in Berlin. The talk is based on reflections which I have had over a number of years on genetic testing and its evaluation and regulation. It presents a thesis, which I hope will generate discussion and comment. A theme which will run through the paper is the need for precise definition of terms before making any normative statement about such terms. Our failure to do so in genetic discourse is at best confusing and at worst capable of resulting in inappropriate (and sometimes harmful) regulatory responses. PMID:22773250

  15. 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

  16. Risk reversals in predictive testing for Huntington disease.

    PubMed Central

    Almqvist, E; Adam, S; Bloch, M; Fuller, A; Welch, P; Eisenberg, D; Whelan, D; Macgregor, D; Meschino, W; Hayden, M R

    1997-01-01

    The first predictive testing for Huntington disease (HD) was based on analysis of linked polymorphic DNA markers to estimate the likelihood of inheriting the mutation for HD. Limits to accuracy included recombination between the DNA markers and the mutation, pedigree structure, and whether DNA samples were available from family members. With direct tests for the HD mutation, we have assessed the accuracy of results obtained by linkage approaches when requested to do so by the test individuals. For six such individuals, there was significant disparity between the tests. Three went from a decreased risk to an increased risk, while in another three the risk was decreased. Knowledge of the potential reasons for these changes in results and impact of these risk reversals on both patients and the counseling team can assist in the development of strategies for the prevention and, where necessary, management of a risk reversal in any predictive testing program. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:9382108

  17. Scoring functions for prediction of protein-ligand interactions.

    PubMed

    Wang, Jui-Chih; Lin, Jung-Hsin

    2013-01-01

    The scoring functions for protein-ligand interactions plays central roles in computational drug design, virtual screening of chemical libraries for new lead identification, and prediction of possible binding targets of small chemical molecules. An ideal scoring function for protein-ligand interactions is expected to be able to recognize the native binding pose of a ligand on the protein surface among decoy poses, and to accurately predict the binding affinity (or binding free energy) so that the active molecules can be discriminated from the non-active ones. Due to the empirical nature of most, if not all, scoring functions for protein-ligand interactions, the general applicability of empirical scoring functions, especially to domains far outside training sets, is a major concern. In this review article, we will explore the foundations of different classes of scoring functions, their possible limitations, and their suitable application domains. We also provide assessments of several scoring functions on weakly-interacting protein-ligand complexes, which will be useful information in computational fragment-based drug design or virtual screening. PMID:23016847

  18. Can quantitative sensory testing predict responses to analgesic treatment?

    PubMed

    Grosen, K; Fischer, I W D; Olesen, A E; Drewes, A M

    2013-10-01

    The role of quantitative sensory testing (QST) in prediction of analgesic effect in humans is scarcely investigated. This updated review assesses the effectiveness in predicting analgesic effects in healthy volunteers, surgical patients and patients with chronic pain. A systematic review of English written, peer-reviewed articles was conducted using PubMed and Embase (1980-2013). Additional studies were identified by chain searching. Search terms included 'quantitative sensory testing', 'sensory testing' and 'analgesics'. Studies on the relationship between QST and response to analgesic treatment in human adults were included. Appraisal of the methodological quality of the included studies was based on evaluative criteria for prognostic studies. Fourteen studies (including 720 individuals) met the inclusion criteria. Significant correlations were observed between responses to analgesics and several QST parameters including (1) heat pain threshold in experimental human pain, (2) electrical and heat pain thresholds, pressure pain tolerance and suprathreshold heat pain in surgical patients, and (3) electrical and heat pain threshold and conditioned pain modulation in patients with chronic pain. Heterogeneity among studies was observed especially with regard to application of QST and type and use of analgesics. Although promising, the current evidence is not sufficiently robust to recommend the use of any specific QST parameter in predicting analgesic response. Future studies should focus on a range of different experimental pain modalities rather than a single static pain stimulation paradigm. PMID:23658120

  19. Allergy to aminophylline: lack of predictability by skin testing.

    PubMed

    Kradjan, W A; Lakshminarayan, S

    1981-07-01

    Problems with determining hypersensitivity to aminophylline, ethylenediamine, and theophylline with intradermal skin tests and patch tests are reported in three patients. Three patients were tested with intradermal injections of 0.9% sodium chloride, 1% aminophylline, 1% ethylenediamine, and 0.5% theophylline following apparent allergic reactions to aminophylline. Patch testing using hydrophilic ointment base, 1% aminophylline, 1% ethylenediamine, and 0.5% theophylline was also done. All three patients had no reaction to intradermal sodium chloride or theophylline; all patch tests were negative. The first patient reacted to ethylenediamine strongly and to aminophylline more weakly; punch biopsy of the ethylenediamine reaction site showed a direct toxic effect with no allergic component. Punch biopsy of the aminophylline site showed a typical hypersensitivity reaction. Two concentrations (0.5% and 1.0%) of ethylenediamine injection were used to test the second patient, and he reacted to both concentrations but not to any other injections. His positive reactions contained blisters rather than the typical wheal-and-flare reaction of hypersensitivity. The third patient had similar responses including reactions to 0.5% and 0.1% ethylenediamine (he was not tested with 1% ethylenediamine). Skin testing may be of value in predicting aminophylline or ethylenediamine allergy, but the nonspecific toxic effect of ethylenediamine makes interpretation difficult. PMID:7258203

  20. 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

  1. 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

  2. A real-life, ecologically valid test of executive functioning: the executive secretarial task.

    PubMed

    Lamberts, Kirsten F; Evans, Jonathan J; Spikman, Jacoba M

    2010-01-01

    A major goal of neuropsychological assessment is predicting a person's level of functioning in daily life. Making predictions about everyday executive functioning based on tests is problematic because of the contrast between demands made in the test environment and demands made in everyday life (Shallice & Burgess, 1991). As executive functions play an important role in independent functioning, tests with robust psychometric properties and ecologically validity are needed. We developed the Executive Secretarial Task (EST) and assessed 92 participants: 35 brain-injured patients and 57 controls. Analyses showed the EST is sensitive to executive problems and has concurrent and ecological validity. PMID:19408184

  3. KNEE EXTENSOR STRENGTH EXHIBITS POTENTIAL TO PREDICT FUNCTION IN SPORADIC INCLUSION-BODY MYOSITIS

    PubMed Central

    LOWES, LINDA PAX; ALFANO, LINDSAY; VIOLLET, LAURENCE; ROSALES, XIOMARA QUINTERO; SAHENK, ZARIFE; KASPAR, BRIAN K.; CLARK, K. REED; FLANIGAN, KEVIN M.; MENDELL, JERRY R.

    2013-01-01

    Introduction In this study we address the challenging issue of potential use of muscle strength to predict function in clinical trials. This has immediate relevance to translational studies that attempt to improve quadriceps strength in sporadic inclusion-body myositis (sIBM). Methods Maximum voluntary isometric contraction testing as a measure of muscle strength and a battery of functional outcomes were tested in 85 ambulatory subjects with sIBM. Results Marked quadriceps weakness was noted in all patients. Strength was correlated with distance walked at 2 and 6 minutes. Additional correlations were found with time to get up from a chair, climb stairs, and step up on curbs. Conclusions Quadriceps (knee extensor) strength correlated with performance in this large cohort of sIBM subjects, which demonstrated its potential to predict function in this disease. These data provide initial support for use of muscle strength as a surrogate for function, although validation in a clinical trial is required. PMID:22246869

  4. Prediction accuracy measurements as a fitness function for software effort estimation.

    PubMed

    Urbanek, Tomas; Prokopova, Zdenka; Silhavy, Radek; Vesela, Veronika

    2015-01-01

    This paper evaluates the usage of analytical programming and different fitness functions for software effort estimation. Analytical programming and differential evolution generate regression functions. These functions are evaluated by the fitness function which is part of differential evolution. The differential evolution requires a proper fitness function for effective optimization. The problem is in proper selection of the fitness function. Analytical programming and different fitness functions were tested to assess insight to this problem. Mean magnitude of relative error, prediction 25 %, mean squared error (MSE) and other metrics were as possible candidates for proper fitness function. The experimental results shows that means squared error performs best and therefore is recommended as a fitness function. Moreover, this work shows that analytical programming method is viable method for calibrating use case points method. All results were evaluated by standard approach: visual inspection and statistical significance. PMID:26697288

  5. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

    PubMed

    Warde-Farley, David; Donaldson, Sylva L; Comes, Ovi; Zuberi, Khalid; Badrawi, Rashad; Chao, Pauline; Franz, Max; Grouios, Chris; Kazi, Farzana; Lopes, Christian Tannus; Maitland, Anson; Mostafavi, Sara; Montojo, Jason; Shao, Quentin; Wright, George; Bader, Gary D; Morris, Quaid

    2010-07-01

    GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist. PMID:20576703

  6. Computational predictions of energy materials using density functional theory

    NASA Astrophysics Data System (ADS)

    Jain, Anubhav; Shin, Yongwoo; Persson, Kristin A.

    2016-01-01

    In the search for new functional materials, quantum mechanics is an exciting starting point. The fundamental laws that govern the behaviour of electrons have the possibility, at the other end of the scale, to predict the performance of a material for a targeted application. In some cases, this is achievable using density functional theory (DFT). In this Review, we highlight DFT studies predicting energy-related materials that were subsequently confirmed experimentally. The attributes and limitations of DFT for the computational design of materials for lithium-ion batteries, hydrogen production and storage materials, superconductors, photovoltaics and thermoelectric materials are discussed. In the future, we expect that the accuracy of DFT-based methods will continue to improve and that growth in computing power will enable millions of materials to be virtually screened for specific applications. Thus, these examples represent a first glimpse of what may become a routine and integral step in materials discovery.

  7. 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

  8. Optimizing Non-Decomposable Loss Functions in Structured Prediction

    PubMed Central

    Ranjbar, Mani; Lan, Tian; Wang, Yang; Robinovitch, Steven N.; Li, Ze-Nian; Mori, Greg

    2012-01-01

    We develop an algorithm for structured prediction with non-decomposable performance measures. The algorithm learns parameters of Markov random fields and can be applied to multivariate performance measures. Examples include performance measures such as Fβ score (natural language processing), intersection over union (object category segmentation), Precision/Recall at k (search engines) and ROC area (binary classifiers). We attack this optimization problem by approximating the loss function with a piecewise linear function. The loss augmented inference forms a quadratic program (QP), which we solve using LP relaxation. We apply this approach to two tasks: object class-specific segmentation and human action retrieval from videos. We show significant improvement over baseline approaches that either use simple loss functions or simple scoring functions on the PASCAL VOC and H3D Segmentation datasets, and a nursing home action recognition dataset. PMID:22868650

  9. Rapid D-Affine Biventricular Cardiac Function with Polar Prediction

    PubMed Central

    Gilbert, Kathleen; Cowan, Brett; Suinesiaputra, Avan; Occleshaw, Christopher; Young, Alistair

    2014-01-01

    Although many solutions have been proposed for left ventricular functional analysis of the heart, right and left (bi-) ventricular function has been problematic due to the complex geometry and large motions. Biventricular function is particularly important in congenital heart disease, the most common type of birth defects. We describe a rapid interactive analysis tool for biventricular function which incorporates 1) a 3D+ time finite element model of biventricular geometry, 2) a fast prediction step which estimates an initial geometry in a polar coordinate system, and 3) a Cartesian update which penalizes deviations from affine transformations (D-Affine) from a prior. Solution times were very rapid, enabling interaction in real time using guide point modeling. The method was applied to 13 patients with congenital heart disease and compared with the clinical gold standard of manual tracing. Results between the methods showed good correlation (R2 > 0.9) and good precision (volume<17ml; mass<11g) for both chambers. PMID:25485422

  10. 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

  11. 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

  12. Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms

    PubMed Central

    Rhee, Soo-Yon; Fessel, W. Jeffrey; Liu, Tommy F.; Marlowe, Natalia M.; Rowland, Charles M.; Rode, Richard A.; Vandamme, Anne-Mieke; Laethem, Kristel Van; Brun-Vezinet, Francçoise; Calvez, Vincent; Taylor, Jonathan; Hurley, Leo; Horberg, Michael; Shafer, Robert W.

    2016-01-01

    Background Interpreting human immunodeficienc virus type 1 (HIV-1) genotypic drug-resistance test results is challenging for clinicians treating HIV-1–infected patients. Multiple drug-resistance interpretation algorithms have been developed, but their predictive value has rarely been evaluated using contemporary clinical data sets. Methods We examined the predictive value of 4 algorithms at predicting virologic response (VR) during 734 treatment-change episodes (TCEs). VR was define as attaining plasma HIV-1 RNA levels below the limit of quantification Drug-specifi genotypic susceptibility scores (GSSs) were calculated by applying each algorithm to the baseline genotype. Weighted GSSs were calculated by multiplying drug-specifi GSSs by antiretroviral (ARV) potency factors. Regimen-specifi GSSs (rGSSs) were calculated by adding unweighted or weighted drug-specif c GSSs for each salvage therapy ARV. The predictive value of rGSSs were estimated by use of multivariate logistic regression. Results Of 734 TCEs, 475 (65%) were associated with VR. The rGSSs for the 4 algorithms were the variables most strongly predictive of VR. The adjusted rGSS odds ratios ranged from 1.6 to 2.2 (P < .001). Using 10-fold cross-validation, the averaged area under the receiver operating characteristic curve for all algorithms increased from 0.76 with unweighted rGSSs to 0.80 with weighted rGSSs. Conclusions Unweighted and weighted rGSSs of 4 genotypic resistance algorithms were the strongest independent predictors of VR. Optimizing ARV weighting may further improve VR predictions. PMID:19552527

  13. 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.

  14. 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. PMID:26400858

  15. Design prediction of pavement skid resistance from laboratory tests

    NASA Astrophysics Data System (ADS)

    Parcells, W. H.; Metheny, T. M.; Maag, R. G.

    1980-08-01

    Methods for preevaluating aggregates and paving mixtures so that predictions can be made covering skid resistance properties of proposed and in service pavement types are discussed. A correlation was established between the field testing using the data from the British Portable Tester and the Locked Wheel Pavement Friction Trailer at speeds of 40 and 55 mph. Core samples were extracted from the Locked Wheel Tester Skid Path and subjected to wear on the small wheel circular track with periodic surface friction testing. The final step was to remix and remold the cored pavement samples or make samples with new materials to obtain an 'as new' surface and again subject these samples to wear on the small wheel circular track with periodic testing.

  16. Ethical issues in predictive genetic testing: a public health perspective.

    PubMed

    Fulda, K G; Lykens, K

    2006-03-01

    As a result of the increase in genetic testing and the fear of discrimination by insurance companies, employers, and society as a result of genetic testing, the disciplines of ethics, public health, and genetics have converged. Whether relatives of someone with a positive predictive genetic test should be notified of the results and risks is a matter urgently in need of debate. Such a debate must encompass the moral and ethical obligations of the diagnosing physician and the patient. The decision to inform or not will vary depending on what moral theory is used. Utilising the utilitarian and libertarian theories produces different outcomes. The principles of justice and non-maleficence will also play an important role in the decision. PMID:16507657

  17. Ethics of a predictive test for Huntington's chorea.

    PubMed Central

    Thomas, S

    1982-01-01

    "Index Medicus" and 18 other publications have been consulted in an attempt to provide an easily assimilated selection of the recently published and widely dispersed material relevant to the ethical debate the editors of the "BMJ" called for on 4 March 1978. The medical profession is shown to be deeply divided on the ethics of a predictive test for Huntington's chorea. Some members are already using the prospect of a reliable test as an inducement to potential transmitters of this incurable hereditary disease to postpone procreation. Other members would prefer to see any future test withheld from every applicant until such time as radically improved means of treatment or a cure is discovered. The evolution of generally acceptable professional guidelines requires further informed debate. PMID:6462188

  18. 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

  19. 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

  20. 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.

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

    PubMed

    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

  2. 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.

  3. 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. PMID:27476848

  4. 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

  5. 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.

  6. 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.

  7. Testing of lithium-ion 18650 cells and characterizing/predicting cell performance

    NASA Astrophysics Data System (ADS)

    Fellner, J. P.; Loeber, G. J.; Sandhu, S. S.

    The performance of lithium-ion cells, as determined from in-house testing, is primarily a function of cell design/materials, charge/discharge rate, ambient temperature, and the number of charge/discharge cycles. Testing of lithium-ion 18650 cells was performed in order to characterize their behavior and to eventually predict the performance of lithium-ion cells of various sizes. AC impedance spectroscopy was used to determine the interfacial resistance of the lithium-ion cells as a function of temperature, state-of-charge, and cycle number. From these results, a nonisothermal mathematical model was developed and preliminary results are presented.

  8. Actual Versus Predicted Cardiovascular Demands in Submaximal Cycle Ergometer Testing

    PubMed Central

    HOEHN, AMANDA M.; MULLENBACH, MEGAN J.; FOUNTAINE, CHARLES J.

    2015-01-01

    The Astrand-Rhyming cycle ergometer test (ARCET) is a commonly administered submaximal test for estimating aerobic capacity. Whereas typically utilized in clinical populations, the validity of the ARCET to predict VO2max in a non-clinical population, especially female, is less clear. Therefore, the purpose of this study was to determine the accuracy of the ARCET in a sample of healthy and physically active college students. Subjects (13 females, 10 males) performed a maximal cycle ergometer test to volitional exhaustion to determine VO2max. At least 48 hours later, subjects performed the ARCET protocol. Predicted VO2max was calculated following the ARCET format using the age corrected factor. There was no significant difference (p=.045) between actual (41.0±7.97 ml/kg/min) and predicted VO2max (40.3±7.58 ml/kg/min). When split for gender there was a significant difference between actual and predicted VO2 for males, (45.1±7.74 vs. 42.7±8.26 ml/kg/min, p=0.029) but no significant difference observed for females, (37.9±6.9 vs. 38.5±6.77 ml/kg/min, p=0.675). The correlation between actual and predicted VO2 was r=0.84, p<0.001 with an SEE= 4.3 ml/kg/min. When split for gender, the correlation for males was r=0.94, p<0.001, SEE=2.72 ml/kg/min; for females, r=0.74, p=0.004, SEE=4.67 ml/kg/min. The results of this study indicate that the ARCET accurately estimated VO2max in a healthy college population of both male and female subjects. Implications of this study suggest the ARCET can be used to assess aerobic capacity in both fitness and clinical settings where measurement via open-circuit spirometry is either unavailable or impractical. PMID:27182410

  9. Quantitative Sensory Testing Predicts Pregabalin Efficacy in Painful Chronic Pancreatitis

    PubMed Central

    Olesen, Søren S.; Graversen, Carina; Bouwense, Stefan A. W.; van Goor, Harry; Wilder-Smith, Oliver H. G.; Drewes, Asbjørn M.

    2013-01-01

    Background A major problem in pain medicine is the lack of knowledge about which treatment suits a specific patient. We tested the ability of quantitative sensory testing to predict the analgesic effect of pregabalin and placebo in patients with chronic pancreatitis. Methods Sixty-four patients with painful chronic pancreatitis received pregabalin (150–300 mg BID) or matching placebo for three consecutive weeks. Analgesic effect was documented in a pain diary based on a visual analogue scale. Responders were defined as patients with a reduction in clinical pain score of 30% or more after three weeks of study treatment compared to baseline recordings. Prior to study medication, pain thresholds to electric skin and pressure stimulation were measured in dermatomes T10 (pancreatic area) and C5 (control area). To eliminate inter-subject differences in absolute pain thresholds an index of sensitivity between stimulation areas was determined (ratio of pain detection thresholds in pancreatic versus control area, ePDT ratio). Pain modulation was recorded by a conditioned pain modulation paradigm. A support vector machine was used to screen sensory parameters for their predictive power of pregabalin efficacy. Results The pregabalin responders group was hypersensitive to electric tetanic stimulation of the pancreatic area (ePDT ratio 1.2 (0.9–1.3)) compared to non-responders group (ePDT ratio: 1.6 (1.5–2.0)) (P = 0.001). The electrical pain detection ratio was predictive for pregabalin effect with a classification accuracy of 83.9% (P = 0.007). The corresponding sensitivity was 87.5% and specificity was 80.0%. No other parameters were predictive of pregabalin or placebo efficacy. Conclusions The present study provides first evidence that quantitative sensory testing predicts the analgesic effect of pregabalin in patients with painful chronic pancreatitis. The method can be used to tailor pain medication based on patient’s individual sensory profile and thus

  10. Developing a Causal Model from Liver Function Test Data

    NASA Astrophysics Data System (ADS)

    Inada, Masanori; Terano, Takao

    As Active Mining is a new concept among data mining and/or knowledge discovery in databases communities, in order to validate the effectiveness, it is important to carry out empirical studies using practical data. Based on the concept of Active User Reaction, this paper develops a causal model from liver function test data in a medical domain. To develop the model, we have set a problem to predict the values of ICG (indocyanine green) test from given observation data and experts' background knowledge. We therefore employ a framework of meta-learning and structural equation modeling. In this paper meta-learning means learning about mined results from multiple data-mining techniques. Structural equation modeling enables us to describe flexible models from background knowledge. The construction of the causal model contains two phases: meta-learning and the model building. The meta-learning phase utilizes both the linear regression and the neural network as data mining techniques, then examines the predictability on the given data set. Mining models are n-folded learned from the training data set. Each of the prediction accuracy of the mining models is compared using with the testing data. On the model building phase, we use structural equation modeling to develop a causal model based on results of meta-learning and background knowledge. We again compare the accuracy of the causal model with each of the mining models. Consequently we have developed the causal model, which is comprehensible and have good predictive performance, via the meta-learning phase. Through the empirical study, we have got the conclusion that the framework of meta-learning is effective in data mining in a difficult medical domain.

  11. 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

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

    PubMed

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

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration. PMID:24524947

  13. Predictive Equations Using Regression Analysis of Pulmonary Function for Healthy Children in Northeast China

    PubMed Central

    Ma, Ya-Nan; Wang, Jing; Dong, Guang-Hui; Liu, Miao-Miao; Wang, Da; Liu, Yu-Qin; Zhao, Yang; Ren, Wan-Hui; Lee, Yungling Leo; Zhao, Ya-Dong; He, Qin-Cheng

    2013-01-01

    Background There have been few published studies on spirometric reference values for healthy children in China. We hypothesize that there would have been changes in lung function that would not have been precisely predicted by the existing spirometric reference equations. The objective of the study was to develop more accurate predictive equations for spirometric reference values for children aged 9 to 15 years in Northeast China. Methodology/Principal Findings Spirometric measurements were obtained from 3,922 children, including 1,974 boys and 1,948 girls, who were randomly selected from five cities of Liaoning province, Northeast China, using the ATS (American Thoracic Society) and ERS (European Respiratory Society) standards. The data was then randomly split into a training subset containing 2078 cases and a validation subset containing 1844 cases. Predictive equations used multiple linear regression techniques with three predictor variables: height, age and weight. Model goodness of fit was examined using the coefficient of determination or the R2 and adjusted R2. The predicted values were compared with those obtained from the existing spirometric reference equations. The results showed the prediction equations using linear regression analysis performed well for most spirometric parameters. Paired t-tests were used to compare the predicted values obtained from the developed and existing spirometric reference equations based on the validation subset. The t-test for males was not statistically significant (p>0.01). The predictive accuracy of the developed equations was higher than the existing equations and the predictive ability of the model was also validated. Conclusion/Significance We developed prediction equations using linear regression analysis of spirometric parameters for children aged 9–15 years in Northeast China. These equations represent the first attempt at predicting lung function for Chinese children following the ATS/ERS Task Force 2005

  14. "Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.

    PubMed

    Marcovitz, Amir; Jia, Robin; Bejerano, Gill

    2016-05-01

    Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their evolutionary profiles against a diverse set of phenotypes recently annotated across multiple mammalian species. We identify 2,759 compelling associations between human CNEs and a diverse set of mammalian phenotypes. We discuss multiple CNEs, including a predicted ear element near BMP7, a pelvic CNE in FBN1, a brain morphology element in UBE4B, and an aquatic adaptation forelimb CNE near EGR2, and provide a full list of our predictions. As more genomes are sequenced and more traits are annotated across species, we expect our method to facilitate the interpretation of noncoding mutations in human disease and expedite the discovery of individual CNEs that play key roles in human evolution and development. PMID:26744417

  15. 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.

  16. 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

  17. 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

  18. 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

  19. AGR-2 Safety Test Predictions Using the PARFUME Code

    SciTech Connect

    Blaise Collin

    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

  20. Pulmonary function tests in children with beta-thalassemia major.

    PubMed

    Abu-Ekteish, F M; Al-Rimawi, H S; Al-Ali, M K; Shehabi, I M

    2007-01-01

    Lung function abnormality is a known complication of thalassemia, but the results of studies in pulmonary function have been inconsistent. This study was conducted to describe the type of lung impairment in thalassemic children. Pulmonary function tests were conducted in 40 children with beta-thalassemia major, 23 males and 17 females. Tests included spirometry, total lung capacity (TLC), single breath diffusing capacity of the lung for carbon monoxide (DL(CO)) and arterial blood gases. Serum ferritin level was measured in all children to study its relationship to lung function impairment. A predominantly restrictive pattern was seen in 14 patients (35%). These patients had a significant reduction in RV, FVC, TLC and PEF with an FEV1/FVC ratio of more than 75%. Obstructive airway disease was found in six patients (15%), with an FEV1/FVC ratio less than 75%, increased RV and reduced FEF(25%-75%). Impairment of diffusion was found in 10 patients (25%), with DL(CO) reduced to less than 80% of the predicted value. Arterial blood gases results showed that no patient was hypoxic. No correlation was found between the severity of restrictive or obstructive disease and the serum ferritin level. There was a significant linear correlation between age and serum ferritin level (P < 0.019). Patients with thalassemia have a predominantly restrictive lung dysfunction pattern. This may be due to pulmonary parenchymal pathology, although the reason for the obstructive pattern seen in a small proportion of patients remains obscure. PMID:17416149

  1. 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

  2. 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.

  3. Contrast sensitivity function calibration based on image quality prediction

    NASA Astrophysics Data System (ADS)

    Han, Yu; Cai, Yunze

    2014-11-01

    Contrast sensitivity functions (CSFs) describe visual stimuli based on their spatial frequency. However, CSF calibration is limited by the size of the sample collection and this remains an open issue. In this study, we propose an approach for calibrating CSFs that is based on the hypothesis that a precise CSF model can accurately predict image quality. Thus, CSF calibration is regarded as the inverse problem of image quality prediction according to our hypothesis. A CSF could be calibrated by optimizing the performance of a CSF-based image quality metric using a database containing images with known quality. Compared with the traditional method, this would reduce the work involved in sample collection dramatically. In the present study, we employed three image databases to optimize some existing CSF models. The experimental results showed that the performance of a three-parameter CSF model was better than that of other models. The results of this study may be helpful in CSF and image quality research.

  4. Prediction of functional residues in water channels and related proteins.

    PubMed Central

    Froger, A.; Tallur, B.; Thomas, D.; Delamarche, C.

    1998-01-01

    In this paper, we present an updated classification of the ubiquitous MIP (Major Intrinsic Protein) family proteins, including 153 fully or partially sequenced members available in public databases. Presently, about 30 of these proteins have been functionally characterized, exhibiting essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators. Sequence alignments were used to predict amino acids and motifs discriminant in channel specificity. The protein sequences were also analyzed using statistical tools (comparisons of means and correspondence analysis). Five key positions were clearly identified where the residues are specific for each functional subgroup and exhibit high dissimilar physico-chemical properties. Moreover, we have found that the putative channels for small neutral solutes clearly differ from the aquaporins by the amino acid content and the length of predicted loop regions, suggesting a substrate filter function for these loops. From these results, we propose a signature pattern for water transport. PMID:9655351

  5. 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

  6. 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. PMID:24696112

  7. FLASH predictions of the MB-2 steamline break tests

    SciTech Connect

    Lincoln, F.W.; Coffield, R.D.; Johnson, E.G. )

    1992-01-01

    If a main streamline from a pressurized water reactor (PWR) steam generator were to rupture, the effect would be a depressurization of the secondary side and a consequential overcooling transient of the primary side. Analyses must accurately predict the effects of the rapid cooldown of the reactor vessel coolant on positive nuclear-kinetic reactivity feedback to the core plus thermal shock to the reactor vessel and other primary system components. Many early studies of the steamline bread (SLB) transient made extremely conservative assumptions to maximize the primary-to-secondary heat transfer, which, in turn, maximized the reactor vessel cooldown rate. Among the more significant of these assumptions was that flow from the break was pure steam and that the tube bundle remained covered until the secondary mass inventory was significantly reduced. The model F commercial PWR steam generator testing performed in the model boiler no. 2 (MB-2) facility located at the Westinghouse Electric Corporation Engineering Test Facility in Tampa, Florida, provided data to better qualify the actual variation in these key parameters. A conclusion of this analysis is that the MS-2 SLB data base is accurate and of sufficient detail, to provide a valuable basis for amking comparisons relative to code predictions. Results obtained using the FLASH transient safety analysis code were found to be in excellent agreement with the data.

  8. 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.

  9. 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

  10. 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

  11. 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…

  12. 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. PMID:26117822

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

    PubMed Central

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

    2012-01-01

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

  14. Predicting clinical responses in major depression using intrinsic functional connectivity.

    PubMed

    Qin, Jian; Shen, Hui; Zeng, Ling-Li; Jiang, Weixiong; Liu, Li; Hu, Dewen

    2015-08-19

    There has been increasing interest in multivariate pattern analysis (MVPA) as a means of distinguishing psychiatric patients from healthy controls using brain imaging. However, it remains unclear whether MVPA methods can accurately estimate the medication status of psychiatric patients. This study aims to develop an MVPA approach to accurately predict the antidepressant medication status of individuals with major depression on the basis of whole-brain resting-state functional connectivity MRI (rs-fcMRI). We investigated data from rs-fcMRI of 24 medication-naive depressed patients, 16 out of whom subsequently underwent antidepressant treatment and achieved clinical recovery, and 29 demographically similar controls. By training a linear support vector machine classifier and combining it with principal component analysis, the medication-naive patients were identified from the healthy controls with 100% accuracy. In addition, we found reliable correlations between MVPA prediction scores and clinical symptom severity. Moreover, the most discriminative functional connections were located within or across the cerebellum and default mode, affective, and sensorimotor networks, indicating that these networks may play important roles in major depression. Most importantly, only ∼30% of these discriminative connections were normalized in clinically recovered patients after antidepressant treatment. The current study may not only show the feasibility of estimating medication status by MVPA of whole-brain rs-fcMRI data in major depression but also shed new light on the pathological mechanism of this disorder. PMID:26164454

  15. Testing the assumptions of linear prediction analysis in normal vowels

    NASA Astrophysics Data System (ADS)

    Little, M. A.

    This paper develops an improved surrogate data test to show experimental evidence, for all the simple vowels of US English, for both male and female speakers, that Gaussian linear prediction analysis, a ubiquitous technique in current speech technologies, cannot be used to extract all the dynamical structure of real speech time series. The test provides robust evidence undermining the validity of these linear techniques, supporting the assumptions of either dynamical nonlinearity and/or non-Gaussianity common to more recent, complex, efforts at dynamical modelling speech time series. However, an additional finding is that the classical assumptions cannot be ruled out entirely, and plausible evidence is given to explain the success of the linear Gaussian theory as a weak approximation to the true, nonlinear/non-Gaussian dynamics. This supports the use of appropriate hybrid linear/nonlinear/non-Gaussian modelling. With a calibrated calculation of statistic and particular choice of experimental protocol, some of the known systematic problems of the method of surrogate data testing are circumvented to obtain results to support the conclusions to a high level of significance.

  16. 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

  17. 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

  18. 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

  19. Ophthalmodynamometry for ICP prediction and pilot test on Mt. Everest

    PubMed Central

    2010-01-01

    Background A recent development in non-invasive techniques to predict intracranial pressure (ICP) termed venous ophthalmodynamometry (vODM) has made measurements in absolute units possible. However, there has been little progress to show utility in the clinic or field. One important application would be to predict changes in actual ICP during adaptive responses to physiologic stress such as hypoxia. A causal relationship between raised intracranial pressure and acute mountain sickness (AMS) is suspected. Several MRI studies report that modest physiologic increases in cerebral volume, from swelling, normally accompany subacute ascent to simulated high altitudes. Objectives 1) Validate and calibrate an advanced, portable vODM instrument on intensive patients with raised intracranial pressure and 2) make pilot, non-invasive ICP estimations of normal subjects at increasing altitudes. Methods The vODM was calibrated against actual ICP in 12 neurosurgical patients, most affected with acute hydrocephalus and monitored using ventriculostomy/pressure transducers. The operator was blinded to the transducer read-out. A clinical field test was then conducted on a variable data set of 42 volunteer trekkers and climbers scaling Mt. Everest, Nepal. Mean ICPs were estimated at several altitudes on the ascent both across and within subjects. Results Portable vODM measurements increased directly and linearly with ICP resulting in good predictability (r = 0.85). We also found that estimated ICP increases normally with altitude (10 ± 3 mm Hg; sea level to 20 ± 2 mm Hg; 6553 m) and that AMS symptoms did not correlate with raised ICP. Conclusion vODM technology has potential to reliably estimate absolute ICP and is portable. Physiologic increases in ICP and mild-mod AMS are separate responses to high altitude, possibly reflecting swelling and vasoactive instability, respectively. PMID:21040572

  20. The alteration of profile analysis to accommodate testing functions

    NASA Technical Reports Server (NTRS)

    Myers, R. H.

    1979-01-01

    The development of a methodology was studied for testing differences among several pilot functions, where the data points represent averages at various frequencies. Topics discussed include: basic assumptions, hypothesis, profile analysis, alteration of profile analysis to accommodate testing functions, test and procedures, and power of tests.

  1. 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.

  2. 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.

  3. 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)

  4. Primary rat hepatocytes in chemical testing and QSAR predictive applicability.

    PubMed

    Tichý, Milon; Pokorná, Adéla; Hanzlíková, Iveta; Nerudová, Jana; Tumová, Jana; Uzlová, Rút

    2010-02-01

    Primary rat hepatocytes were used to test acute toxicities of 16 neutral aliphatic alcohols, ketones and esters. Their effects on cell viability and metabolic function (ureogenesis, i.e. biotransformation of ornithine to urea) were measured and expressed as EC50 values. Log EC50 values from both tests correlated with the log partition coefficients for the chemicals between n-octanol and water and log P(ow)-based QSAR models were derived. Log EC50 (viability) tightly correlates with log EC50 (ureogenesis): log EC50 (viability)=0.91 log EC50 (ureogenesis)+0.06. Each of these toxic indices can be substituted by the other one. The toxic indices for both cell viability and metabolic disorder can be estimated using log EC50 for movement inhibition in the oligochaete Tubifex tubifex and the respective QSAR equation. It eliminates a usage of rats. Their correlations were proved and justified. PMID:19735719

  5. 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.

  6. 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

  7. 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 Kohler 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. Furthermore, 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

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

    SciTech Connect

    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.

  9. Predicting individual brain maturity using dynamic functional connectivity

    PubMed Central

    Qin, Jian; Chen, Shan-Guang; Hu, Dewen; Zeng, Ling-Li; Fan, Yi-Ming; Chen, Xiao-Ping; Shen, Hui

    2015-01-01

    Neuroimaging-based functional connectivity (FC) analyses have revealed significant developmental trends in specific intrinsic connectivity networks linked to cognitive and behavioral maturation. However, knowledge of how brain functional maturation is associated with FC dynamics at rest is limited. Here, we examined age-related differences in the temporal variability of FC dynamics with data publicly released by the Nathan Kline Institute (NKI; n = 183, ages 7–30) and showed that dynamic inter-region interactions can be used to accurately predict individual brain maturity across development. Furthermore, we identified a significant age-dependent trend underlying dynamic inter-network FC, including increasing variability of the connections between the visual network, default mode network (DMN) and cerebellum as well as within the cerebellum and DMN and decreasing variability within the cerebellum and between the cerebellum and DMN as well as the cingulo-opercular network. Overall, the results suggested significant developmental changes in dynamic inter-network interaction, which may shed new light on the functional organization of typical developmental brains. PMID:26236224

  10. 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

  11. 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.

  12. CLAES cryostat on-orbit performance versus ground test predictions. [Cryogenic Limb Array Etalon Spectrometer

    NASA Technical Reports Server (NTRS)

    Bell, Greg A.; Burriesci, Larry G.; Naes, Larry G., Jr.

    1993-01-01

    The paper describes the Cryogenic Limb Array Etalon Spectrometer (CLAES) launched on September 12, 1991 aboard the NASA Goddard's Upper Atmosphere Research Satellite the purpose of which is to measure the global concentrations of stratospheric species and their temperature, as a function of altitude. Particular attention is given to the design-level thermal predictions and their correlation to the results of ground tests, and to the on-orbit performance of CLAES. Also presented are data on the cryostat's thermal performance during ground operations, at spacecraft integration and during launch preparations. The CLAES functional block diagram and the cryostat schematic diagram are included.

  13. 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

  14. Trait impulsivity predicts D-KEFS tower test performance in university students.

    PubMed

    Lyvers, Michael; Basch, Vanessa; Duff, Helen; Edwards, Mark S

    2015-01-01

    The present study examined a widely used self-report index of trait impulsiveness in relation to performance on a well-known neuropsychological executive function test in 70 university undergraduate students (50 women, 20 men) aged 18 to 24 years old. Participants completed the Barratt Impulsiveness Scale (BIS-11) and the Frontal Systems Behavior Scale (FrSBe), after which they performed the Tower Test of the Delis-Kaplan Executive Function System. Hierarchical linear regression showed that after controlling for gender, current alcohol consumption, age at onset of weekly alcohol use, and FrSBe scores, BIS-11 significantly predicted Tower Test Achievement scores, β = -.44, p < .01. The results indicate that self-reported impulsiveness is associated with poorer executive cognitive performance even in a sample likely to be characterized by relatively high general cognitive functioning (i.e., university students). The results also support the role of inhibition as a key aspect of executive task performance. Elevated scores on the BIS-11 and FrSBe are known to be linked to risky drinking in young adults as confirmed in this sample; however, only BIS-11 predicted Tower Test performance. PMID:24927380

  15. Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

    PubMed

    Chen, Brian Y; Bryant, Drew H; Cruess, Amanda E; Bylund, Joseph H; Fofanov, Viacheslav Y; Kristensen, David M; Kimmel, Marek; Lichtarge, Olivier; Kavraki, Lydia E

    2007-01-01

    The study of disease often hinges on the biological function of proteins, but determining protein function is a difficult experimental process. To minimize duplicated effort, algorithms for function prediction seek characteristics indicative of possible protein function. One approach is to identify substructural matches of geometric and chemical similarity between motifs representing known active sites and target protein structures with unknown function. In earlier work, statistically significant matches of certain effective motifs have identified functionally related active sites. Effective motifs must be carefully designed to maintain similarity to functionally related sites (sensitivity) and avoid incidental similarities to functionally unrelated protein geometry (specificity). Existing motif design techniques use the geometry of a single protein structure. Poor selection of this structure can limit motif effectiveness if the selected functional site lacks similarity to functionally related sites. To address this problem, this paper presents composite motifs, which combine structures of functionally related active sites to potentially increase sensitivity. Our experimentation compares the effectiveness of composite motifs with simple motifs designed from single protein structures. On six distinct families of functionally related proteins, leave-one-out testing showed that composite motifs had sensitivity comparable to the most sensitive of all simple motifs and specificity comparable to the average simple motif. On our data set, we observed that composite motifs simultaneously capture variations in active site conformation, diminish the problem of selecting motif structures, and enable the fusion of protein structures from diverse data sources. PMID:17951837

  16. 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

  17. 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.

  18. 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

  19. Predicting stability constants for uranyl complexes using density functional theory.

    PubMed

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

    2015-04-20

    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 use density functional theory (B3LYP) and the integral equation formalism polarizable continuum model (IEF-PCM) to compute aqueous stability constants for UO2(2+) 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 chelating capability to uranyl. PMID:25835578

  20. 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.

  1. Updates on Functional Characterization of Bronchopulmonary Dysplasia – The Contribution of Lung Function Testing

    PubMed Central

    Greenough, Anne; Pahuja, Anoop

    2015-01-01

    Bronchopulmonary dysplasia (BPD) is a chronic lung disease that predominantly affects prematurely born infants. Initially, BPD was described in infants who had suffered severe respiratory failure and required high pressure, mechanical ventilation with high concentrations of supplementary oxygen. Now, it also occurs in very prematurely born infants who initially had minimal or even no signs of lung disease. These differences impact the nature of the lung function abnormalities suffered by “BPD” infants, which are also influenced by the criteria used to diagnose BPD and the oxygen saturation level used to determine the supplementary oxygen requirement. Key also to interpreting lung function data in this population is whether appropriate lung function tests have been used and in an adequately sized population to make meaningful conclusions. It should also be emphasized that BPD is a poor predictor of long-term respiratory morbidity. Bearing in mind those caveats, studies have consistently demonstrated that infants who develop BPD have low compliance and functional residual capacities and raised resistances in the neonatal period. There is, however, no agreement with regard to which early lung function measurement predicts the development of BPD, likely reflecting different techniques were used in different populations in often underpowered studies. During infancy, lung function generally improves, but importantly airflow limitation persists and small airway function appears to decline. Improvements in lung function following administration of diuretics or bronchodilators have not translated into long-term improvements in respiratory outcomes. By contrast, early differences in lung function related to different ventilation modes have led to investigation and demonstration that prophylactic, neonatal high-frequency oscillation appears to protect small airway function. PMID:26131449

  2. 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

  3. 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.

  4. 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. PMID:26627261

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

    PubMed Central

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

    2015-01-01

    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. PMID:26627261

  6. Pulmonary physiology: future directions for lung function testing in COPD.

    PubMed

    Brusasco, Vito; Barisione, Giovanni; Crimi, Emanuele

    2015-02-01

    Chronic obstructive pulmonary disease (COPD) is a term that encompasses different pathological conditions having excessive airflow limitation in common. A wide body of knowledge has been accumulated over the last century explaining the mechanisms by which airway (chronic bronchitis) and parenchymal (emphysema) diseases lead to an indistinguishable spirometric abnormality. Although the definition of emphysema is anatomical, early studies showed that its presence can be inferred with good approximation from measurements of lung mechanics and gas exchange, in addition to simple spirometry. Studies using tests of ventilation distribution showed that abnormalities are present in smokers with normal spirometry, although these tests were not predictive of development of COPD. At the beginning of the third millennium, new documents and guidelines for diagnosis and treatment of COPD were developed, in which the functional diagnosis of COPD was restricted, for the sake of simplicity, to simple spirometry. In recent years, there has been a resurgence of interest in separating bronchitic from emphysematous phenotype of COPD. For this purpose, high-resolution computed tomography scanning has been added to diagnostic work-up. At the same time, methods for lung function testing have been refined and seem promising for detection of early small airways abnormalities. Among them are the forced oscillation technique and the nitrogen phase III slope analysis of the multiple-breath washout test, which may provide information on ventilation inhomogeneity. Moreover, the combined assessment of diffusing capacity for nitric oxide and carbon monoxide may be more sensitive than the latter alone for partitioning diffusive components at parenchymal level. PMID:25257934

  7. Cumulative-strain-damage model of ductile fracture: simulation and prediction of engineering fracture tests

    SciTech Connect

    Wilkins, M.L.; Streit, R.D.; Reaugh, J.E.

    1980-10-03

    A cumulative-strain-damage criterion is used to predict the initiation and propagation of fracture in ductile materials. The model is consistent with a model of ductile rupture that involves void growth and coalescence. Two- and three-dimensional finite difference computer codes, which use incremental-plasticity theory to describe large strains with rotation, are used to trace the history of damage in a material due to external forces. Fracture begins when the damage exceeds a critical value over a critical distance and proceeds as the critical-damage state is reached elsewhere. This unified approach to failure prediction can be applied to an arbitrary geometry if the material behavior has been adequately characterized. The damage function must be calibrated for a particular material using various material property tests. The fracture toughness of 6061-T651 aluminum is predicted.

  8. Ecological Relevance of Memory Tests and the Prediction of Relapse in Alcoholics.

    ERIC Educational Resources Information Center

    Sussman, Steve; And Others

    Recent research suggests that alcoholic inpatients' performance on neuropsychological tests is predictive of their drinking status following discharge from alcohol rehabilitation programs, although no single test itself has been predictive of relapse. This study seeks to develop a ecologically relevant memory test that would predict relapse and…

  9. 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

  10. A continuous function model for path prediction of entities

    NASA Astrophysics Data System (ADS)

    Nanda, S.; Pray, R.

    2007-04-01

    As militaries across the world continue to evolve, the roles of humans in various theatres of operation are being increasingly targeted by military planners for substitution with automation. Forward observation and direction of supporting arms to neutralize threats from dynamic adversaries is one such example. However, contemporary tracking and targeting systems are incapable of serving autonomously for they do not embody the sophisticated algorithms necessary to predict the future positions of adversaries with the accuracy offered by the cognitive and analytical abilities of human operators. The need for these systems to incorporate methods characterizing such intelligence is therefore compelling. In this paper, we present a novel technique to achieve this goal by modeling the path of an entity as a continuous polynomial function of multiple variables expressed as a Taylor series with a finite number of terms. We demonstrate the method for evaluating the coefficient of each term to define this function unambiguously for any given entity, and illustrate its use to determine the entity's position at any point in time in the future.

  11. Local functional descriptors for surface comparison based binding prediction

    PubMed Central

    2012-01-01

    Background Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to predict interactions without regard to the underlying structural scaffold that creates the surface. Results We present a new descriptor for protein functional surfaces and algorithms for using these descriptors to compare protein surface regions to identify ligand binding interfaces. Our approach uses descriptors of local regions of the surface, and assembles collections of matches to compare larger regions. Our approach uses a variety of physical, chemical, and geometric properties, adaptively weighting these properties as appropriate for different regions of the interface. Our approach builds a classifier based on a training corpus of examples of binding sites of the target ligand. The constructed classifiers can be applied to a query protein providing a probability for each position on the protein that the position is part of a binding interface. We demonstrate the effectiveness of the approach on a number of benchmarks, demonstrating performance that is comparable to the state-of-the-art, with an approach with more generality than these prior methods. Conclusions Local functional descriptors offer a new method for protein surface comparison that is sufficiently flexible to serve in a variety of applications. PMID:23176080

  12. Structure-based activity prediction for an enzyme of unknown function

    PubMed Central

    Hermann, Johannes C.; Marti-Arbona, Ricardo; Fedorov, Alexander A.; Fedorov, Elena; Almo, Steven C.; Shoichet, Brian K.; Raushel, Frank M.

    2008-01-01

    With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (105 M−1s−1). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function. PMID:17603473

  13. OAIS Functional Model Conformance Test: A Proposed Measurement

    ERIC Educational Resources Information Center

    Laughton, Paul

    2012-01-01

    Purpose: The purpose of this paper is to develop a test for data centres, repositories and archives to determine OAIS functional model conformance. The test developed was carried out among the World Data Centre (WDC) member data centres. The method used to develop the OAIS functional model conformance test is discussed, along with the test…

  14. 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)…

  15. 20 CFR 718.103 - Pulmonary function tests.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... (MVV) is reported, the results of such test shall be obtained independently rather than calculated from the results of the FEV1. (b) All pulmonary function test results submitted in connection with a claim... within 10% of each other shall be sufficient. Pulmonary function test results developed in...

  16. LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

    PubMed Central

    Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew

    2011-01-01

    Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains. PMID:21789174

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. Prediction Accuracy of a Novel Dynamic Structure–Function Model for Glaucoma Progression

    PubMed Central

    Hu, Rongrong; Marín-Franch, Iván; Racette, Lyne

    2014-01-01

    Purpose. To assess the prediction accuracy of a novel dynamic structure–function (DSF) model to monitor glaucoma progression. Methods. Longitudinal data of paired rim area (RA) and mean sensitivity (MS) from 220 eyes with ocular hypertension or primary open-angle glaucoma enrolled in the Diagnostic Innovations in Glaucoma Study or the African Descent and Glaucoma Evaluation Study were included. Rim area and MS were expressed as percent of mean normal based on an independent dataset of 91 healthy eyes. The DSF model uses centroids as estimates of the current state of the disease and velocity vectors as estimates of direction and rate of change over time. The first three visits were used to predict the fourth visit; the first four visits were used to predict the fifth visit, and so on up to the 11th visit. The prediction error (PE) was compared to that of ordinary least squares linear regression (OLSLR) using Wilcoxon signed-rank test. Results. For predictions at visit 4 to visit 7, the average PE for the DSF model was significantly lower than OLSLR by 1.19% to 3.42% of mean normal. No significant difference was observed for the predictions at visit 8 to visit 11. The DSF model had lower PE than OLSLR for 70% of eyes in predicting visit 4 and approximately 60% in predicting visits 5, 6, and 7. Conclusions. The two models had similar prediction capabilities, and the DSF model performed better in shorter time series. The DSF model could be clinically useful when only limited follow-ups are available. (ClinicalTrials.gov numbers, NCT00221923, NCT00221897.) PMID:25358735

  5. "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…

  6. 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…

  7. 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.

  8. 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

  9. 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

  10. The Lung Physiome: merging imaging-based measures with predictive computational models of structure and function

    PubMed Central

    Tawhai, Merryn H; Hoffman, Eric A; Lin, Ching-Long

    2009-01-01

    Global measurements of the lung provided by standard pulmonary function tests do not give insight into the regional basis of lung function and lung disease. Advances in imaging methodologies, computer technologies, and subject-specific simulations are creating new opportunities for studying structure-function relationships in the lung through multi-disciplinary research. The digital Human Lung Atlas is an imaging-based resource compiled from male and female subjects spanning several decades of age. The Atlas comprises both structural and functional measures, and includes computational models derived to match individual subjects for personalized prediction of function. The computational models in the Atlas form part of the Lung Physiome project, which is an international effort to develop integrative models of lung function at all levels of biological organization. The computational models provide mechanistic interpretation of imaging measures; the Atlas provides structural data upon which to base model geometry, and functional data against which to test hypotheses. The example of simulating air flow on a subject-specific basis is considered. Methods for deriving multi-scale models of the airway geometry for individual subjects in the Atlas are outlined, and methods for modeling turbulent flows in the airway are reviewed. PMID:20835982

  11. Axial force measurement for esophageal function testing.

    PubMed

    Gravesen, Flemming H; Funch-Jensen, Peter; Gregersen, Hans; Drewes, Asbjørn Mohr

    2009-01-14

    The esophagus serves to transport food and fluid from the pharynx to the stomach. Manometry has been the "golden standard" for the diagnosis of esophageal motility diseases for many decades. Hence, esophageal function is normally evaluated by means of manometry even though it reflects the squeeze force (force in radial direction) whereas the bolus moves along the length of esophagus in a distal direction. Force measurements in the longitudinal (axial) direction provide a more direct measure of esophageal transport function. The technique used to record axial force has developed from external force transducers over in-vivo strain gauges of various sizes to electrical impedance based measurements. The amplitude and duration of the axial force has been shown to be as reliable as manometry. Normal, as well as abnormal, manometric recordings occur with normal bolus transit, which have been documented using imaging modalities such as radiography and scintigraphy. This inconsistency using manometry has also been documented by axial force recordings. This underlines the lack of information when diagnostics are based on manometry alone. Increasing the volume of a bag mounted on a probe with combined axial force and manometry recordings showed that axial force amplitude increased by 130% in contrast to an increase of 30% using manometry. Using axial force in combination with manometry provides a more complete picture of esophageal motility, and the current paper outlines the advantages of using this method. PMID:19132762

  12. Bradykinesia-Akinesia Incoordination Test: Validating an Online Keyboard Test of Upper Limb Function

    PubMed Central

    Noyce, Alastair J.; Nagy, Anna; Acharya, Shami; Hadavi, Shahrzad; Bestwick, Jonathan P.; Fearnley, Julian; Lees, Andrew J.; Giovannoni, Gavin

    2014-01-01

    Background The Bradykinesia Akinesia Incoordination (BRAIN) test is a computer keyboard-tapping task that was developed for use in assessing the effect of symptomatic treatment on motor function in Parkinson's disease (PD). An online version has now been designed for use in a wider clinical context and the research setting. Methods Validation of the online BRAIN test was undertaken in 58 patients with Parkinson's disease (PD) and 93 age-matched, non-neurological controls. Kinesia scores (KS30, number of key taps in 30 seconds), akinesia times (AT30, mean dwell time on each key in milliseconds), incoordination scores (IS30, variance of travelling time between key presses) and dysmetria scores (DS30, accuracy of key presses) were compared between groups. These parameters were correlated against total motor scores and sub-scores from the Unified Parkinson's Disease Rating Scale (UPDRS). Results Mean KS30, AT30 and IS30 were significantly different between PD patients and controls (p≤0.0001). Sensitivity for 85% specificity was 50% for KS30, 40% for AT30 and 29% for IS30. KS30, AT30 and IS30 correlated significantly with UPDRS total motor scores (r = −0.53, r = 0.27 and r = 0.28 respectively) and motor UPDRS sub-scores. The reliability of KS30, AT30 and DS30 was good on repeated testing. Conclusions The BRAIN test is a reliable, convenient test of upper limb motor function that can be used routinely in the outpatient clinic, at home and in clinical trials. In addition, it can be used as an objective longitudinal measurement of emerging motor dysfunction for the prediction of PD in at-risk cohorts. PMID:24781810

  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. PMID:24145400

  14. 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.

  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. 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

  19. 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

  20. Relating Phylogenetic and Functional Diversity among Denitrifiers and Quantifying their Capacity to Predict Community Functioning

    PubMed Central

    Salles, Joana Falcão; Le Roux, Xavier; Poly, Franck

    2012-01-01

    Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear to what extent functional diversity (FD), gene sequence diversity and community functioning are linked. For a range of denitrifying bacteria, we analyzed the relationships between (i) the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates) or from N2O accumulation patterns on different carbon sources and (ii) the similarity of phylogenetic (16S rRNA gene) or functional (nir gene) markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic (16S rRNA gene) or functional similarities (based either on metabolic profiles or N2O accumulation patterns), and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence was weakly correlated with the variation in metabolic patterns (ρ = 0.35) and was not related to N2O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analyzed separately, the similarity in amino acids coded by the nirS genes was highly correlated with the observed patterns of N2O accumulation (ρ = 0.62), whereas nirK amino acid residues were unrelated to N2O accumulation. For bacterial assemblages, phylogenetic diversity (average similarity among species in a community) and mean community dissimilarity (average distance between species) calculated using 16S rRNA gene sequences, and FD measures associated with metabolic profiles, poorly predicted the variation in the functioning of assembled communities (≤15%). In contrast, the proxies of FD based on N2O accumulation patterns performed better and explained from 23 to 42% of the variation in denitrification. Amongst those, community niche was the best metric, indicating the importance of complementarity for

  1. 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

  2. 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

  3. 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

  4. Efficiency test of earthquake prediction around Thessaloniki from electrotelluric precursors

    NASA Astrophysics Data System (ADS)

    Meyer, K.; Varotsos, P.; Alexopoulos, K.; Nomicos, K.

    1985-11-01

    Since the completion of the network in January 1983, the electric field of the earth has been continuously monitored at four sites near Thessaloniki, the capital of northern Greece. From the present study and from previous investigations by similar measurements in Greece, it is evident that transient changes of the electrotelluric field occur prior to earthquakes. The analysis of these electric forerunners leads in many cases to a successful prediction of the epicentral area, the magnitude and the time of the impending event. Predictions prior to regional earthquakes are issued and documented with telegrams. From November 1983 until the end of May 1984 twelve earthquakes ( M L > 3.5 ) occurred in the vicinity of Thessaloniki. Ten of these were predicted and warnings given by telegram, whereas two smaller seismic events were missed. Two additional predictions were unsuccessful. Independent of their magnitudes, predicted events took place within a time window of 6 hrs to 6 days after the observations of the electrotelluric anomalies. The accuracy of the predicted epicenters in eight cases is better than 100 km, which corresponds roughly to the mean distance between the electric stations. Magnitude estimates deviate by less than 0.5 magnitude units from the seismically observed ones. Considering the two largest earthquakes, it is shown that the probability of making each of these predictions by chance is of the order of 10 -2.

  5. 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.

  6. 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

  7. 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.

  8. 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…

  9. 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.

  10. 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. We developed a method to estimate spatial variation in energy availability in the context of a topographically complex, high-elevation watershed, which we used to test the explanatory power of environmental gradients both with and without snow cover in relation to taxonomic and functional plant diversity. Methods We mapped snow cover at 15 m resolution using Landsat imagery for five recent years and fitted a generalized additive model (GAM) for each year linking snow to time and topography. Predicted snow cover maps were combined with air temperature and solar radiation 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 to without led to an average gain in R2 of 0.26 and also reversed slope direction to more intuitive relationships for several diversity metrics. Conclusions We 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. Our results further indicate that studies seeking to predict the response

  11. Significance tests for functional data with complex dependence structure

    PubMed Central

    Lahiri, Soumen N.; Carroll, Raymond J.

    2015-01-01

    We propose an L2-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups–clusters or subjects–units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment. PMID:26023253

  12. Coaching patients during pulmonary function testing: A practical guide.

    PubMed

    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

  13. 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

  14. PREDICTING THE EFFECTIVENESS OF CHEMICAL-PROTECTIVE CLOTHING MODEL AND TEST METHOD DEVELOPMENT

    EPA Science Inventory

    A predictive model and test method were developed for determining the chemical resistance of protective polymeric gloves exposed to liquid organic chemicals. The prediction of permeation through protective gloves by solvents was based on theories of the solution thermodynamics of...

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

    PubMed

    Kennedy, R S; Baltzley, D R; Turnage, J J; Jones, M B

    1989-12-01

    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. PMID:2622715

  16. 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.

  17. 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…

  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. 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…

  20. 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…

  1. Test Bias and the Prediction of Grades in Law School

    ERIC Educational Resources Information Center

    Linn, Robert L.

    1975-01-01

    Use of the Law School Admission Test (LSAT) and undergraduate grade point average for members of minority groups are examined in relationship to recent LSAT studies and related research on admissions tests and test bias. Traditional predictors of law school grades were found to be as accurate for minority as for majority persons. (JT)

  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. 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. PMID:26108101

  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. 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

  6. 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.

  7. 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…

  8. 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

  9. 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

  10. 21 CFR 868.1890 - Predictive pulmonary-function value calculator.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Predictive pulmonary-function value calculator. 868.1890 Section 868.1890 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... pulmonary-function value calculator. (a) Identification. A predictive pulmonary-function value calculator...

  11. 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

  12. Resting-state functional connectivity predicts impulsivity in economic decision-making.

    PubMed

    Li, Nan; Ma, Ning; Liu, Ying; He, Xiao-Song; Sun, De-Lin; Fu, Xian-Ming; Zhang, Xiaochu; Han, Shihui; Zhang, Da-Ren

    2013-03-13

    Increasing neuroimaging evidence suggests an association between impulsive decision-making behavior and task-related brain activity. However, the relationship between impulsivity in decision-making and resting-state brain activity remains unknown. To address this issue, we used functional MRI to record brain activity from human adults during a resting state and during a delay discounting task (DDT) that requires choosing between an immediate smaller reward and a larger delayed reward. In experiment I, we identified four DDT-related brain networks. The money network (the striatum, posterior cingulate cortex, etc.) and the time network (the medial and dorsolateral prefrontal cortices, etc.) were associated with the valuation process; the frontoparietal network and the dorsal anterior cingulate cortex-anterior insular cortex network were related to the choice process. Moreover, we found that the resting-state functional connectivity of the brain regions in these networks was significantly correlated with participants' discounting rate, a behavioral index of impulsivity during the DDT. In experiment II, we tested an independent group of subjects and demonstrated that this resting-state functional connectivity was able to predict individuals' discounting rates. Together, these findings suggest that resting-state functional organization of the human brain may be a biomarker of impulsivity and can predict economic decision-making behavior. PMID:23486959

  13. 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. PMID:25107302

  14. 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

  15. 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

  16. Newton force from wave function collapse: speculation and test

    NASA Astrophysics Data System (ADS)

    Diósi, Lajos

    2014-04-01

    The Diosi-Penrose model of quantum-classical boundary postulates gravity-related spontaneous wave function collapse of massive degrees of freedom. The decoherence effects of the collapses are in principle detectable if not masked by the overwhelming environmental decoherence. But the DP (or any other, like GRW, CSL) spontaneous collapses are not detectable themselves, they are merely the redundant formalism of spontaneous decoherence. To let DP collapses become testable physics, recently we extended the DP model and proposed that DP collapses are responsible for the emergence of the Newton gravitational force between massive objects. We identified the collapse rate, possibly of the order of 1/ms, with the rate of emergence of the Newton force. A simple heuristic emergence (delay) time was added to the Newton law of gravity. This non-relativistic delay is in peaceful coexistence with Einstein's relativistic theory of gravitation, at least no experimental evidence has so far surfaced against it. We derive new predictions of such a 'lazy' Newton law that will enable decisive laboratory tests with available technologies. The simple equation of 'lazy' Newton law deserves theoretical and experimental studies in itself, independently of the underlying quantum foundational considerations.

  17. 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

  18. Can three incongruence tests predict when data should be combined?

    PubMed

    Cunningham, C W

    1997-07-01

    Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tests of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies. Of the three tests, the most useful was the incongruence length difference test (ILD, also called the partition homogeneity test). This test distinguished between cases in which combining the data generally improved phylogenetic accuracy (P > 0.01) and cases in which accuracy of the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tests detected highly significant incongruence (P < 0.001) even though combining the incongruent partitions actually increased phylogenetic accuracy. All three tests identified cases in which improving the reconstruction model would improve the phylogenetic accuracy of the individual partitions. PMID:9214746

  19. 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…

  20. The Validity of the "Boehm Test of Basic Concepts" in Predicting Achievement.

    ERIC Educational Resources Information Center

    Olinger, Clarice K.

    To determine the validity of the Boehm Test of Basic Concepts in predicting reading achievement as measured by the reading scores of the Iowa Test of Basic Skills, the Boehm test was given to 55 kindergarten children and the Iowa test was given to 42 of the same children in second grade. The results indiciated that the Boehm test appeared to be of…

  1. 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…

  2. Predicting Transfer Performance: A Comparison of Competing Function Learning Models

    ERIC Educational Resources Information Center

    McDaniel, Mark A.; Dimperio, Eric; Griego, Jacqueline A.; Busemeyer, Jerome R.

    2009-01-01

    The population of linear experts (POLE) model suggests that function learning and transfer are mediated by activation of a set of prestored linear functions that together approximate the given function (Kalish, Lewandowsky, & Kruschke, 2004). In the extrapolation-association (EXAM) model, an exemplar-based architecture associates trained input…

  3. 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 ...

  4. 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

  5. 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. PMID:23971032

  6. Do preoperative pulmonary function indices predict morbidity after coronary artery bypass surgery?

    PubMed Central

    Najafi, Mahdi; Sheikhvatan, Mehrdad; Mortazavi, Seyedeh Hamideh

    2015-01-01

    Context: The reported prevalence of chronic obstructive pulmonary disease (COPD) varies among different groups of cardiac surgical patients. Moreover, the prognostic value of preoperative COPD in outcome prediction is controversial. Aims: The present study assessed the morbidity in the different levels of COPD severity and the role of pulmonary function indices in predicting morbidity in patients undergoing coronary artery bypass graft (CABG). Settings and Design: Patients who were candidates for isolated CABG with cardiopulmonary bypass who were recruited for Tehran Heart Center-Coronary Outcome Measurement Study. Methods: Based on spirometry findings, diagnosis of COPD was considered based on Global Initiative for Chronic Obstructive Lung Disease category as forced expiratory volume in 1 s [FEV1]/forced vital capacity <0.7 (absolute value, not the percentage of the predicted). Society of Thoracic Surgeons (STS) definition was used for determining COPD severity and the patients were divided into three groups: Control group (FEV1 >75% predicted), mild (FEV1 60–75% predicted), moderate (FEV1 50–59% predicted), severe (FEV1<50% predicted). The preoperative pulmonary function indices were assessed as predictors, and postoperative morbidity was considered the surgical outcome. Results: This study included 566 consecutive patients. Patients with and without COPD were similar regarding baseline characteristics and clinical data. Hypertension, recent myocardial infarction, and low ejection fraction were higher in patients with different degrees of COPD than the control group while male gender was more frequent in control patients than the others. Restrictive lung disease and current cigarette smoking did not have any significant impact on postoperative complications. We found a borderline P = 0.057 with respect to respiratory failure among different patients of COPD severity so that 14.1% patients in control group, 23.5% in mild, 23.4% in moderate, and 21.9% in severe

  7. Structure based function prediction of proteins using fragment library frequency vectors

    PubMed Central

    Yadav, Akshay; Jayaraman, Valadi Krishnamoorthy

    2012-01-01

    The function of the protein is primarily dictated by its structure. Therefore it is far more logical to find the functional clues of the protein in its overall 3-dimensional fold or its global structure. In this paper, we have developed a novel Support Vector Machines (SVM) based prediction model for functional classification and prediction of proteins using features extracted from its global structure based on fragment libraries. Fragment libraries have been previously used for abintio modelling of proteins and protein structure comparisons. The query protein structure is broken down into a collection of short contiguous backbone fragments and this collection is discretized using a library of fragments. The input feature vector is frequency vector that counts the number of each library fragment in the collection of fragments by all-to-all fragment comparisons. SVM models were trained and optimised for obtaining the best 10-fold Cross validation accuracy for classification. As an example, this method was applied for prediction and classification of Cell Adhesion molecules (CAMs). Thirty-four different fragment libraries with sizes ranging from 4 to 400 and fragment lengths ranging from 4 to 12 were used for obtaining the best prediction model. The best 10-fold CV accuracy of 95.25% was obtained for library of 400 fragments of length 10. An accuracy of 87.5% was obtained on an unseen test dataset consisting of 20 CAMs and 20 NonCAMs. This shows that protein structure can be accurately and uniquely described using 400 representative fragments of length 10. PMID:23144557

  8. Exercise Ventilatory Inefficiency Adds to Lung Function in Predicting Mortality in COPD.

    PubMed

    Neder, J Alberto; Alharbi, Abdullah; Berton, Danilo C; Alencar, Maria Clara N; Arbex, Flavio F; Hirai, Daniel M; Webb, Katherine A; O'Donnell, Denis E

    2016-08-01

    Severity of resting functional impairment only partially predicts the increased risk of death in chronic obstructive pulmonary disease (COPD). Increased ventilation during exercise is associated with markers of disease progression and poor prognosis, including emphysema extension and pulmonary vascular impairment. Whether excess exercise ventilation would add to resting lung function in predicting mortality in COPD, however, is currently unknown. After an incremental cardiopulmonary exercise test, 288 patients (forced expiratory volume in one second ranging from 18% to 148% predicted) were followed for a median (interquartile range) of 57 (47) months. Increases in the lowest (nadir) ventilation to CO2 output (VCO2) ratio determined excess exercise ventilation. Seventy-seven patients (26.7%) died during follow-up: 30/77 (38.9%) deaths were due to respiratory causes. Deceased patients were older, leaner, had a greater co-morbidity burden (Charlson Index) and reported more daily life dyspnea. Moreover, they had poorer lung function and exercise tolerance (p < 0.05). A logistic regression analysis revealed that ventilation/VCO2 nadir was the only exercise variable that added to age, body mass index, Charlson Index and resting inspiratory capacity (IC)/total lung capacity (TLC) ratio to predict all-cause and respiratory mortality (p < 0.001). Kaplan-Meier analyses showed that survival time was particularly reduced when ventilation/VCO2 nadir > 34 was associated with IC/TLC ≤ 0.34 or IC/TLC ≤ 0.31 for all-cause and respiratory mortality, respectively (p < 0.001). Excess exercise ventilation is an independent prognostic marker across the spectrum of COPD severity. Physiological abnormalities beyond traditional airway dysfunction and lung mechanics are relevant in determining the course of the disease. PMID:27077955

  9. sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections.

    PubMed

    Hoque, Md Tamjidul; Yang, Yuedong; Mishra, Avdesh; Zhou, Yaoqi

    2016-05-01

    An important unsolved problem in molecular and structural biology is the protein folding and structure prediction problem. One major bottleneck for solving this is the lack of an accurate energy to discriminate near-native conformations against other possible conformations. Here we have developed sDFIRE energy function, which is an optimized linear combination of DFIRE (the Distance-scaled Finite Ideal gas Reference state based Energy), the orientation dependent (polar-polar and polar-nonpolar) statistical potentials, and the matching scores between predicted and model structural properties including predicted main-chain torsion angles and solvent accessible surface area. The weights for these scoring terms are optimized by three widely used decoy sets consisting of a total of 134 proteins. Independent tests on CASP8 and CASP9 decoy sets indicate that sDFIRE outperforms other state-of-the-art energy functions in selecting near native structures and in the Pearson's correlation coefficient between the energy score and structural accuracy of the model (measured by TM-score). © 2016 Wiley Periodicals, Inc. PMID:26849026

  10. 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. PMID:18415810

  11. 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

  12. 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.

  13. 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

  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. Platelet Function Tests: A Review of Progresses in Clinical Application

    PubMed Central

    Choi, Jae-Lim; Li, Shuhua

    2014-01-01

    The major goal of traditional platelet function tests has been to screen and diagnose patients who present with bleeding problems. However, as the central role of platelets implicated in the etiology of arterial thrombotic diseases such as myocardial infarction and stroke became widely known, platelet function tests are now being promoted to monitor the efficacy of antiplatelet drugs and also to potentially identify patients at increased risk of thrombosis. Beyond hemostasis and thrombosis, an increasing number of studies indicate that platelets play an integral role in intercellular communication, are mediators of inflammation, and have immunomodulatory activity. As new potential biomarkers and technologies arrive at the horizon, platelet functions testing appears to take on a new aspect. This review article discusses currently available clinical application of platelet function tests, placing emphasis on essential characteristics. PMID:24895576

  16. 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.

  17. A Semi-Automated Functional Test Data Analysis Tool

    SciTech Connect

    Xu, Peng; Haves, Philip; Kim, Moosung

    2005-05-01

    The growing interest in commissioning is creating a demand that will increasingly be met by mechanical contractors and less experienced commissioning agents. They will need tools to help them perform commissioning effectively and efficiently. The widespread availability of standardized procedures, accessible in the field, will allow commissioning to be specified with greater certainty as to what will be delivered, enhancing the acceptance and credibility of commissioning. In response, a functional test data analysis tool is being developed to analyze the data collected during functional tests for air-handling units. The functional test data analysis tool is designed to analyze test data, assess performance of the unit under test and identify the likely causes of the failure. The tool has a convenient user interface to facilitate manual entry of measurements made during a test. A graphical display shows the measured performance versus the expected performance, highlighting significant differences that indicate the unit is not able to pass the test. The tool is described as semiautomated because the measured data need to be entered manually, instead of being passed from the building control system automatically. However, the data analysis and visualization are fully automated. The tool is designed to be used by commissioning providers conducting functional tests as part of either new building commissioning or retro-commissioning, as well as building owners and operators interested in conducting routine tests periodically to check the performance of their HVAC systems.

  18. 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.

  19. 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. PMID:10951925

  20. 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.

  1. Does cognitive functioning predict chronic pain? Results from a prospective surgical cohort.

    PubMed

    Attal, Nadine; Masselin-Dubois, Anne; Martinez, Valéria; Jayr, Christian; Albi, Aline; Fermanian, Jacques; Bouhassira, Didier; Baudic, Sophie

    2014-03-01

    It is well established that chronic pain impairs cognition, particularly memory, attention and mental flexibility. Overlaps have been found between the brain regions involved in pain modulation and cognition, including in particular the prefrontal cortex and the anterior cingulate cortex, which are involved in executive function, attention and memory. However, whether cognitive function may predict chronic pain has not been investigated. We addressed this question in surgical patients, because such patients can be followed prospectively and may have no pain before surgery. In this prospective longitudinal study, we investigated the links between executive function, visual memory and attention, as assessed by clinical measurements and the development of chronic pain, its severity and neuropathic symptoms (based on the 'Douleur Neuropathique 4' questionnaire), 6 and 12 months after surgery (total knee arthroplasty for osteoarthritis or breast surgery for cancer). Neuropsychological tests included the Trail-Making Test A and B, and the Rey-Osterrieth Complex Figure copy and immediate recall, which assess cognitive flexibility, visuospatial processing and visual memory. Anxiety, depression and coping strategies were also evaluated. In total, we investigated 189 patients before surgery: 96% were re-evaluated at 6 months, and 88% at 12 months. Multivariate logistic regression (stepwise selection) for the total group of patients indicated that the presence of clinical meaningful pain at 6 and 12 months (pain intensity ≥ 3/10) was predicted by poorer cognitive performance in the Trail Making Test B (P = 0.0009 and 0.02 for pain at 6 and 12 months, respectively), Rey-Osterrieth Complex Figure copy (P = 0.015 and 0.006 for pain at 6 and 12 months, respectively) and recall (P = 0.016 for pain at 12 months), independently of affective variables. Linear regression analyses indicated that impaired scores on these tests predicted pain intensity (P < 0.01) and neuropathic

  2. 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

  3. Recent improvements in prediction of protein structure by global optimization of a potential energy function

    PubMed Central

    Pillardy, Jarosław; Czaplewski, Cezary; Liwo, Adam; Lee, Jooyoung; Ripoll, Daniel R.; Kaźmierkiewicz, Rajmund; Ołdziej, Stanisław; Wedemeyer, William J.; Gibson, Kenneth D.; Arnautova, Yelena A.; Saunders, Jeff; Ye, Yuan-Jie; Scheraga, Harold A.

    2001-01-01

    Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence. PMID:11226239

  4. 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.

  5. 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…

  6. 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.

  7. 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

  8. 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...

  9. Do Attachment Style and Emotion Regulation Strategies Indicate Distress in Predictive Testing?

    PubMed

    van der Meer, Lucienne B; van Duijn, Erik; Giltay, Erik J; Tibben, Aad

    2015-10-01

    Predictive genetic testing for a neurogenetic disorder evokes strong emotions, and may lead to distress. The aim of this study is to investigate whether attachment style and emotion regulation strategies are associated with distress in persons who present for predictive testing for a neurogenetic disorder, and whether these psychological traits predict distress after receiving test results. Self-report scales were used to assess attachment insecurity (anxiety and avoidance) and maladaptive emotion regulation strategies (self-blame, rumination, catastrophizing) in adults at 50 % risk for Huntington's Disease (HD), Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL), and Hereditary Cerebral Hemorrhage With Amyloidosis - Dutch type (HCHWA-D), when they presented for predictive testing. Distress was measured before testing and twice (within 2 months and between 6 and 8 months) after receiving test results. Pearson correlations and linear regression were used to analyze whether attachment style and emotion regulation strategies indicated distress. In 98 persons at risk for HD, CADASIL, or HCHWA-D, attachment anxiety and catastrophizing were associated with distress before predictive testing. Attachment anxiety predicted distress up to 2 months after testing. Clinicians may consider looking for signs of attachment anxiety and catastrophizing in persons who present for predictive testing, to see who may be vulnerable for distress during and after testing. PMID:25641254

  10. 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.

  11. 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.

  12. 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

  13. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

    PubMed Central

    Kristensen, David M; Ward, R Matthew; Lisewski, Andreas Martin; Erdin, Serkan; Chen, Brian Y; Fofanov, Viacheslav Y; Kimmel, Marek; Kavraki, Lydia E; Lichtarge, Olivier

    2008-01-01

    Background Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates. Results Based on evolutionary information and heuristics, an Evolutionary Trace Annotation (ETA) pipeline built templates for 98 enzymes, half taken from the PSI, and sought matches in a non-redundant structure database. On average each template matched 2.7 distinct proteins, of which 2.0 share the first three Enzyme Commission digits as the template's enzyme of origin. In many cases (61%) a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy. ETA was also found to be complementary to sequence homology-based annotations. When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable. Conclusion These data suggest that knowledge of evolutionarily important residues improves functional annotation among distant enzyme homologs. Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome. PMID:18190718

  14. Aptitude Testing: A Critical Examination of the Differential Aptitude Tests, Alternative Batteries, and Problems in Prediction.

    ERIC Educational Resources Information Center

    Toronto Board of Education (Ontario). Research Dept.

    In addition to a review of the Differential Aptitude Tests (DAT), a number of other aptitude tests are examined. They are: (1) Flanagan Aptitude Classification Tests, (2) Holzinger-Crowder Uni-Factor Tests, (3) Employee Aptitude Survey, (4) Revised Minnesota Paper Form Board Test, (5) Minnesota Clerical Test, and (6) Turse Clerical Aptitudes Test.…

  15. Intrinsic functional connectivity predicts individual differences in distractibility.

    PubMed

    Poole, Victoria N; Robinson, Meghan E; Singleton, Omar; DeGutis, Joseph; Milberg, William P; McGlinchey, Regina E; Salat, David H; Esterman, Michael

    2016-06-01

    Distractor suppression, the ability to filter and ignore task-irrelevant information, is critical for efficient task performance. While successful distractor suppression relies on a balance of activity in neural networks responsible for attention maintenance (dorsal attention network; DAN), reorientation (ventral attention network; VAN), and internal thought (default mode network, DMN), the degree to which intrinsic connectivity within and between these networks contributes to individual differences in distractor suppression ability is not well-characterized. For the purposes of understanding these interactions, the current study collected resting-state fMRI data from 32 Veterans and, several months later (7±5 months apart), performance on the additional singleton paradigm, a measure of distractor suppression. Using multivariate support vector regression models composed of resting state connectivity between regions of the DAN, VAN, and DMN, and a leave-one-subject-out cross-validation procedure, we were able to predict an individual's task performance, yielding a significant correlation between the actual and predicted distractor suppression (r=0.48, p=0.0053). Network-level analyses revealed that greater within-network DMN connectivity was predictive of better distractor suppression, while greater connectivity between the DMN and attention networks was predictive of poorer distractor suppression. The strongest connection hubs were determined to be the right frontal eye field and temporoparietal junction of the DAN and VAN, respectively, and medial (ventromedial prefrontal and posterior cingulate cortices) and bilateral prefrontal regions of the DMN. These results are amongst a small but growing number of studies demonstrating that resting state connectivity is related to stable individual differences in cognitive ability, and suggest that greater integrity and independence of the DMN is related to better attentional ability. PMID:27132070

  16. 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

  17. 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…

  18. Selective Citation Mars Conclusions about Test Validity and Predictive Bias

    ERIC Educational Resources Information Center

    Kuncel, Nathan R.; Sackett, Paul R.

    2007-01-01

    Comments on the article by Vasquez and Jones, in which they put forward the argument that standardized tests do not evaluate much of anything worthwhile and do not assess merit. The current authors argue that Vasquez and Jones support their argument only through highly selective citations from the literature, and they discuss Vasquez and Jones'…

  19. A Computerized Test of Self-Control Predicts Classroom Behavior

    ERIC Educational Resources Information Center

    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…

  20. [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. PMID:26657268

  1. Testing the predictive power of cognitive atypicalities in autistic children: evidence from a 3-year follow-up study.

    PubMed

    Pellicano, Elizabeth

    2013-08-01

    This follow-up study investigated the predictive power of early cognitive atypicalities. Specifically, it examined whether early individual differences in specific cognitive skills, including theory of mind, executive function, and central coherence, could uniquely account for variation in autistic children's behaviors-social communication, repetitive behaviors, and interests and insistence on sameness-at follow-up. Thirty-seven cognitively able children with an autism spectrum condition were assessed on tests tapping verbal and nonverbal ability, theory of mind (false-belief prediction), executive function (planning ability, cognitive flexibility, and inhibitory control), and central coherence (local processing) at intake and their behavioral functioning (social communication, repetitive behaviors and interests, insistence on sameness) 3 years later. Individual differences in early executive but not theory of mind skills predicted variation in children's social communication. Individual differences in children's early executive function also predicted the degree of repetitive behaviors and interests at follow-up. There were no predictive relationships between early central coherence and children's insistence on sameness. These findings challenge the notion that distinct cognitive atypicalities map on to specific behavioral features of autism. Instead, early variation in executive function plays a key role in helping to shape autistic children's emerging behaviors, including their social communication and repetitive behaviors and interests. PMID:23495146

  2. Quantitative reactivity profiling predicts functional cysteines in proteomes

    PubMed Central

    Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M.; Richter, Florian; Khare, Sagar; Dillon, Myles B.D.; Bachovchin, Daniel A.; Mowen, Kerri; Baker, David; Cravatt, Benjamin F.

    2010-01-01

    Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here, we describe a proteomics method to quantitatively profile the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyperreactivity was a rare feature among cysteines and found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyperreactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and involved in iron-sulfur protein biogenesis. Finally, we demonstrate that quantitative reactivity profiling can also form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs. PMID:21085121

  3. Quantitative reactivity profiling predicts functional cysteines in proteomes.

    PubMed

    Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M; Richter, Florian; Khare, Sagar; Dillon, Myles B D; Bachovchin, Daniel A; Mowen, Kerri; Baker, David; Cravatt, Benjamin F

    2010-12-01

    Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs. PMID:21085121

  4. 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

  5. Baseline burnout symptoms predict visuospatial executive function during survival school training in special operations military personnel.

    PubMed

    Morgan, Charles A; Russell, Bartlett; McNeil, Jeff; Maxwell, Jeff; Snyder, Peter J; Southwick, Steven M; Pietrzak, Robert H

    2011-05-01

    Burnout symptoms, which are characterized by exhaustion, cynicism, and a reduced sense of professional efficacy, may deleteriously affect cognitive function in military personnel. A total of 32 U.S. Military Special Operations personnel enrolled in Survival School completed measures of trauma history, dissociation, and burnout before training. They then completed the Groton Maze Learning Test (GMLT), a neuropsychological measure of integrative visuospatial executive function during three field-based phases of Survival School-enemy evasion, captivity/interrogation, and escape/release from captivity. Lower pre-training perceptions of professional efficacy were associated with reduced executive function during all of the field-based phases of Survival School, even after adjustment for years of education, cynicism, and baseline GMLT scores. Magnitudes of decrements in executive function in Marines with low efficacy relative to those with high efficacy increased as training progressed and ranged from .58 during enemy evasion to .99 during escape/release from captivity. Pre-training perceptions of burnout may predict visuospatial executive function during naturalistic training-related stress in military personnel. Assessment of burnout symptoms, particularly perceptions of professional efficacy, may help identify military personnel at risk for stress-related executive dysfunction. PMID:21466738

  6. Wiggle—Predicting Functionally Flexible Regions from Primary Sequence

    PubMed Central

    Gu, Jenny; Gribskov, Michael; Bourne, Philip E

    2006-01-01

    The Wiggle series are support vector machine–based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity. PMID:16839194

  7. 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.

  8. SP-100 nuclear assembly test - Test assembly functional requirements and system arrangement

    NASA Astrophysics Data System (ADS)

    Fallas, T. T.; Gluck, Robert; Motwani, Kumar; Clay, Harold; O'Neill, Gerald

    This paper describes the functional requirements and the system that will be tested to validate the reactor, flight shield, and flight controller of the SP-100 Generic Flight System. The Nuclear Assembly Test consists of the test article (SP-100 reactor with control devices and the flight shield) and its supporting systems.

  9. Why species matter: an experimental assessment of assumptions and predictive ability of two functional-group models.

    PubMed

    Fong, Caitlin R; Fong, Peggy

    2014-08-01

    Community ecologists use functional groups based on the rarely tested assumption that within-group responses to ecological processes are similar and thus members are functionally equivalent. However, recent research suggests that functional equivalency may break down with human impacts. We tested the equivalency assumption and model predictions of responses to simulated human alterations in nutrients and large herbivores for two models of coral reef algae, the Relative Dominance Model (RDM) and the Functional Group Model (FGM). Results of both mesocosm and field experiments using assembled communities were compared to model predictions, and within- and between-group variability were assessed. Both models' predictions of group response to herbivory matched experimental outcomes, but only the RDM predicted response to nutrients. However, within-group variability was dramatic, because the RDM grouped species with opposite responses to herbivory and the FGM grouped species with unique responses to nutrients. These heterogeneous responses resulted in loss of information and masked strong interactions between herbivory and nutrients that were not included in the models. As humans continue to impact major ecological processes in ecosystems globally, we postulate that functional-group models may need to be reformulated to account for shifting baselines. PMID:25230457

  10. Predicting tree diversity across the United States as a function of modeled gross primary production.

    PubMed

    Nightingale, Joanne M; Fan, Weihong; Coops, Nicholas C; Waring, Richard H

    2008-01-01

    At the regional and continental scale, ecologists have theorized that spatial variation in biodiversity can be interpreted as a response to differences in climate. To test this theory we assumed that ecological constraints associated with current climatic conditions (2000-2004) might best be correlated with tree richness if expressed through satellite-derived measures of gross primary production (GPP), rather than the more commonly used, but less consistently derived, net primary production. To evaluate current patterns in tree diversity across the contiguous United States we acquired information on tree composition from the USDA Forest Service's Forest Inventory and Analysis program that represented more than 17,4000 survey plots. We selected 2693 cells of 1000 km2 within which a sufficient number of plots were available to estimate tree richness per hectare. Our estimates of forest productivity varied from simple vegetation indices indicative of the fraction of light intercepted by canopies at 16-d intervals, a product from the MODIS (Moderate Resolution Imaging Spectro-radiometer), to 8- and 10-d GPP products derived with minimal climatic data (MODIS) and SPOT-Vegetation (Systeme Pour l'Observation de la Terre), to 3-PGS (Physiological Principles Predicting Growth with Satellites), which requires both climate and soil data. Across the contiguous United States, modeled predictions of gross productivity accounted for between 51% and 77% of the recorded spatial variation in tree diversity, which ranged from 2 to 67 species per hectare. When the analyses were concentrated within nine broadly defined ecoregions, predictive relations largely disappeared. Only 3-PGS predictions fit a theorized unimodal function by being able to distinguish highly productive forests in the Pacific Northwest that support lower than expected tree diversity. Other models predicted a continuous steep rise in tree diversity with increasing productivity, and did so with generally better or

  11. 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

  12. Prediction of mandibular rotation: an empirical test of clinician performance.

    PubMed

    Baumrind, S; Korn, E L; West, E E

    1984-11-01

    An experiment was conducted in an attempt to determine empirically how effective a number of expert clinicians were at differentiating "backward rotators" from "forward rotators" on the basis of head-film information which might reasonably have been available to them prior to instituting treatment for the correction of Class II malocclusion. As a result of a previously reported ongoing study, pre- and posttreatment head films were available for 188 patients treated in the mixed dentition for the correction of Class II malocclusion and for 50 untreated Class II subjects. These subjects were divided into 14 groups (average size of group, 17; range, 6 to 23) solely on the basis of type of treatment and the clinician from whose clinic the records had originated. From within each group, we selected the two or three subjects who had exhibited the most extreme backward rotation and the two or three subjects who had exhibited the most extreme forward rotation of the mandible during the interval between films. The sole criterion for classification was magnitude of change in the mandibular plane angle of Downs between the pre- and posttreatment films of each patient. The resulting sample contained 32 backward-rotator subjects and 32 forward-rotator subjects. Five expert judges (mean clinical experience, 28 years) were asked to identify the backward-rotator subjects by examination of the pretreatment films. The findings may be summarized as follows: (1) No judge performed significantly better than chance. (2) There was strong evidence that the judges used a shared, though relatively ineffective, set of rules in making their discriminations between forward and backward rotators. (3) Statistical analysis of the predictive power of a set of standard cephalometric measurements which had previously been made for this set of subjects indicated that the numerical data also failed to identify potential backward rotators at a rate significantly better than chance. We infer from these

  13. 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

  14. 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.

  15. 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

  16. Energy functions for knots: Beginning to predict physical behavior

    SciTech Connect

    Simon, J.

    1996-12-31

    Several definitions have been proposed for the {open_quotes}energy{close_quotes} of a knot. The intuitive goal is to define a number u(K) that somehow measures how {open_quotes}tangled{close_quotes} or {open_quotes}crumpled{close_quotes} a knot K is. Typically, one starts with the idea that a small piece of the knot somehow repels other pieces, and then adds up the contributions from all the pieces. From a purely mathematical standpoint, one may hope to define new knot-type invariants, e.g by considering the minimum of u(K) as K ranges over all the knots of a given knot-type. We also are motivated by the desire to understand and predict how knot-type affects the behavior of physically real knots, in particular DNA loops in gel electrophoresis or random knotting experiments. Despite the physical naivete of recently studied knot energies, there now is enough laboratory data on relative gel velocity, along with computer calculations of idealized knot energies, to justify the assertion that knot energies can predict relative knot behavior in physical systems. The relationships between random knot frequencies and either gel velocities or knot energies is less clear at this time. 50 refs., 8 figs., 2 tabs.

  17. 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.

  18. Predicting the Academic Functioning of Youth Involved in Residential Care

    ERIC Educational Resources Information Center

    Griffith, Annette K.; Trout, Alexandra L.; Epstein, Michael H.; Garbin, Calvin P.; Pick, Robert; Wright, Tanya

    2010-01-01

    Youth involved in residential care programs present with significant difficulties across behavioral and mental health domains. Although this is a group that is also at considerable risk for academic failure, very little research has been done to understand the academic functioning of this population. The current study sought to expand what is…

  19. 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

  20. On the use of back propagation and radial basis function neural networks in surface roughness prediction

    NASA Astrophysics Data System (ADS)

    Markopoulos, Angelos P.; Georgiopoulos, Sotirios; Manolakos, Dimitrios E.

    2016-03-01

    Various artificial neural networks types are examined and compared for the prediction of surface roughness in manufacturing technology. The aim of the study is to evaluate different kinds of neural networks and observe their performance and applicability on the same problem. More specifically, feed-forward artificial neural networks are trained with three different back propagation algorithms, namely the adaptive back propagation algorithm of the steepest descent with the use of momentum term, the back propagation Levenberg-Marquardt algorithm and the back propagation Bayesian algorithm. Moreover, radial basis function neural networks are examined. All the aforementioned algorithms are used for the prediction of surface roughness in milling, trained with the same input parameters and output data so that they can be compared. The advantages and disadvantages, in terms of the quality of the results, computational cost and time are identified. An algorithm for the selection of the spread constant is applied and tests are performed for the determination of the neural network with the best performance. The finally selected neural networks can satisfactorily predict the quality of the manufacturing process performed, through simulation and input-output surfaces for combinations of the input data, which correspond to milling cutting conditions.

  1. Executive Functioning Skills Uniquely Predict Chinese Word Reading

    ERIC Educational Resources Information Center

    Chung, Kevin K. H.; McBride-Chang, Catherine

    2011-01-01

    Eighty-five Hong Kong Chinese children were tested across both the 2nd and 3rd years of kindergarten (ages 4-5 years) on tasks of inhibitory control, working memory, vocabulary knowledge, phonological awareness, morphological awareness, and word reading. With age, vocabulary knowledge, and metalinguistic skills statistically controlled, the…

  2. 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)…

  3. 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. PMID:25323464

  4. 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

  5. Psychometric tests for assessment of brain function after solvent exposure.

    PubMed

    Rasmussen, K; Jeppesen, H J; Sabroe, S

    1993-11-01

    Psychometric testing is a key issue in neuropsychological toxicology assessment. Evaluation of methods for assessing general intellectual impairment is necessary as conventional neurology has been shown to be insensitive to the neurotoxic effects of solvents and metals. This study presents an analysis of a psychometric test battery from an investigation of psycho-organic syndrome in a historical cohort of 96 metal degreasers with long-term exposure to solvents, particularly trichloroethylene. The neuropsychological test battery was a combination of Wechsler Adult Intelligence Scale (WAIS), Luria, and tests developed in Scandinavia. Linear regression analysis showed a significant dose-response relation between increasing cumulative solvent exposure and impaired psychometric test performance in 9 out of 15 tests. Multivariate analysis, however, suggests that much of the variance was due to confounding variables, especially age, and to a lesser degree, primary intellectual function and word blindness. After control for confounding factors the strongest association with solvent exposure occurred for the following three tests: acoustic-motor function, Paced Auditory Serial Addition Test (PASAT), and the visual gestalt test. PMID:8266931

  6. Predictive Validity Study of the APS Writing and Reading Tests [and] Validating Placement Rules for the APS Writing Test.

    ERIC Educational Resources Information Center

    College of the Canyons, Valencia, CA. Office of Institutional Development.

    California's College of the Canyons has used the College Board Assessment and Placement Services (APS) test to assess students' abilities in basic and college English since spring 1993. These two reports summarize data from a May 1994 study of the predictive validity of the APS writing and reading tests and a June 1994 effort to validate the cut…

  7. The Prediction of Success in Engineering Graphics Using the Group Embedded Figures Test and the Hidden Figures Test.

    ERIC Educational Resources Information Center

    Wilson, Russell C.; Davis, Paul D.

    1985-01-01

    A study was conducted to continue the assessment of the Group Embedded Figures Test (GEFT), to assess the value of the Hidden Figures Test (HFT), and to assess the usefulness of the two instruments used in combination as tools for predicting student success and early identification of students who may need special assistance in engineering…

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  10. Effect of Load Rate on Tensile Strength of Various CFCCs at Elevated Temperatures: An Approach to Life Prediction Testing

    NASA Technical Reports Server (NTRS)

    Choi, Sung R.; Gyekenyesi, John P.

    2001-01-01

    Strength of three continuous fiber-reinforced ceramic composites, including SiC/CAS-11, SiC/MAS-5 and SiC/SiC, was determined as a function of test rate in air at 1100 - 1200 C. All three composite materials exhibited a strong dependency of strength on test rate, similar to the behavior observed in many advanced monolithic ceramics at elevated temperatures. The application of the preloading technique as well as the prediction of life from one loading configuration (constant stress-rate) to another (constant stress loading) suggested that the overall macroscopic failure mechanism of the composites would be the one governed by a power-law tyw of damage evolution/accumulation, analogous to slow crack growth commonly observed in advanced monolithic ceramics. It was further found that constant stress-rate testing could be used as an alternative to life prediction test methodology even for the composite materials at least for the short range of lifetime.

  11. Predicting Functional Status Following Amputation After Lower Extremity Bypass

    PubMed Central

    Suckow, Bjoern D.; Goodney, Philip P.; Cambria, Robert A.; Bertges, Daniel J.; Eldrup-Jorgensen, Jens; Indes, Jeffrey E.; Schanzer, Andres; Stone, David H.; Kraiss, Larry W.; Cronenwett, Jack L.

    2012-01-01

    Background Some patients who undergo lower extremity bypass (LEB) for critical limb ischemia ultimately require amputation. The functional outcome achieved by these patients after amputation is not well known. Therefore, we sought to characterize the functional outcome of patients who undergo amputation after LEB, and to describe the pre- and perioperative factors associated with independent ambulation at home after lower extremity amputation. Methods Within a cohort of 3,198 patients who underwent an LEB between January, 2003 and December, 2008, we studied 436 patients who subsequently received an above-knee (AK), below-knee (BK), or minor (forefoot or toe) ipsilateral or contralateral amputation. Our main outcome measure consisted of a “good functional outcome,” defined as living at home and ambulating independently. We calculated univariate and multivariate associations among patient characteristics and our main outcome measure, as well as overall survival. Results Of the 436 patients who underwent amputation within the first year following LEB, 224 of 436 (51.4%) had a minor amputation, 105 of 436 (24.1%) had a BK amputation, and 107 of 436 (24.5%) had an AK amputation. The majority of AK (75 of 107, 72.8%) and BK amputations (72 of 105, 70.6%) occurred in the setting of bypass graft thrombosis, whereas nearly all minor amputations (200 of 224, 89.7%) occurred with a patent bypass graft. By life-table analysis at 1 year, we found that the proportion of surviving patients with a good functional outcome varied by the presence and extent of amputation (proportion surviving with good functional outcome = 88% no amputation, 81% minor amputation, 55% BK amputation, and 45% AK amputation, p = 0.001). Among those analyzed at long-term follow-up, survival was slightly lower for those who had a minor amputation when compared with those who did not receive an amputation after LEB (81 vs. 88%, p = 0.02). Survival among major amputation patients did not significantly

  12. 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.

  13. Executive function on the Psychology Experiment Building Language tests.

    PubMed

    Piper, Brian J; 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; Raber, Jacob

    2012-03-01

    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

  14. Ethical dilemmas in genetic testing: examples from the Cuban program for predictive diagnosis of hereditary ataxias.

    PubMed

    Mariño, Tania Cruz; Armiñán, Rubén Reynaldo; Cedeño, Humberto Jorge; Mesa, José Miguel Laffita; Zaldivar, Yanetza González; Rodríguez, Raúl Aguilera; Santos, Miguel Velázquez; Mederos, Luis Enrique Almaguer; Herrera, Milena Paneque; Pérez, Luis Velázquez

    2011-06-01

    Predictive testing protocols are intended to help patients affected with hereditary conditions understand their condition and make informed reproductive choices. However, predictive protocols may expose clinicians and patients to ethical dilemmas that interfere with genetic counseling and the decision making process. This paper describes ethical dilemmas in a series of five cases involving predictive testing for hereditary ataxias in Cuba. The examples herein present evidence of the deeply controversial situations faced by both individuals at risk and professionals in charge of these predictive studies, suggesting a need for expanded guidelines to address such complexities. PMID:21264501

  15. In vitro gene regulatory networks predict in vivo function of liver

    PubMed Central

    2010-01-01

    Background Evolution of toxicity testing is predicated upon using in vitro cell based systems to rapidly screen and predict how a chemical might cause toxicity to an organ in vivo. However, the degree to which we can extend in vitro results to in vivo activity and possible mechanisms of action remains to be fully addressed. Results Here we use the nitroaromatic 2,4,6-trinitrotoluene (TNT) as a model chemical to compare and determine how we might extrapolate from in vitro data to in vivo effects. We found 341 transcripts differentially expressed in common among in vitro and in vivo assays in response to TNT. The major functional term corresponding to these transcripts was cell cycle. Similarly modulated common pathways were identified between in vitro and in vivo. Furthermore, we uncovered the conserved common transcriptional gene regulatory networks between in vitro and in vivo cellular liver systems that responded to TNT exposure, which mainly contain 2 subnetwork modules: PTTG1 and PIR centered networks. Interestingly, all 7 genes in the PTTG1 module were involved in cell cycle and downregulated by TNT both in vitro and in vivo. Conclusions The results of our investigation of TNT effects on gene expression in liver suggest that gene regulatory networks obtained from an in vitro system can predict in vivo function and mechanisms. Inhibiting PTTG1 and its targeted cell cyle related genes could be key machanism for TNT induced liver toxicity. PMID:21073692

  16. Can we predict community-wide effects of herbicides from toxicity tests on macrophyte species?

    PubMed

    Coutris, Claire; Merlina, Georges; Silvestre, Jérôme; Pinelli, Eric; Elger, Arnaud

    2011-01-17

    Macrophyte communities play an essential role in the way freshwater ecosystems function. It is thus of great concern to understand how environmental factors, especially anthropogenic ones, influence their composition and diversity. The aim of this study was to examine whether the effects of a herbicide mixture (50% atrazine, 35% isoproturon, 15% alachlor) on single macrophyte species can be used to predict its impact at a community level. In a first experiment we tested the sensitivity of six species (Azolla filiculoides, Ceratophyllum demersum, Elodea canadensis, Lemna minor, Myriophyllum spicatum and Vallisneria spiralis) grown separately and exposed to 0.6-600 μg L(-1) of the herbicide mixture. In a second experiment, conducted in microcosms, we tested the effects of herbicides on macrophyte assemblages composed of the same six species exposed to 0, 6 or 60 μg L(-1) of the herbicide mixture. Species grown separately exhibited growth inhibition at 60 and 600 μg L(-1). At 600 μg L(-1) the sensitivity differed significantly between species. V. spiralis was the most resistant species, C. demersum, M. spicatum and E. canadensis exhibited intermediate sensitivities, and A. filiculoides and L. minor were the most sensitive species. In microcosms, community biomass and Shannon evenness index were reduced after 8 weeks at 60 μg L(-1). Communities also exhibited changes in their composition: the relative and absolute abundance of C. demersum increased at 6 μg L(-1), while the relative abundance of V. spiralis increased at 60 μg L(-1). These results are in agreement with the individual responses of these species to the herbicides. It is therefore concluded that short-term effects of herbicides on simple macrophyte communities can be predicted from the sensitivity of individual species. However, further investigations are required to examine whether longer term effects can be predicted as well, especially in more complex communities. PMID:20926143

  17. [Diagnosis and examination for COPD. Pulmonary function tests].

    PubMed

    Kubota, Masaru

    2016-05-01

    Pulmonary function tests are essential for the diagnosis and management of COPD. It is important to understand the inspection method of tests and the interpretation of test results. The presence of a post-bronchodilator FEV1/FVC<0.70 confirms the presence of persistent airflow limitation and the diagnosis of COPD. On the other hand, the classification of severity of airflow limitation in COPD is based on %FEV1. In COPD patients, as airflow limitation worsens gas trapping and static hyperinflation occurs. These changes can be documented by lung volume measurement as increases in functional residual capacity, residual volume and total lung capacity. Measurement of diffusing capacity (DLco) provides information on the functional impact of emphysema in COPD. PMID:27254943

  18. 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

  19. Measuring individuals' response quality in self-administered psychological tests: an introduction to Gendre's functional method

    PubMed Central

    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. PMID:26136693

  20. Predicting Functional Resilience Among Young-Adult Children of Opiate-Addicted Parents

    PubMed Central

    Skinner, Martie L.; Haggerty, Kevin P.; Fleming, Charles B.; Catalano, Richard F.

    2009-01-01

    Purpose This study describes the adversities experienced by a sample of children of opiate-addicted parents, examines criteria for young adulthood functional resilience, and tests parent, child, and school predictors of resilience. Methods The Focus on Families (FOF) project was a randomized trial of a family-focused intervention with opiate addicts in methadone treatment and their children. Analyses were conducted on data from the children in treatment and control families during the original study (1991–1995) and a long-term follow-up interview (2005–2006). Results While all participants had an opiate-addicted parent, 70% experienced 2 or more and 20% experienced 4 or more additional types of childhood adversity. Twenty-four percent met the following three criteria for functional resilience at the time of their young-adult interview: (1) working or being enrolled in school, (2) no history of substance abuse or dependence, and (3) no adult criminal charges in the prior 5 years. The FOF intervention did not significantly predict functional resilience. Girls were approximately four times more likely to exhibit resilience than boys. Experiencing a wider range of adversities in addition to having an opiate-addicted parent did not reduce the likelihood of functional resilience. Of the 5 child, family, and school predictors tested after, only externalizing or internalizing problems in childhood were significantly associated with the likelihood of functional resilience (OR = .30, p = .04) as a young adult. Conclusions These findings suggest that early intervention with families with addicted parents to prevent and reduce internalizing and externalizing problems in their children holds the most promise of supporting resilient adaptation in early adulthood. PMID:19237115

  1. Adolescents’ Functional Numeracy Is Predicted by Their School Entry Number System Knowledge

    PubMed Central

    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. PMID:23382934

  2. 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. PMID:23382934

  3. SP-100 nuclear assembly test: Test assembly functional requirements and system arrangement

    NASA Astrophysics Data System (ADS)

    Fallas, T. Ted; Gluck, Robert; Motwani, Kumar; Clay, Harold; O'Neill, Gerald

    1991-01-01

    This paper describes the functional requirements and the system that will be tested to validate the reactor, flight shield, and flight controller of the SP-100 Generic Flight System (GFS). The Nuclear Assembly Test (NAT) consists of the test article (SP-100 reactor with control devices and the flight shield) and its supporting systems. The NAT test assembly is being designed by GE. Westinghouse Hanford Company (WHC) is designing the test cell and vacuum vessel system that will contain the NAT test assembly (Renkey et al. 1989). Preliminary design reviews have been completed and the final design is under way.

  4. 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

  5. The Proteome Folding Project: Proteome-scale prediction of structure and function

    PubMed Central

    Drew, Kevin; Winters, Patrick; Butterfoss, Glenn L.; Berstis, Viktors; Uplinger, Keith; Armstrong, Jonathan; Riffle, Michael; Schweighofer, Erik; Bovermann, Bill; Goodlett, David R.; Davis, Trisha N.; Shasha, Dennis; Malmström, Lars; Bonneau, Richard

    2011-01-01

    The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions. PMID:21824995

  6. Structural and functional protein network analyses predict novel signaling functions for rhodopsin

    PubMed Central

    Kiel, Christina; Vogt, Andreas; Campagna, Anne; Chatr-aryamontri, Andrew; Swiatek-de Lange, Magdalena; Beer, Monika; Bolz, Sylvia; Mack, Andreas F; Kinkl, Norbert; Cesareni, Gianni; Serrano, Luis; Ueffing, Marius

    2011-01-01

    Orchestration of signaling, photoreceptor structural integrity, and maintenance needed for mammalian vision remain enigmatic. By integrating three proteomic data sets, literature mining, computational analyses, and structural information, we have generated a multiscale signal transduction network linked to the visual G protein-coupled receptor (GPCR) rhodopsin, the major protein component of rod outer segments. This network was complemented by domain decomposition of protein–protein interactions and then qualified for mutually exclusive or mutually compatible interactions and ternary complex formation using structural data. The resulting information not only offers a comprehensive view of signal transduction induced by this GPCR but also suggests novel signaling routes to cytoskeleton dynamics and vesicular trafficking, predicting an important level of regulation through small GTPases. Further, it demonstrates a specific disease susceptibility of the core visual pathway due to the uniqueness of its components present mainly in the eye. As a comprehensive multiscale network, it can serve as a basis to elucidate the physiological principles of photoreceptor function, identify potential disease-associated genes and proteins, and guide the development of therapies that target specific branches of the signaling pathway. PMID:22108793

  7. A function approximation approach to anomaly detection in propulsion system test data

    NASA Astrophysics Data System (ADS)

    Whitehead, Bruce A.; Hoyt, W. A.

    1993-06-01

    Ground test data from propulsion systems such as the Space Shuttle Main Engine (SSME) can be automatically screened for anomalies by a neural network. The neural network screens data after being trained with nominal data only. Given the values of 14 measurements reflecting external influences on the SSME at a given time, the neural network predicts the expected nominal value of a desired engine parameter at that time. We compared the ability of three different function-approximation techniques to perform this nominal value prediction: a novel neural network architecture based on Gaussian bar basis functions, a conventional back propagation neural network, and linear regression. These three techniques were tested with real data from six SSME ground tests containing two anomalies. The basis function network trained more rapidly than back propagation. It yielded nominal predictions with, a tight enough confidence interval to distinguish anomalous deviations from the nominal fluctuations in an engine parameter. Since the function-approximation approach requires nominal training data only, it is capable of detecting unknown classes of anomalies for which training data is not available.

  8. A function approximation approach to anomaly detection in propulsion system test data

    NASA Technical Reports Server (NTRS)

    Whitehead, Bruce A.; Hoyt, W. A.

    1993-01-01

    Ground test data from propulsion systems such as the Space Shuttle Main Engine (SSME) can be automatically screened for anomalies by a neural network. The neural network screens data after being trained with nominal data only. Given the values of 14 measurements reflecting external influences on the SSME at a given time, the neural network predicts the expected nominal value of a desired engine parameter at that time. We compared the ability of three different function-approximation techniques to perform this nominal value prediction: a novel neural network architecture based on Gaussian bar basis functions, a conventional back propagation neural network, and linear regression. These three techniques were tested with real data from six SSME ground tests containing two anomalies. The basis function network trained more rapidly than back propagation. It yielded nominal predictions with, a tight enough confidence interval to distinguish anomalous deviations from the nominal fluctuations in an engine parameter. Since the function-approximation approach requires nominal training data only, it is capable of detecting unknown classes of anomalies for which training data is not available.

  9. 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

  10. 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

  11. [Problems of lung function testing in the laboratory].

    PubMed

    Tojo, Naoko

    2006-08-01

    Spirometry is indispensable for the screening test of general respiratory function, and measurements of lung volume and diffusing capacity play an important role in the assessment of disease severity, functional disability, disease activity and response to treatment. Pulmonary function testing requires cooperation between the subjects and the examiner, and the results obtained depend on technical as well as personal factors. In order to diminish the variability of results and improve measurement accuracy, the Japan Respiratory Society published the first guidelines on the standardization of spirometry and diffusing capacity for both technical and clinical staff in 2004. It is therefore essential to distribute the guidelines to both laboratory personnel and general physicians. Furthermore, training workshops are mandatory to improve their understanding of the basics of lung function testing. Recently, there has been increasing interest in noninvasive methods of lung function testing without requiring the patient's cooperation during spontaneous breathing. Three alternative techniques, i.e. the negative expiratory pressure (NEP) method to detect expiratory flow limitation, impulse oscillation system (IOS) to measure respiratory system resistance (Rrs) and reactance (Xrs), and interruption resistance (Rint) to measure respiratory resistance have been introduced. Further study is required to determine the advantage of these methods. PMID:16989403

  12. 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.

  13. 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

  14. 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

  15. VALIDITY OF EFFLUENT AND AMBIENT TOXICITY TESTS FOR PREDICTING BIOLOGICAL IMPACT, BACK RIVER, BALTIMORE HARBOR, MARYLAND

    EPA Science Inventory

    The purpose for the study was to measure the toxicity of effluents discharged to an estuary using freshwater test species and compare the predictions with the receiving water biological impact. In addition, ambient tests were done in conjunction with salinity tolerance tests to c...

  16. 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…

  17. The Use of Psychological Tests in Predicting Vocational Success of Disadvantaged Adults.

    ERIC Educational Resources Information Center

    Stanley, Charlton S.

    A study of the relationship between certain test scores and probable training and vocational success was made. Examined were three major training areas: power sewing machine, nurse aide, and clerical office work. Six tests were tested for their ability to predict success: the WAIS Revised Beta; Purdue Pegboard; English, California Surveys of…

  18. 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…

  19. Repeated mobility testing for later artificial visual function evaluation

    NASA Astrophysics Data System (ADS)

    Velikay-Parel, M.; Ivastinovic, D.; Koch, M.; Hornig, R.; Dagnelie, G.; Richard, G.; Langmann, A.

    2007-03-01

    The study investigates the utility of a newly designed mobility test for repeated testing of visual function in patients with severe visual impairment and future application in evaluating functional progress in patients with artificial vision. Ten subjects divided into three groups based on visual acuity (VA) ranging from light perception to 20/200 and reduced visual field (VF) were included in the study. The mobility test consisted of using a set of four different but structurally similar and relatively short mazes having a constant number of obstacles of various sizes. The subjects, divided into three groups by acuity, passed through each course several times. In general, the patients with better VA had a larger extent of VF. Average speed and number of contacts were recorded as measures of performance. The average passing times of the groups through the courses were significantly different (p = 0.03), which was influenced by VA and VF. There was no significant difference in average number of contacts between the groups (p = 0.15). The mobility test proved to be appropriate for gaining statistically relevant results in repeated individual testing of patients with severe vision impairment. Results show promise for use this mobility test as a tool for assessing visual function of patients undergoing implantation of a visual prosthesis for artificial vision.

  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. Does human presynaptic striatal dopamine function predict social conformity?

    PubMed

    Stokes, Paul R A; Benecke, Aaf; Puraite, Julita; Bloomfield, Michael A P; Shotbolt, Paul; Reeves, Suzanne J; Lingford-Hughes, Anne R; Howes, Oliver; Egerton, Alice

    2014-03-01

    Socially desirable responding (SDR) is a personality trait which reflects either a tendency to present oneself in an overly positive manner to others, consistent with social conformity (impression management (IM)), or the tendency to view one's own behaviour in an overly positive light (self-deceptive enhancement (SDE)). Neurochemical imaging studies report an inverse relationship between SDR and dorsal striatal dopamine D₂/₃ receptor availability. This may reflect an association between SDR and D₂/₃ receptor expression, synaptic dopamine levels or a combination of the two. In this study, we used a [¹⁸F]-DOPA positron emission tomography (PET) image database to investigate whether SDR is associated with presynaptic dopamine function. Striatal [¹⁸F]-DOPA uptake, (k(i)(cer), min⁻¹), was determined in two independent healthy participant cohorts (n=27 and 19), by Patlak analysis using a cerebellar reference region. SDR was assessed using the revised Eysenck Personality Questionnaire (EPQ-R) Lie scale, and IM and SDE were measured using the Paulhus Deception Scales. No significant associations were detected between Lie, SDE or IM scores and striatal [¹⁸F]-DOPA k(i)(cer). These results indicate that presynaptic striatal dopamine function is not associated with social conformity and suggests that social conformity may be associated with striatal D₂/₃ receptor expression rather than with synaptic dopamine levels. PMID:24257812

  2. Filtered selection coupled with support vector machines generate a functionally relevant prediction model for colorectal cancer

    PubMed Central

    Gabere, Musa Nur; Hussein, Mohamed Aly; Aziz, Mohammad Azhar

    2016-01-01

    Purpose There has been considerable interest in using whole-genome expression profiles for the classification of colorectal cancer (CRC). The selection of important features is a crucial step before training a classifier. Methods In this study, we built a model that uses support vector machine (SVM) to classify cancer and normal samples using Affymetrix exon microarray data obtained from 90 samples of 48 patients diagnosed with CRC. From the 22,011 genes, we selected the 20, 30, 50, 100, 200, 300, and 500 genes most relevant to CRC using the minimum-redundancy–maximum-relevance (mRMR) technique. With these gene sets, an SVM model was designed using four different kernel types (linear, polynomial, radial basis function [RBF], and sigmoid). Results The best model, which used 30 genes and RBF kernel, outperformed other combinations; it had an accuracy of 84% for both ten fold and leave-one-out cross validations in discriminating the cancer samples from the normal samples. With this 30 genes set from mRMR, six classifiers were trained using random forest (RF), Bayes net (BN), multilayer perceptron (MLP), naïve Bayes (NB), reduced error pruning tree (REPT), and SVM. Two hybrids, mRMR + SVM and mRMR + BN, were the best models when tested on other datasets, and they achieved a prediction accuracy of 95.27% and 91.99%, respectively, compared to other mRMR hybrid models (mRMR + RF, mRMR + NB, mRMR + REPT, and mRMR + MLP). Ingenuity pathway analysis was used to analyze the functions of the 30 genes selected for this model and their potential association with CRC: CDH3, CEACAM7, CLDN1, IL8, IL6R, MMP1, MMP7, and TGFB1 were predicted to be CRC biomarkers. Conclusion This model could be used to further develop a diagnostic tool for predicting CRC based on gene expression data from patient samples. PMID:27330311

  3. Stability of executive function and predictions to adaptive behavior from middle childhood to pre-adolescence

    PubMed Central

    Harms, Madeline B.; Zayas, Vivian; Meltzoff, Andrew N.; Carlson, Stephanie M.

    2014-01-01

    The shift from childhood to adolescence is characterized by rapid remodeling of the brain and increased risk-taking behaviors. Current theories hypothesize that developmental enhancements in sensitivity to affective environmental cues in adolescence may undermine executive function (EF) and increase the likelihood of problematic behaviors. In the current study, we examined the extent to which EF in childhood predicts EF in early adolescence. We also tested whether individual differences in neural responses to affective cues (rewards/punishments) in childhood serve as a biological marker for EF, sensation-seeking, academic performance, and social skills in early adolescence. At age 8, 84 children completed a gambling task while event-related potentials (ERPs) were recorded. We examined the extent to which selections resulting in rewards or losses in this task elicited (i) the P300, a post-stimulus waveform reflecting the allocation of attentional resources toward a stimulus, and (ii) the SPN, a pre-stimulus anticipatory waveform reflecting a neural representation of a “hunch” about an outcome that originates in insula and ventromedial PFC. Children also completed a Dimensional Change Card-Sort (DCCS) and Flanker task to measure EF. At age 12, 78 children repeated the DCCS and Flanker and completed a battery of questionnaires. Flanker and DCCS accuracy at age 8 predicted Flanker and DCCS performance at age 12, respectively. Individual differences in the magnitude of P300 (to losses vs. rewards) and SPN (preceding outcomes with a high probability of punishment) at age 8 predicted self-reported sensation seeking (lower) and teacher-rated academic performance (higher) at age 12. We suggest there is stability in EF from age 8 to 12, and that childhood neural sensitivity to reward and punishment predicts individual differences in sensation seeking and adaptive behaviors in children entering adolescence. PMID:24795680

  4. [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 simultaneously detect the integrity of the sperm head and tail and sperm membrane structure and function. As a widely used method in clinical laboratories in China, the Eosin Y-water test is methodologically characterized by three advantages. Firstly, both the sperm head and tail can be detected at the same time, which allows easy and comprehensive assessment of membrane damage in different parts of sperm. Secondly, distilled water is used instead of the usual formula solution to simplify and standardize the test by eliminating any potential effects on the water molecules through the sperm membrane due to different osmotic pressure or different sugar proportions and electrolyte solutions. Thirdly, the test takes less time and thus can be repeated before and after treatment. This article focuses on the fundamental principles and modification of the Eosin Y-water test and its application in sperm function examination and routine semen analysis for male infertility, assessment of the quality of sperm retrieved by testicular fine needle aspiration, semen cryopreservation program development, and evaluation of sperm membrane integrity after microwave radiation. PMID:26242051

  5. The challenge of developmentally appropriate care: predictive genetic testing in young people for familial adenomatous polyposis.

    PubMed

    Duncan, Rony E; Gillam, Lynn; Savulescu, Julian; Williamson, Robert; Rogers, John G; Delatycki, Martin B

    2010-03-01

    Predictive genetic tests for familial adenomatous polyposis (FAP) are routinely offered to young people during early adolescence. While this is not controversial, due to the medical benefit conferred by the test, it is nonetheless challenging as a consequence of the stage of life of the young people, and the simultaneous involvement of multiple family members. Despite these challenges, it is possible to ensure that the test is offered in such a way that it actively acknowledges and facilitates young people's developing autonomy and psychosocial well-being. In this paper we present findings from ten in-depth interviews with young people who have undergone predictive genetic testing for FAP (four male, six female; five gene-positive, five gene-negative; aged 10-17 years at the time of their predictive test; aged 12-25 years at the time of their research interview). We present five themes that emerged from the interviews which highlight key ethical challenges associated with such testing. These are: (1) the significance of the test; (2) young people's lack of involvement in the decision to be tested; (3) young people's limited understanding; (4) provision of the blood test at the first visit; and (5) group testing of family members. We draw on these themes to make eight recommendations for future practice. Together, these recommendations highlight the importance of providing developmentally appropriate care to young people undergoing predictive genetic testing for FAP. PMID:19760114

  6. The Functional Task Test (FTT): An Interdisciplinary Testing Protocol to Investigate the Factors Underlying Changes in Astronaut Functional Performance

    NASA Technical Reports Server (NTRS)

    Bloomberg, J. J.; Lawrence, E. L.; Arzeno, N. M.; Buxton, R. E.; Feiveson, A. H.; Kofman, I. S.; Lee, S. M. C.; Mulavara, A. P.; Peters, B. T.; Platts. S. H.; Ploutz-Snyder, L. L.; Reschke, M. F.; Ryder, J. W.; Spiering, B. A.; Stenger, M. B.; Taylor, L. C.; Wood, S. J.

    2011-01-01

    Exposure to space flight causes adaptations in multiple physiological systems including changes in sensorimotor, cardiovascular, and neuromuscular systems. These changes may affect a crewmember s ability to perform critical mission tasks immediately after landing on a planetary surface. The overall goal of this project is to determine the effects of space flight on functional tests that are representative of high priority exploration mission tasks and to identify the key underlying physiological factors that contribute to decrements in performance. To achieve this goal we developed an interdisciplinary testing protocol (Functional Task Test, FTT) that evaluates both astronaut functional performance and related physiological changes. Functional tests include ladder climbing, hatch opening, jump down, manual manipulation of objects and tool use, seat egress and obstacle avoidance, recovery from a fall and object translation tasks. Physiological measures include assessments of postural and gait control, dynamic visual acuity, fine motor control, plasma volume, orthostatic intolerance, upper- and lower-body muscle strength, power, endurance, control, and neuromuscular drive. Crewmembers perform this integrated test protocol before and after short (Shuttle) and long-duration (ISS) space flight. Data are collected on two sessions before flight, on landing day (Shuttle only) and 1, 6 and 30 days after landing. Preliminary results from both Shuttle and ISS crewmembers indicate decrement in performance of the functional tasks after both short and long-duration space flight. On-going data collection continues to improve the statistical power required to map changes in functional task performance to alterations in physiological systems. The information obtained from this study will be used to design and implement countermeasures that specifically target the physiological systems most responsible for the altered functional performance associated with space flight.

  7. 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.

  8. 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.

  9. Frequency importance functions for a feature recognition test material.

    PubMed

    Duggirala, V; Studebaker, G A; Pavlovic, C V; Sherbecoe, R L

    1988-06-01

    The relative importance of different parts of the auditory spectrum to recognition of the Diagnostic Rhyme Test (DRT) and its six speech feature subtests was determined. Three normal hearing subjects were tested twice in each of 70 experimental conditions. The analytical procedures of French and Steinberg [J. Acoust. Soc. Am. 19, 90-119 (1947)] were applied to the data to derive frequency importance functions for each of the DRT subtests and the test as a whole over the frequency range 178-8912 Hz. For the DRT as a whole, the low frequencies were found to be more important than is the case for nonsense syllables. Importance functions for the feature subtests also differed from those for nonsense syllables and from each other as well. These results suggest that test materials loaded with different proportions of particular phonemes have different frequency importance functions. Comparison of the results with those from other studies suggests that importance functions depend to a degree on the available response options as well. PMID:3411027

  10. Executive Function in Preschool Children: Test-Retest Reliability

    ERIC Educational Resources Information Center

    Beck, Danielle M.; Schaefer, Catherine; Pang, Karen; Carlson, Stephanie M.

    2011-01-01

    Research suggests that executive function (EF) may distinguish between children who are well- or ill-prepared for kindergarten; however, little is known about the test-retest reliability of measures of EF for children. We aimed to establish a battery of EF measures that are sensitive to both development and individual differences across the…

  11. Testing for Differential Item Functioning with Measures of Partial Association

    ERIC Educational Resources Information Center

    Woods, Carol M.

    2009-01-01

    Differential item functioning (DIF) occurs when an item on a test or questionnaire has different measurement properties for one group of people versus another, irrespective of mean differences on the construct. There are many methods available for DIF assessment. The present article is focused on indices of partial association. A family of average…

  12. Advances in the Detection of Differentially Functioning Test Items.

    ERIC Educational Resources Information Center

    Hambleton, Ronald K.; And Others

    The development and evaluation of methods for detecting potentially biased items or differentially functioning items (DIF) represent a critical area of research for psychometricians because of the negative impact of biased items on test validity. A summary is provided of the authors' 12 years of research at the University of Massachusetts…

  13. Testing anatomically specified hypotheses in functional imaging using cytoarchitectonic maps.

    PubMed

    Eickhoff, Simon B; Heim, Stefan; Zilles, Karl; Amunts, Katrin

    2006-08-15

    The statistical inference on functional imaging data is severely complicated by the embedded multiple testing problem. Defining a region of interest (ROI) where the activation is hypothesized a priori helps to circumvent this problem, since in this case the inference is restricted to fewer simultaneous tests, rendering it more sensitive. Cytoarchitectonic maps obtained from postmortem brains provide objective, a priori ROIs that can be used to test anatomically specified hypotheses about the localization of functional activations. We here analyzed three methods for the definition of ROIs based on probabilistic cytoarchitectonic maps. (1) ROIs defined by the volume assigned to a cytoarchitectonic area in the summary map of all areas (maximum probability map, MPM), (2) ROIs based on thresholding the individual probabilistic maps and (3) spherical ROIs build around the cytoarchitectonic center of gravity. The quality with which the thus defined ROIs represented the respective cytoarchitectonic areas as well as their sensitivity for detecting functional activations was subsequently statistically evaluated. Our data showed that the MPM method yields ROIs, which reflect most adequately the underlying anatomical hypotheses. These maps also show a high degree of sensitivity in the statistical analysis. We thus propose the use of MPMs for the definition of ROIs. In combination with thresholding based on the Gaussian random field theory, these ROIs can then be applied to test anatomically specified hypotheses in functional neuroimaging studies. PMID:16781166