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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. 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).

  3. Predicting functional capacity during treadmill testing independent of exercise protocol.

    PubMed

    Foster, C; Crowe, A J; Daines, E; Dumit, M; Green, M A; Lettau, S; Thompson, N N; Weymier, J

    1996-06-01

    Clinically useful estimates of VO2max from treadmill tests (GXT) may be made using protocol-specific equations. In many cases, GXT may proceed more effectively if the clinician is free to adjust speed and grade independent of a specific protocol. We sought to determine whether VO2max could be predicted from the estimated steady-state VO2 of the terminal exercise stage. Seventy clinically stable individuals performed GXT with direct measurement of VO2. Exercise was incremented each minute to optimize clinical examination. Measured VO2max was compared to the estimated steady-state VO2 of the terminal stage based on ACSM equations. Equations for walking or running were used based on the patient's observed method of ambulation. The measured VO2max was always less than the ACSM estimate, with a regular relationship between measured and estimated VO2max. No handrail support: VO2max = 0.869.ACSM -0.07; R2 = 0.955, SEE = 4.8 ml.min-1.kg-1 (N = 30). With handrail support: VO2max = 0.694.ACSM + 3.33; R2 = 0.833, SEE = 4.4 ml.min-1.kg-1 (N = 40). The equations were cross-validated with 20 patients. The correlation between predicted and observed values was r = 0.98 and 0.97 without and with handrail support, respectively. The mean absolute prediction error (3.1 and 4.1 ml.min-1.kg-1) were similar to protocol-specific equations. We conclude that VO2max can be predicted independent of treadmill protocol with approximately the same error as protocol-specific equations.

  4. CAN UPPER EXTREMITY FUNCTIONAL TESTS PREDICT THE SOFTBALL THROW FOR DISTANCE: A PREDICTIVE VALIDITY INVESTIGATION

    PubMed Central

    Hanney, William J.; Kolber, Morey J.; Davies, George J.; Riemann, Bryan

    2011-01-01

    Introduction: Understanding the relationships between performance tests and sport activity is important to the rehabilitation specialist. The purpose of this study was two- fold: 1) To identify if relationships exist between tests of upper body strength and power (Single Arm Seated Shot Put, Timed Push-Up, Timed Modified Pull-Up, and The Davies Closed Kinetic Chain Upper Extremity Stability Test, and the softball throw for distance), 2) To determine which variable or group of variables best predicts the performance of a sport specific task (the softball throw for distance). Methods: One hundred eighty subjects (111 females and 69 males, aged 18-45 years) performed the 5 upper extremity tests. The Pearson product moment correlation and a stepwise regression were used to determine whether relationships existed between performance on the tests and which upper extremity test result best explained the performance on the softball throw for distance. Results: There were significant correlations (r=.33 to r=.70, p=0.001) between performance on all of the tests. The modified pull-up test was the best predictor of the performance on the softball throw for distance (r2= 48.7), explaining 48.7% of variation in performance. When weight, height, and age were added to the regression equation the r2 values increased to 64.5, 66.2, and 67.5 respectively. Conclusion: The results of this study indicate that several upper extremity tests demonstrate significant relationships with one another and with the softball throw for distance. The modified pull up test was the best predictor of performance on the softball throw for distance. PMID:21712942

  5. 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 ...

  6. PREDICTION OF FUNCTIONAL MOVEMENT SCREEN™ PERFORMANCE FROM LOWER EXTREMITY RANGE OF MOTION AND CORE TESTS.

    PubMed

    Chimera, Nicole J; Knoeller, Shelby; Cooper, Ron; Kothe, Nicholas; Smith, Craig; Warren, Meghan

    2017-04-01

    There are varied reports in the literature regarding the association of the Functional Movement Screen™ (FMS™) with injury. The FMS™ has been correlated with hamstring range of motion and plank hold times; however, limited research is available on the predictability of lower extremity range of motion (ROM) and core function on FMS™ performance. The purpose of this study was to examine whether active lower extremity ROM measurements and core functional tests predict FMS™ performance. The authors hypothesized that lower extremity ROM and core functional tests would predict FMS™ composite score (CS) and performance on individual FMS™ fundamental movement patterns. Descriptive cohort study. Forty recreationally active participants had active lower extremity ROM measured, performed two core functional tests, the single leg wall sit hold (SLWS) and the repetitive single leg squat (RSLS), and performed the FMS™. Independent t tests were used to assess differences between right and left limb ROM measures and outcomes of core functional tests. Linear and ordinal logistic regressions were used to determine the best predictors of FMS™ CS and fundamental movement patterns, respectively. On the left side, reduced DF and SLWS significantly predicted lower FMS™ CS. On the right side only reduced DF significantly predicted lower FMS™ CS. Ordinal logistic regression models for the fundamental movement patterns demonstrated that reduced DF ROM was significantly associated with lower performance on deep squat. Reduced left knee extension was significantly associated with better performance in left straight leg raise; while reduced right hip flexion was significantly associated with reduced right straight leg raise. Lower SLWS was associated with reduced trunk stability performance. FMS™ movement patterns were affected by lower extremity ROM and core function. Researchers should consider lower FMS™ performance as indicative of underlying issues in ROM and

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  8. Predictions of the Reliability Coefficients and Standard Errors of Measurement Using the Test Information Function and Its Modifications.

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    Because the test information function and its two modified formulas provide useful information, the reliability coefficient of a test is no longer necessary in modern mental test theory. Yet it is interesting to know how to predict the coefficient using the test information function and its modifications, tailored for each separate population of…

  9. Fine motor skills predict performance in the Jebsen Taylor Hand Function Test after stroke.

    PubMed

    Allgöwer, Kathrin; Hermsdörfer, Joachim

    2017-10-01

    To determine factors characterizing the differences in fine motor performance between stroke patients and controls. To confirm the relevance of the factors by analyzing their predictive power with regard to the Jebsen Taylor Hand Function Test (JTHFT), a common clinical test of fine motor control. Twenty-two people with slight paresis in an early chronic phase following stroke and twenty-two healthy controls were examined. Performance on the JTHFT, Nine-Hole Peg Test and 2-point discrimination was evaluated. To analyze object manipulation skills, grip forces and temporal measures were examined during (1) lifting actions with variations of weight and surface (2) cyclic movements (3) predictive/reactive catching tasks. Three other aspects of force control included (4) visuomotor tracking (5) fast force changes and (6) grip strength. Based on 9 parameters which significantly distinguished fine motor performance in the two groups, we identified three principal components (factors): grip force scaling, motor coordination and speed of movement. The three factors are shown to predict JTHFT scores via linear regression (R(2)=0.687, p<0.001). We revealed a factor structure behind fine motor impairments following stroke and showed that it explains JTHFT results to a large extend. This result can serve as a basis for improving diagnostics and enabling more targeted therapy. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

  10. 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.

  11. 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

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

    PubMed

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

    2013-12-01

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

  13. 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.

  14. Predicting therapeutic response to secondary treatment with bupropion: dichotic listening tests of functional brain asymmetry.

    PubMed

    Bruder, Gerard E; Stewart, Jonathan W; Schaller, Jennifer D; McGrath, Patrick J

    2007-10-31

    Studies using neuroimaging, electrophysiologic and cognitive measures have raised hopes for developing predictors of therapeutic response to antidepressants. Pretreatment measures of functional brain asymmetry have been found to be related to response to the selective serotonin reuptake inhibitor fluoxetine. This report examines the extent to which dichotic listening tests also predict clinical response to an antidepressant with a different mechanism of action, i.e., bupropion. Dichotic listening data were obtained for 17 unmedicated depressed patients who were subsequently treated with bupropion. Right-handed outpatients were tested on dichotic fused-words and complex-tones tests. Seven patients who responded to bupropion and 10 nonresponders did not differ in gender, age or education. Bupropion responders had significantly larger left-hemisphere advantage for perceiving words when compared to nonresponders, but there was no difference in their right-hemisphere advantage for tones. All patients having a left-hemisphere advantage above the normal mean responded to bupropion, whereas only 9% of patients below the normal mean responded to treatment. These findings should encourage further study of the clinical value of dichotic listening and other measures of functional brain asymmetry for identifying depressed patients who most benefit from treatment with different classes of antidepressants.

  15. Impairment in Occupational Functioning and Adult ADHD: The Predictive Utility of Executive Function (EF) Ratings Versus EF Tests

    PubMed Central

    Barkley, Russell A.; Murphy, Kevin R.

    2010-01-01

    Attention deficit hyperactivity disorder (ADHD) is associated with deficits in executive functioning (EF). ADHD in adults is also associated with impairments in major life activities, particularly occupational functioning. We investigated the extent to which EF deficits assessed by both tests and self-ratings contributed to the degree of impairment in 11 measures involving self-reported occupational problems, employer reported workplace adjustment, and clinician rated occupational adjustment. Three groups of adults were recruited as a function of their severity of ADHD: ADHD diagnosis (n = 146), clinical controls self-referring for ADHD but not diagnosed with it (n = 97), and community controls (n = 109). Groups were combined and regression analyses revealed that self-ratings of EF were significantly predictive of impairments in all 11 measures of occupational adjustment. Although several tests of EF also did so, they contributed substantially less than did the EF ratings, particularly when analyzed jointly with the ratings. We conclude that EF deficits contribute to the impairments in occupational functioning that occur in conjunction with adult ADHD. Ratings of EF in daily life contribute more to such impairments than do EF tests, perhaps because, as we hypothesize, each assesses a different level in the hierarchical organization of EF as a meta-construct. PMID:20197297

  16. Do simple beside lung function tests predict morbidity after rib fractures?

    PubMed

    Butts, Christopher A; Brady, John J; Wilhelm, Sara; Castor, Laura; Sherwood, Alicia; McCall, Abby; Patch, John; Jones, Pamela; Cortes, Vicente; Ong, Adrian W

    2017-03-01

    We evaluated if incentive spirometry volume (ISV) and peak expiratory flow rate (PEFR) could predict acute respiratory failure (ARF) in patients with rib fractures. Normotensive, co-operative patients were enrolled prospectively. ISV and PEFR were measured on admission, at 24 h and at 48 h by taking the best of three readings each time. The primary outcome, ARF, was defined as requiring invasive or noninvasive positive pressure ventilation. 99 patients were enrolled (median age, 77 years). ARF occurred in 9%. Of the lung function tests, only a low median ISV at admission was associated with ARF (500 ml vs 1250 ml, p = 0.04). Three of 69 patients with ISV of ≥1000 ml versus six of 30 with ISV <1000 ml developed ARF (p = 0.01). Other significant factors were: number of rib fractures, tube thoracostomy, any lower-third rib fracture, flail segment. PEFR did not predict ARF. Admission ISV may have value in predicting ARF. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. 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

    2016-03-23

    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.

  18. 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.

  19. Accuracy of liver function tests for predicting adverse maternal and fetal outcomes in women with preeclampsia: a systematic review.

    PubMed

    Thangaratinam, Shakila; Koopmans, Corine M; Iyengar, Shalini; Zamora, Javier; Ismail, Khaled M K; Mol, Ben W J; Khan, Khalid S

    2011-06-01

    Liver function tests are routinely performed in women as part of a battery of investigations to assess severity at admission and later to guide appropriate management. To determine the accuracy with which liver function tests predict complications in women with preeclampsia by a systematic review. We conducted electronic searches without language restrictions in (1951-2010), (1980-2010) and the Cochrane Library (2009). Primary articles that evaluated the accuracy of liver function tests in predicting complications in women with preeclampsia were chosen. Data was extracted by two reviewers independently. A bivariate model estimated area under the curve, sensitivity and specificity. There were 13 primary articles including a total of 3 497 women assessing maternal (30 2×2 tables) and fetal (19 2×2 tables) outcomes. For predicting adverse maternal outcome, the point estimates of specificity were >70% in 18 tables with 0.79 (95%CI 0.51, 0.93). For predicting adverse fetal outcomes the specificity of the test was >70% in 2×2 tables. Sensitivity of the test was poor for both maternal and fetal outcomes. In women with preeclampsia, function tests performed better in predicting adverse maternal than fetal outcomes. The presence of increased liver enzymes was associated with an increased probability of maternal and fetal complications, but normal liver enzyme levels did not rule out disease, as specificity was often higher than sensitivity. © 2011 The Authors Acta Obstetricia et Gynecologica Scandinavica© 2011 Nordic Federation of Societies of Obstetrics and Gynecology.

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

    PubMed Central

    Lee, A-Jin; Kim, Sang-Gyung

    2016-01-01

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

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

    PubMed

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

    1996-09-01

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

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

    PubMed Central

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

    1996-01-01

    For people at risk for Huntington's disease, the anxiety and uncertainty about the future may be very burdensome and may be an obstacle to personal decision making about important life issues, for example, procreation. For some at risk persons, this situation is the reason for requesting predictive DNA testing. The aim of this paper is two-fold. First, we want to evaluate whether knowing one's carrier status reduces anxiety and uncertainty and whether it facilitates decision making about procreation. Second, we endeavour to identify pretest predictors of psychological adaptation one year after the predictive test (psychometric evaluation of general anxiety, depression level, and ego strength). The impact of the predictive test result was assessed in 53 subjects tested, using pre- and post-test psychometric measurement and self-report data of follow up interviews. Mean anxiety and depression levels were significantly decreased one year after a good test result; there was no significant change in the case of a bad test result. The mean personality profile, including ego strength, remained unchanged one year after the test. The study further shows that the test result had a definite impact on reproductive decision making. Stepwise multiple regression analyses were used to select the best predictors of the subject's post-test reactions. The results indicate that a careful evaluation of pretest ego strength, depression level, and coping strategies may be helpful in predicting post-test reactions, independently of the carrier status. Test result (carrier/ non-carrier), gender, and age did not significantly contribute to the prediction. About one third of the variance of post-test anxiety and depression level and more than half of the variance of ego strength was explained, implying that other psychological or social aspects should also be taken into account when predicting individual post-test reactions. PMID:8880572

  3. 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

  4. 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

  5. The critical power function is dependent on the duration of the predictive exercise tests chosen.

    PubMed

    Bishop, D; Jenkins, D G; Howard, A

    1998-02-01

    The linear relationship between work accomplished (W(lim)) and time to exhaustion (t(lim)) can be described by the equation: W(lim) = a + CP x t(lim). Critical power (CP) is the slope of this line and is thought to represent a maximum rate of ATP synthesis without exhaustion, presumably an inherent characteristic of the aerobic energy system. The present investigation determined whether the choice of predictive tests would elicit significant differences in the estimated CP. Ten female physical education students completed, in random order and on consecutive days, five all-out predictive tests at preselected constant-power outputs. Predictive tests were performed on an electrically-braked cycle ergometer and power loadings were individually chosen so as to induce fatigue within approximately 1-10 mins. CP was derived by fitting the linear W(lim)-t(lim) regression and calculated three ways: 1) using the first, third and fifth W(lim)-t(lim) coordinates (I135), 2) using coordinates from the three highest power outputs (I123; mean t(lim) = 68-193 s) and 3) using coordinates from the lowest power outputs (I345; mean t(lim) = 193-485 s). Repeated measures ANOVA revealed that CPI123 (201.0+/-37.9W) > CPI135 (176.1+/-27.6W) > CPI345 (164.0+/-22.8W) (P<0.05). When the three sets of data were used to fit the hyperbolic Power-t(lim) regression, statistically significant differences between each CP were also found (P<0.05). The shorter the predictive trials, the greater the slope of the W(lim)-t(lim) regression; possibly because of the greater influence of 'aerobic inertia' on these trials. This may explain why CP has failed to represent a maximal, sustainable work rate. The present findings suggest that if CP is to represent the highest power output that an individual can maintain "for a very long time without fatigue" then CP should be calculated over a range of predictive tests in which the influence of aerobic inertia is minimised.

  6. Accuracy of indocyanine green pulse spectrophotometry clearance test for liver function prediction in transplanted patients

    PubMed Central

    Hsieh, Chung-Bao; Chen, Chung-Jueng; Chen, Teng-Wei; Yu, Jyh-Cherng; Shen, Kuo-Liang; Chang, Tzu-Ming; Liu, Yao-Chi

    2004-01-01

    AIM: To investigate whether the non-invasive real-time Indocynine green (ICG) clearance is a sensitive index of liver viability in patients before, during, and after liver transplantation. METHODS: Thirteen patients were studied, two before, three during, and eight following liver transplantation, with two patients suffering acute rejection. The conventional invasive ICG clearance test and ICG pulse spectrophotometry non-invasive real-time ICG clearance test were performed simultaneously. Using linear regression analysis we tested the correlation between these two methods. The transplantation condition of these patients and serum total bilirubin (T. Bil), alanine aminotransferase (ALT), and platelet count were also evaluated. RESULTS: The correlation between these two methods was excellent (r2 = 0.977). CONCLUSION: ICG pulse spectrophotometry clearance is a quick, non-invasive, and reliable liver function test in transplantation patients. PMID:15285026

  7. Flow cytometry-based platelet function testing is predictive of symptom burden in a cohort of bleeders.

    PubMed

    Boknäs, Niklas; Ramström, Sofia; Faxälv, Lars; Lindahl, Tomas L

    2017-09-12

    Platelet function disorders (PFDs) are common in patients with mild bleeding disorders (MBDs), yet the significance of laboratory findings suggestive of a PFD remain unclear due to the lack of evidence for a clinical correlation between the test results and the patient phenotype. Herein, we present the results from a study evaluating the potential utility of platelet function testing using whole-blood flow cytometry in a cohort of 105 patients undergoing investigation for MBD. Subjects were evaluated with a test panel comprising two different activation markers (fibrinogen binding and P-selectin exposure) and four physiologically relevant platelet agonists (ADP, PAR1-AP, PAR4-AP, and CRP-XL). Abnormal test results were identified by comparison with reference ranges constructed from 24 healthy controls or with the fifth percentile of the entire patient cohort. We found that the abnormal test results are predictive of bleeding symptom severity, and that the greatest predictive strength was achieved using a subset of the panel, comparing measurements of fibrinogen binding after activation with all four agonists with the fifth percentile of the patient cohort (p = 0.00008, hazard ratio 8.7; 95% CI 2.5-40). Our results suggest that whole-blood flow cytometry-based platelet function testing could become a feasible alternative for the investigation of MBDs. We also show that platelet function testing using whole-blood flow cytometry could provide a clinically relevant quantitative assessment of platelet-related hemostasis.

  8. 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

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

    PubMed

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

    2015-01-01

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

  10. Preoperative prediction of inpatient recovery of function after total hip arthroplasty using performance-based tests: a prospective cohort study.

    PubMed

    Oosting, Ellen; Hoogeboom, Thomas J; Appelman-de Vries, Suzan A; Swets, Adam; Dronkers, Jaap J; van Meeteren, Nico L U

    2016-01-01

    The aim of this study was to evaluate the value of conventional factors, the Risk Assessment and Predictor Tool (RAPT) and performance-based functional tests as predictors of delayed recovery after total hip arthroplasty (THA). A prospective cohort study in a regional hospital in the Netherlands with 315 patients was attending for THA in 2012. The dependent variable recovery of function was assessed with the Modified Iowa Levels of Assistance scale. Delayed recovery was defined as taking more than 3 days to walk independently. Independent variables were age, sex, BMI, Charnley score, RAPT score and scores for four performance-based tests [2-minute walk test, timed up and go test (TUG), 10-meter walking test (10 mW) and hand grip strength]. Regression analysis with all variables identified older age (>70 years), Charnley score C, slow walking speed (10 mW >10.0 s) and poor functional mobility (TUG >10.5 s) as the best predictors of delayed recovery of function. This model (AUC 0.85, 95% CI 0.79-0.91) performed better than a model with conventional factors and RAPT scores, and significantly better (p = 0.04) than a model with only conventional factors (AUC 0.81, 95% CI 0.74-0.87). The combination of performance-based tests and conventional factors predicted inpatient functional recovery after THA. Two simple functional performance-based tests have a significant added value to a more conventional screening with age and comorbidities to predict recovery of functioning immediately after total hip surgery. Patients over 70 years old, with comorbidities, with a TUG score >10.5 s and a walking speed >1.0 m/s are at risk for delayed recovery of functioning. Those high risk patients need an accurate discharge plan and could benefit from targeted pre- and postoperative therapeutic exercise programs.

  11. LIVER FUNCTION TESTS IN PREDICTING CBD STONES IN ACUTE BILIARY PANCREATITIS.

    PubMed

    Thomson, J T; Smith, M D; Omoshoro-Jones, J A O; Devar, J D; Gaylard, P D; Khan, Z K; Jugmohan, B J

    2017-06-01

    Acute biliary pancreatitis is a significant cause of pancreatitis. The role and timing of endoscopic retrograde cholangiopancreatography in the setting of acute biliary pancreatitis is still controversial. Persistent choledocholithiasis in acute biliary pancreatitis occurs and establishing which patients require an endoscopic retrograde cholangiopancreatography based on liver function tests only can be challenging. Retrospective analysis of the Chris Hani Baragwanath Academic Hospital's ERCP database was performed. All ERCPs performed in patients with acute biliary pancreatitis were identified and analysed. A total of 2830 ERCPs were performed during the study period. In total 99 (3%) were performed for suspected choledocholithiasis in acute biliary pancreatitis with abnormal liver function tests. Thirty (30%) of the ERCPs confirmed choledocholithiasis while the remaining 69 (70%) yielded no choledocholithiasis. A significantly higher proportion of patients with choledocholithiasis required a needle knife sphincterotomy for deep biliary cannulation. The incidence of immediate complications, such as bleeding, false tract formation and perforation were comparable between the two groups. Two models were developed to determine specific cut-off values for conjugated bilirubin, ALP, GGT, AST and ALT. The calculated cut-off values yielded poor correlation between sensitivity and specificity. Determining persistent choledocholithiasis in acute biliary pancreatitis based on liver function test alone is not ideal. Using conjugated bilirubin, ALP, GGT, AST and ALT to guide one to perform an ERCP in acute biliary pancreatitis can be misleading.

  12. Hospital for Special Surgery Pediatric Functional Activity Brief Scale predicts physical fitness testing performance.

    PubMed

    Fabricant, Peter D; Robles, Alex; McLaren, Son H; Marx, Robert G; Widmann, Roger F; Green, Daniel W

    2014-05-01

    An eight-item activity scale was recently developed and validated for use as a prognostic tool in clinical research in children and adolescents. It is unclear, however, if this brief questionnaire is predictive of quantitative metrics of physical activity and fitness. The purposes of this study were to prospectively administer the Hospital for Special Surgery Pediatric Functional Activity Brief Scale to a large cohort of healthy adolescents to determine (1) if the activity scale exhibits any floor or ceiling effects; (2) if scores on the activity scale are correlated with standardized physical fitness metrics; and if so, (3) to determine the discrimination ability of the activity scale to differentiate between adolescents with healthy or unhealthy levels of aerobic capacity and calculate an appropriate cutoff value for its use as a screening tool. One hundred eighty-two adolescents (mean, 15.3 years old) prospectively completed the activity scale and four standardized metrics of physical fitness: pushups, sit-ups, shuttle run exercise (Progressive Aerobic Cardiovascular Endurance Run), and calculated VO2-max. Age, sex, and body mass index were also recorded. Pearson correlations, regression analyses, and receiver operating characteristic analyses were used to evaluate activity scale performance. The activity scale did not exhibit any floor or ceiling effects. Pushups (ρ = 0.28), sit-ups (ρ = 0.23), performance on the Progressive Aerobic Cardiovascular Endurance Run (ρ = 0.44), and VO2-max (ρ = 0.43) were all positively correlated with the activity scale score (Pearson correlations, all p < 0.001). Receiver operating characteristic analysis revealed that those with an activity score of ≤ 14 were at higher risk of having low levels of aerobic capacity. In the current study, activity score was free of floor and ceiling effects and predictive of all four physical fitness metrics. An activity score of ≤ 14 was associated with at-risk aerobic capacity previously

  13. 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

  14. De-novo protein function prediction using DNA binding and RNA binding proteins as a test case.

    PubMed

    Peled, Sapir; Leiderman, Olga; Charar, Rotem; Efroni, Gilat; Shav-Tal, Yaron; Ofran, Yanay

    2016-11-21

    Of the currently identified protein sequences, 99.6% have never been observed in the laboratory as proteins and their molecular function has not been established experimentally. Predicting the function of such proteins relies mostly on annotated homologs. However, this has resulted in some erroneous annotations, and many proteins have no annotated homologs. Here we propose a de-novo function prediction approach based on identifying biophysical features that underlie function. Using our approach, we discover DNA and RNA binding proteins that cannot be identified based on homology and validate these predictions experimentally. For example, FGF14, which belongs to a family of secreted growth factors was predicted to bind DNA. We verify this experimentally and also show that FGF14 is localized to the nucleus. Mutating the predicted binding site on FGF14 abrogated DNA binding. These results demonstrate the feasibility of automated de-novo function prediction based on identifying function-related biophysical features.

  15. De-novo protein function prediction using DNA binding and RNA binding proteins as a test case

    PubMed Central

    Peled, Sapir; Leiderman, Olga; Charar, Rotem; Efroni, Gilat; Shav-Tal, Yaron; Ofran, Yanay

    2016-01-01

    Of the currently identified protein sequences, 99.6% have never been observed in the laboratory as proteins and their molecular function has not been established experimentally. Predicting the function of such proteins relies mostly on annotated homologs. However, this has resulted in some erroneous annotations, and many proteins have no annotated homologs. Here we propose a de-novo function prediction approach based on identifying biophysical features that underlie function. Using our approach, we discover DNA and RNA binding proteins that cannot be identified based on homology and validate these predictions experimentally. For example, FGF14, which belongs to a family of secreted growth factors was predicted to bind DNA. We verify this experimentally and also show that FGF14 is localized to the nucleus. Mutating the predicted binding site on FGF14 abrogated DNA binding. These results demonstrate the feasibility of automated de-novo function prediction based on identifying function-related biophysical features. PMID:27869118

  16. Predicting Differential Item Functioning in Cross-Lingual Testing: The Case of a High Stakes Test in the Kyrgyz Republic

    ERIC Educational Resources Information Center

    Drummond, Todd W.

    2011-01-01

    Cross-lingual tests are assessment instruments created in one language and adapted for use with another language group. Practitioners and researchers use cross-lingual tests for various descriptive, analytical and selection purposes both in comparative studies across nations and within countries marked by linguistic diversity (Hambleton, 2005).…

  17. Predicting Differential Item Functioning in Cross-Lingual Testing: The Case of a High Stakes Test in the Kyrgyz Republic

    ERIC Educational Resources Information Center

    Drummond, Todd W.

    2011-01-01

    Cross-lingual tests are assessment instruments created in one language and adapted for use with another language group. Practitioners and researchers use cross-lingual tests for various descriptive, analytical and selection purposes both in comparative studies across nations and within countries marked by linguistic diversity (Hambleton, 2005).…

  18. Testing the trait-based community framework: Do functional traits predict competitive outcomes?

    PubMed

    Funk, Jennifer L; Wolf, Amelia A

    2016-09-01

    Plant traits can be used to understand a range of ecological processes, including competition with invasive species. The extent to which native and invasive species are competing via limiting similarity or trait hierarchies has important implications for the management of invaded communities. We screened 47 native species that co-occur with Festuca perennis, a dominant invader in California serpentine grassland, for traits pertaining to resource use and acquisition. We then grew F. perennis with 10 species spanning a range of functional similarity in pairwise competition trials. Functionally similar species did not have a strong adverse effect on F. perennis performance as would be expected by limiting similarity theory. Phylogenetic relatedness, which may integrate a number of functional traits, was also a poor predictor of competitive outcome. Instead, species with high specific root length, low root-to-shoot biomass ratio, and low leaf nitrogen concentration were more effective at suppressing the growth of F. perennis. Our results suggest that fitness differences (i.e., trait hierarchies) may be more important than niche differences (i.e., limiting similarity) in structuring competitive outcomes in this system and may be a promising approach for the restoration of invaded systems.

  19. 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.

  20. Early prediction of functional recovery after experimental stroke: functional magnetic resonance imaging, electrophysiology, and behavioral testing in rats.

    PubMed

    Weber, Ralph; Ramos-Cabrer, Pedro; Justicia, Carlos; Wiedermann, Dirk; Strecker, Cordula; Sprenger, Christiane; Hoehn, Mathias

    2008-01-30

    Therapeutic success of treatment of cerebral diseases must be assessed in terms of functional outcome. In experimental stroke studies, this has been limited to behavioral studies combined with morphological evaluations and single time point functional magnetic resonance imaging (fMRI) measurements but lacking the access to understanding underlying mechanisms for alterations in brain activation. Using a recently developed blood oxygenation level-dependent fMRI protocol to study longitudinal and intraindividual profiles of functional brain activation in the somatosensory system, we have demonstrated activation reemergence in the original representation field as the basic principle of functional recovery from experimental stroke. No plastic reorganization has been observed at any time point during 7 weeks after stroke induction. Applying combined recording of fMRI and somatosensory evoked potentials, we observed a tight coupling of electrical brain activity and hemodynamic response at all times, indicating persistent preservation of neurovascular coupling. Identification of functional brain recovery mechanisms has important implications for the understanding of brain plasticity after cerebral lesions, whereas preservation of neurovascular coupling is important for the clinical translation of fMRI.

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

    PubMed

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

    2010-07-01

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

  2. Testing predictions from density functional theory at finite temperatures: β2-like ground states in Co-Pt

    NASA Astrophysics Data System (ADS)

    Decolvenaere, Elizabeth; Gordon, Michael J.; Van der Ven, Anton

    2015-08-01

    We perform a critical assessment of the accuracy of density functional theory (DFT) based methods in predicting stable phases within the Co-Pt binary alloy. Statistical mechanical analysis applied to zero kelvin DFT predictions yields finite-temperature results that can be directly compared with experimental measurements. The predicted temperature-composition phase diagram is qualitatively incompatible with experimental observations, indicating that the predicted stability of long-period superstructures as ground states in the Co-Pt binary is incorrect. We also show that recently suggested methods to better align DFT and experiment via the hybrid functional HSE06 are unable to resolve the discrepancies in this system. Our results indicate a need for better verification of DFT based phase stability predictions, and highlight fundamental flaws in the ability of DFT to treat late 3 d -5 d binary alloys.

  3. 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.

    2015-01-01

    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.

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

    PubMed Central

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

    2014-01-01

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

  5. Platelet Function Tests.

    PubMed

    Lordkipanidzé, Marie

    2016-04-01

    Traditionally developed for diagnosis of bleeding disorders, platelet function assays have become increasingly used in basic research on platelet physiology, in phenotype-genotype associations in bleeding disorders, in drug development as surrogate endpoints of efficacy of new antiplatelet therapy, and to an extent, in the monitoring of antiplatelet therapy in clinical practice to predict thrombotic and bleeding risk. A multiplicity of platelet function assays is available to measure the level of platelet activity in various settings. These include assays that are restricted to a specialized laboratory as well as point-of-care instruments meant to investigate platelet function at patient bedside. Unlike tests that determine a defined quantity or measurement of a clinical biomarker (e.g., cholesterol or blood pressure), platelet function testing assesses the dynamics of living cells, which immediately presents a series of unique problems to any laboratory or clinic. This article presents currently used platelet function assays and discusses important variables to take into account when performing these assays, including preanalytical issues and difficulties in interpreting platelet function test results.

  6. Comparison of the visual function index to the Snellen Visual Acuity Test in predicting older adult self-restricted driving.

    PubMed

    Lotfipour, Shahram; Patel, Bhakti Harishchandra; Grotsky, Thomas Aaron; Anderson, Craig L; Carr, Erin M; Ahmed, Suleman Syed; Chakravarthy, Bharath; Fox, John Christian; Vaca, Federico E

    2010-10-01

    In this observational study, a modified version of the Visual Function Index (VF-14) and the Snellen Visual Acuity Test were compared in how well they correlated with self-restricted driving habits in older adults. The VF-14 was originally designed to assess vision in cataract patients; however, in this study, a modified version (mVF-14) was evaluated as a tool for predicting self-restricted driving in older drivers. During a 3-month period, 151 drivers over the age of 65 were screened at the local senior center. In addition to the Snellen Visual Acuity Test and mVF-14, each participant was given a questionnaire about their driving habits, previously used in self-restriction studies. Out of 151 total participants, 134 were included and 7 nondrivers and 10 subjects who did not complete all questionnaires were excluded. One hundred one participants exhibited normal visual acuity of 20/40 or better (75%), and 110 scored over 90 on the mVF-14 (82%). Spearman's rank sum correlation coefficient was used to analyze the data and showed significant negative correlation of the mVF-14 and Snellen with self-restricted driving. Individuals with normal vision (20/40 or better on the Snellen eye test) had both high and low mVF-14 scores. The study shows that poor vision, as indicated by the Snellen scale and low mVF-14 scores, correlates to self-imposed driving limitations. The mVF-14 showed further distinctions of self-restriction between individuals in the same Snellen Visual Acuity category. Therefore, using the mVF-14 in addition to the Snellen Visual Acuity Test can be helpful to further differentiate visual ability within older drivers who appear to have normal vision.

  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. Cross-Sectional Analysis of the Utility of Pulmonary Function Tests in Predicting Emphysema in Ever-Smokers

    PubMed Central

    Hesselbacher, Sean E.; Ross, Robert; Schabath, Matthew B.; Smith, E. O’Brian; Perusich, Sarah; Barrow, Nadia; Smithwick, Pamela; Mammen, Manoj J.; Coxson, Harvey; Krowchuk, Natasha; Corry, David B.; Kheradmand, Farrah

    2011-01-01

    Emphysema is largely an under-diagnosed medical condition that can exist in smokers in the absence of airway obstruction. We aimed to determine the sensitivity and specificity of pulmonary function tests (PFTs) in assessing emphysema using quantitative CT scans as the reference standard. We enrolled 224 ever-smokers (current or former) over the age of 40. CT of thorax was used to quantify the low attenuation area (% emphysema), and to measure the standardized airway wall thickness. PFTs were used individually and in combination to predict their ability to discriminate radiographic emphysema. Significant emphysema (>7%) was detected in 122 (54%) subjects. Twenty six (21%) emphysema subjects had no evidence of airflow obstruction (FEV1/FVC ratio <70%), while all subjects with >23% emphysema showed airflow obstruction. The sensitivity and specificity of spirometry for detecting radiographic emphysema were 79% and 75%, respectively. Standardized airway wall thickness was increased in subjects with airflow obstruction, but did not correlate with emphysema severity. In this cohort of lifetime ever-smokers, PFTs alone were inadequate for diagnosing emphysema. Airway wall thickness quantified by CT morphometry was associated with airflow limitation, but not with emphysema indicating that the heterogeneous nature of lung disease in smokers may represent distinct phenotypes. PMID:21655122

  9. Kidney function tests

    MedlinePlus

    Kidney function tests are common lab tests used to evaluate how well the kidneys are working. Such tests include: ... Oh MS, Briefel G. Evaluation of renal function, water, electrolytes ... and Management by Laboratory Methods . 23rd ed. Philadelphia, ...

  10. Liver function tests

    MedlinePlus

    Liver function tests are common tests that are used to see how well the liver is working. Tests include: ... M, Bowne WB, Bluth MH. Evaluation of liver function. In: McPherson RA, Pincus MR, eds. Henry's Clinical ...

  11. Gravity-assisted pivot-shift test can predict the function of the reconstructed anterior cruciate ligament.

    PubMed

    Sakai, Hiroya; Hiraoka, Hisatada; Yashiki, Motohisa

    2011-04-01

    The gravity-assisted pivot-shift (GAPS) test is a newly advocated test for anterior cruciate ligament (ACL) injury. We retrospectively investigated the relationships between the result of preoperative GAPS test and the function of the reconstructed ACL using autogenous hamstring tendon grafts. Seventy-eight patients with unilateral ACL injury and a minimum of 1-year follow-up were enrolled in this study. According to the result of preoperative GAPS test, they were divided into two groups, i.e., positive test group (Group P) and negative test group (Group N). At the time of follow-up, the operated knee was examined manually and using KT-1000 arthrometer. According to these results, the function of the reconstructed ACL was classified. The proportion of the knees with a negative abnormal laxity test was less in Group P than Group N with the significant difference in Lachman test (P = 0.0029) and N-test (P = 0.0081). The proportion of the cases having greater than 3 mm of the side-to-side difference in anterior knee laxity using KT-1000 arthrometer was greater in Group P, in spite of no statistically significant difference. Regarding the classification of the function of the reconstructed ACL, Group P was worse than Group N (P = 0.0187), and all 4 knees classified as failed belonged to Group P. The knees with a preoperative positive GAPS test showed worse postoperative function of the reconstructed ACL than those with a negative test. Preoperative positive GAPS test is considered to be a predisposing factor to poor functional outcome after ACL reconstruction. It is possible that the use of hamstring tendons as a graft source should be avoided for the ACL-injured patients with a positive GAPS test.

  12. 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.

  13. Liver Function Tests

    MedlinePlus

    ... Your Liver > Liver Disease Information > Liver Function Tests Liver Function Tests Explore this section to learn more ... including a description and diagnosis. Why is the liver important? The liver is the second largest organ ...

  14. 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

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

    DOE PAGES

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

    2015-01-01

    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

  16. Computed Tomography or Functional Stress Testing for the Prediction of Risk: Can I Have My Cake and Eat It?

    PubMed

    Newby, David E

    2017-08-28

    The clinician now has an overwhelming array of investigations at their disposal for patients with suspected coronary heart disease. These tests are used to diagnose or to risk stratify patients, and thereby enable the clinician to treat their symptoms and to reduce their future risk. Ultimately, these investigations assess either risk factors (such as lipid, glucose and c-reactive protein concentrations) and proxies for disease (such as carotid intima-media thickness and coronary artery calcium score), or they are looking to provide circumstantial downstream evidence of disease (such as markers of ischemia and infarction: Q waves on an electrocardiogram, fibrosis on magnetic resonance imaging or functional stress testing). In this issue of Circulation, Budoff and colleagues compare two of the most widely used approaches, coronary artery calcium scoring and functional stress testing, within the framework of the PROspective Multicenter Imaging Study for Evaluation of chest pain (PROMISE) trial.

  17. Prediction of effective thermal conductivity of porous consolidated media as a function of temperature: a test example of limestones

    NASA Astrophysics Data System (ADS)

    Aurangzeb; Khan, Liaqat Ali; Maqsood, Asghari

    2007-08-01

    The thermal conductivity, thermal diffusivity and heat capacity per unit volume of sedimentary rocks (limestones) taken from Nammal Gorge sections, Western Salt Range, Pakistan, have been measured simultaneously using the transient plane source technique. The temperature dependence of thermal transport properties was studied in the temperature range 293 to 443 K. Different relations for the estimation of thermal conductivity are applied. A proposal for the prediction of thermal conductivity as a function of temperature is also given. It is observed that the values of effective thermal conductivity predicted by the proposed model are in agreement with the experimental thermal conductivity data within 8%. Furthermore, the errors in experimental calculations of thermal conductivity, thermal diffusivity and volumetric heat capacity are around 5%, 7% and 10%, respectively.

  18. Questionnaire, walking time and button test measures of functional capacity as predictive markers for mortality in rheumatoid arthritis.

    PubMed

    Pincus, T; Callahan, L F; Vaughn, W K

    1987-04-01

    Mortality over 9 years in rheumatoid arthritis was studied according to baseline demographic, disease, therapy and comorbidity variables, and measures of functional capacity variables. Significant differences between patients who survived and died over the next 9 years were seen for 8 variables: age, joint count, oral corticosteroid use, presence of concurrent heart disease, formal educational level, and 3 quantitative measures of functional capacity, questionnaire responses regarding activities of daily living, modified walking time and the button test. Five-year survivals of 50% or less were seen in patients with severely dysfunctional values for the 3 quantitative measures of functional capacity. Increased relative risk of mortality according to functional capacity measures was not explained by age, sex, duration of disease, smoking history, joint count, hand radiograph score, grip strength, morning stiffness, formal educational level, oral corticosteroid or parenteral gold use, or various comorbidities, and was not expected by a majority of physicians.

  19. Hypothesis testing and earthquake prediction.

    PubMed Central

    Jackson, D D

    1996-01-01

    Requirements for testing include advance specification of the conditional rate density (probability per unit time, area, and magnitude) or, alternatively, probabilities for specified intervals of time, space, and magnitude. Here I consider testing fully specified hypotheses, with no parameter adjustments or arbitrary decisions allowed during the test period. Because it may take decades to validate prediction methods, it is worthwhile to formulate testable hypotheses carefully in advance. Earthquake prediction generally implies that the probability will be temporarily higher than normal. Such a statement requires knowledge of "normal behavior"--that is, it requires a null hypothesis. Hypotheses can be tested in three ways: (i) by comparing the number of actual earth-quakes to the number predicted, (ii) by comparing the likelihood score of actual earthquakes to the predicted distribution, and (iii) by comparing the likelihood ratio to that of a null hypothesis. The first two tests are purely self-consistency tests, while the third is a direct comparison of two hypotheses. Predictions made without a statement of probability are very difficult to test, and any test must be based on the ratio of earthquakes in and out of the forecast regions. PMID:11607663

  20. Hypothesis testing and earthquake prediction.

    PubMed

    Jackson, D D

    1996-04-30

    Requirements for testing include advance specification of the conditional rate density (probability per unit time, area, and magnitude) or, alternatively, probabilities for specified intervals of time, space, and magnitude. Here I consider testing fully specified hypotheses, with no parameter adjustments or arbitrary decisions allowed during the test period. Because it may take decades to validate prediction methods, it is worthwhile to formulate testable hypotheses carefully in advance. Earthquake prediction generally implies that the probability will be temporarily higher than normal. Such a statement requires knowledge of "normal behavior"--that is, it requires a null hypothesis. Hypotheses can be tested in three ways: (i) by comparing the number of actual earth-quakes to the number predicted, (ii) by comparing the likelihood score of actual earthquakes to the predicted distribution, and (iii) by comparing the likelihood ratio to that of a null hypothesis. The first two tests are purely self-consistency tests, while the third is a direct comparison of two hypotheses. Predictions made without a statement of probability are very difficult to test, and any test must be based on the ratio of earthquakes in and out of the forecast regions.

  1. 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.; hide

    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.

  2. Evaluation of Timed Up and Go Test as a tool to measure postoperative function and prediction of one year walking ability for patients with hip fracture.

    PubMed

    Nygard, Heid; Matre, Kjell; Fevang, Jonas Meling

    2016-05-01

    To evaluate if the Timed Up and Go Test is a useful tool to measure postoperative function and to predict one-year results of rehabilitation in patients operated owing to hip fracture. Prospective cohort study. The department of orthopaedic surgery at five hospitals in Norway. Patients were assessed five days postoperatively and after one year. A total of 684 patients over 60 years with trochanteric or subtrochanteric hip fractures were included. A total of 171 (25%) patients died within a year and 373 (73% of patients still alive) attended follow-up one year after surgery. Timed Up and Go Test and walking ability. A total of 258 (38%) patients passed the postoperative Timed Up and Go Test. A total of 217 (56%) patients with a prefracture independent outdoor walking ability, passed the test. The average Timed Up and Go Test score was 71 seconds. A total of 171 (25%) patients could not rise from a chair without assistance; 8% of the patients with cognitive impairment, and 8% of those admitted from nursing homes, were able to pass the postoperative Timed Up and Go Test. The sensitivity and specificity of the Timed Up and Go Test in predicting walking ability one year after the operation were low. At one year follow-up, 38% of the patients not able to perform the postoperative Timed Up and Go Test, passed the test. A total of 81 (21%) patients did not use any walking-aid, 17 of them did not pass the postoperative Timed Up and Go Test. The Timed Up and Go Test performed the fifth postoperative day was not a suitable tool to assess functional mobility for the majority of the patients with hip fractures in our study. Neither was the postoperative Timed Up and Go Test a suitable tool to predict the walking ability one year after the operation. © The Author(s) 2015.

  3. Evaluation of Timed Up and Go Test as a tool to measure postoperative function and prediction of one year walking ability for patients with hip fracture

    PubMed Central

    Nygard, Heid; Matre, Kjell; Fevang, Jonas Meling

    2015-01-01

    Objective: To evaluate if the Timed Up and Go Test is a useful tool to measure postoperative function and to predict one-year results of rehabilitation in patients operated owing to hip fracture. Design: Prospective cohort study. Setting: The department of orthopaedic surgery at five hospitals in Norway. Patients were assessed five days postoperatively and after one year. Subjects: A total of 684 patients over 60 years with trochanteric or subtrochanteric hip fractures were included. A total of 171 (25%) patients died within a year and 373 (73% of patients still alive) attended follow-up one year after surgery. Main measures: Timed Up and Go Test and walking ability. Results: A total of 258 (38%) patients passed the postoperative Timed Up and Go Test. A total of 217 (56%) patients with a prefracture independent outdoor walking ability, passed the test. The average Timed Up and Go Test score was 71 seconds. A total of 171 (25%) patients could not rise from a chair without assistance; 8% of the patients with cognitive impairment, and 8% of those admitted from nursing homes, were able to pass the postoperative Timed Up and Go Test. The sensitivity and specificity of the Timed Up and Go Test in predicting walking ability one year after the operation were low. At one year follow-up, 38% of the patients not able to perform the postoperative Timed Up and Go Test, passed the test. A total of 81 (21%) patients did not use any walking-aid, 17 of them did not pass the postoperative Timed Up and Go Test. Conclusion: The Timed Up and Go Test performed the fifth postoperative day was not a suitable tool to assess functional mobility for the majority of the patients with hip fractures in our study. Neither was the postoperative Timed Up and Go Test a suitable tool to predict the walking ability one year after the operation. PMID:26109590

  4. Dexamethasone suppression test predicts later development of an impaired adrenal function after a 14-day course of prednisone in healthy volunteers.

    PubMed

    Neidert, Stefanie; Schuetz, Philipp; Mueller, Beat; Christ-Crain, Mirjam

    2010-05-01

    Suppression of the adrenal function after glucocorticoid treatment is common, potentially dangerous, and unpredictable. Identification of patients at risk is of clinical importance. We hypothesized that the dexamethasone suppression test predicts the development of corticosteroid-induced impaired adrenal function. We included 39 healthy male volunteers. After a 1-microg ACTH test, all participants underwent an overnight 0.5-mg dexamethasone suppression test. Participants then took prednisone, 0.5 mg/kg body weight, for 14-day. After the withdrawal of prednisone, a 1-microg ACTH test was performed and a clinical score was assessed on days 1, 3, 7, and 21. On days 1, 3, 7, and 21, 100, 50, 26.5 and 32.4% of the participants had a suppressed adrenal function. The risk of developing suppressed adrenal function decreased from 44 to 0% in patients with cortisol levels after the administration of dexamethasone in the lowest and highest quartiles respectively. Receiver operating curve (ROC) analysis performed to predict a suppressed adrenal function on day 7 after the withdrawal of prednisone showed an area under the curve (AUC) of 0.76 (95% confidence interval (CI) 0.58-0.89) for cortisol after the administration of dexamethasone, which was in the range of the AUC of 0.78 (95% CI 0.6-0.9) for pre-intervention cortisol after the administration of ACTH. Basal cortisol before intake of prednisone (AUC 0.62 (95% CI 0.44-0.78)) and the clinical score (AUC 0.64 (95% CI 0.45-0.79)) had significantly lower AUCs. Circulating cortisol levels after a dexamethasone suppression test and a pre-intervention-stimulated cortisol level are predictive of later development of a suppressed adrenal function after a 14-day course of prednisone, and are superior to a clinical score or basal cortisol levels. This may allow a more targeted concept for the need of stress prophylaxis after cessation of steroid therapy.

  5. Pancreatic exocrine function testing

    SciTech Connect

    Goff, J.S.

    1981-11-01

    It is important to understand which pancreatic function tests are available and how to interpret them when evaluating patients with malabsorption. Available direct tests are the secretin stimulation test, the Lundh test meal, and measurement of serum or fecal enzymes. Indirect tests assess pancreatic exocrine function by measuring the effect of pancreatic secretion on various nutrients. These include triglycerides labeled with carbon 14, cobalamin labeled with cobalt 57 and cobalt 58, and para-aminobenzoic acid bound to a dipeptide. Of all these tests the secretin stimulation test is the most accurate and reliable if done by experienced personnel. However, the indirect tests are simpler to do and appear to be comparable to the secretin test at detecting pancreatic exocrine insufficiency. These indirect tests are becoming clinically available and clinicians should familiarize themselves with the strengths and weaknesses of each.

  6. 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

  7. 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

  8. Pulmonary function tests

    MedlinePlus

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

  9. Left atrial mechanics strongly predict functional capacity assessed by cardiopulmonary exercise testing in subjects without structural heart disease.

    PubMed

    Leite, Luís; Mendes, Sofia Lázaro; Baptista, Rui; Teixeira, Rogério; Oliveira-Santos, Manuel; Ribeiro, Nelson; Coutinho, Rosa; Monteiro, Victor; Martins, Rui; Castro, Graça; Ferreira, Maria João; Pego, Mariano

    2017-05-01

    Left atrium function is essential for cardiovascular performance and is evaluable by two-dimensional speckle-tracking echocardiography (2D-STE). Our aim was to determine how echocardiographic parameters interrelate with exercise capacity and ventilatory efficiency in subjects with no structural heart disease. Asymptomatic volunteers, in sinus rhythm and with normal biventricular size and function, were recruited from a community-based population. Individuals with moderate-to-severe valvular disease, pulmonary hypertension, and history of cardiac disease were excluded. We performed a transthoracic echocardiogram and assessed left atrial (LA) and left ventricular (LV) mechanics via 2D-STE. Cardiopulmonary exercise testing by treadmill took place immediately thereafter. Peak oxygen uptake (VO2) served as measure of functional capacity and ventilation/carbon dioxide output (VE/VCO2) slope as surrogate of ventilation/perfusion mismatch. 20 subjects were included (age 51 ± 14 years, male gender 65%). Peak VO2 strongly correlated with age (r = -0.83; P < 0.01), with E/e' ratio (r = -0.72; P < 0.01), and with LA reservoir- and conduit-phase mechanics, particularly with LA conduit strain rate (SR) (r = -0.82; P < 0.01), but showed no correlation with LA volume index or LV mechanics. A similar pattern of associations was identified for VE/VCO2 slope. In multivariate analysis, LA conduit SR (β = -0.69; P = 0.02) emerged as sole independent correlate of peak VO2, adjusted for age and for E/e' ratio (adjusted r (2)  = 0.76; P < 0.01). Conduit and reservoir components of LA mechanics displayed strong associations with peak VO2 and VE/VCO2 slope. LA conduit-phase SR seems best suited as echocardiographic marker of functional capacity in subjects with no structural heart disease.

  10. Pulmonary function testing.

    PubMed

    Ruppel, Gregg L; Enright, Paul L

    2012-01-01

    Pulmonary function testing is often considered the basis for diagnosis in many categories of pulmonary disease. Although most of the testing methodologies are well established and widely employed, there are still many questions regarding how tests should be performed, how to ensure that reliable data are produced, what reference values and rules should be used, and how pulmonary function tests (PFTs) should be interpreted to best support clinical decision making. This conference was organized around a set of questions aimed at many of these issues. Each presenter was asked to address a specific topic regarding what tests should be done, how those test should be performed to answer a particular clinical question, and to relate test results to an accurate diagnosis and appropriate treatment of the patient. These topics included testing of adults and children, with concentration on important disease entities such as COPD, asthma, and unexplained dyspnea. Special emphasis was given to discussing reference values, lower limits of normal, interpretive strategies to optimize disease classification, and those factors directly affecting data quality. Established techniques for spirometry, lung volumes, diffusing capacity, exercise testing, and bronchial challenges were compared and contrasted with new technologies, and with technologies that might be part of pulmonary function laboratories in the near future.

  11. 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

  12. 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.

  13. Predictive testing for Huntington's disease.

    PubMed

    Tibben, Aad

    2007-04-30

    Worldwide, predictive testing for Huntington's disease has become an accepted clinical application that has allowed many individuals from HD-families to proceed with their life without the uncertainty of being at risk. International guidelines have extensively contributed to establishing counselling programmes of high quality, and have served as a model for other genetic disorders. Psychological follow-up studies have increased the insight into the far-reaching impact of test results for all individuals involved. Although the guidelines have served as a useful frame of reference, clinical experience has shown the importance of a case-by-case approach to do justice to the specific needs of the individual test candidate. Issues such as ambiguous test results, lack of awareness in a test candidate of early signs of the disease, non-compliance to the test protocol, or the test candidate's need for information on the relationship between age at onset and CAG-repeat require careful consideration. Receiving a test result is only one of the transition points in the life of an individual at risk; such result needs to be valued from a life-cycle perspective.

  14. Modern vestibular function testing.

    PubMed Central

    Baloh, R W; Furman, J M

    1989-01-01

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

  15. 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

    2013-12-06

    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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-04-01

    Functional Movement Screen (FMS) scores of ≤14 have been used to predict injury in athletic populations. Movement asymmetries and poor-quality movement patterns in other functional tests have been shown to predict musculoskeletal injury (MSI). Therefore, movement asymmetry or poor-quality movement patterns on the FMS may have more utility in predicting MSI than the composite score. To determine if an asymmetry or score of 1 on an individual FMS test would predict MSI in collegiate athletes. Cohort study. National Collegiate Athletic Association Division II university athletic program. A total of 84 Division II rowers, volleyball players, and soccer players (men: n = 20, age = 20.4 ± 1.3 years, height = 1.77 ± 0.04 m, mass = 73.5 ± 4.8 kg; women: n = 64, age = 19.1 ± 1.2 years, height = 1.69 ± 0.09 m, mass = 64.8 ± 9.4 kg). The FMS was administered during preseason preparticipation examinations. Injury-incidence data were tracked for an academic year by each team's certified athletic trainer via computer software. An MSI was defined as physical damage to the body secondary to athletic activity or an event for which the athlete sought medical care, and resulted in modified training or required protective splitting or taping. Composite FMS scores were categorized as low (≤14) or high (>14). Pearson χ(2) analyses were used to determine if MSI could be predicted by the composite FMS score or an asymmetry or score of 1 on an individual FMS test (P < .05). Athletes with FMS scores of ≤14 were not more likely to sustain an injury than those with higher scores (relative risk = 0.68, 95% confidence interval = 0.39, 1.19; P = .15). However, athletes with an asymmetry or individual score of 1 were 2.73 times more likely to sustain an injury than those without (relative risk = 2.73, 95% confidence interval = 1.36, 5.4; P = .001). Asymmetry or a low FMS individual test score was a better predictor of MSI than the composite FMS score.

  18. 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.

  19. 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…

  20. 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…

  1. Predicting Social Functioning in Schizotypy

    PubMed Central

    McCleery, Amanda; Divilbiss, Marielle; St-Hilaire, Annie; Aakre, Jennifer M.; Seghers, James P.; Bell, Emily K.; Docherty, Nancy M.

    2015-01-01

    Theory of mind (ToM) is an aspect of social cognition that refers to the ability to make inferences about the thoughts, feelings, and intentions of other people. It is believed to be related to social functioning. Previous investigations of ToM in schizotypy have yielded mixed results. Using a correlational approach, the present study explored the relationship between schizotypal traits, ToM, neurocognition, depressed mood, and social functioning in a sample of 50 undergraduate students. Schizotypy was related to poor social functioning. Contrary to predictions, schizotypal traits were not associated with impaired ToM. In fact, schizotypal traits were associated with enhanced performance on a ToM task that involved detection of ironic statements. However, strong relationships emerged among schizotypy, depressed mood, and social functioning, highlighting the need to also examine depression when assessing the relations between elevated schizotypy and poor social functioning. PMID:22297312

  2. Testing Noncollinear Spin-Flip, Collinear Spin-Flip, and Conventional Time-Dependent Density Functional Theory for Predicting Electronic Excitation Energies of Closed-Shell Atoms.

    PubMed

    Xu, Xuefei; Yang, Ke R; Truhlar, Donald G

    2014-05-13

    Conventional time-dependent density functional theory (TDDFT) is based on a closed-shell Kohn-Sham (KS) singlet ground state with the adiabatic approximation, using either linear response (KS-LR) or the Tamm-Dancoff approximation (KS-TDA); these methods can only directly predict singly excited states. This deficiency can be overcome by using a triplet state as the reference in the KS-TDA approximation and "exciting" the singlet by a spin flip (SF) from the triplet; this is the method suggested by Krylov and co-workers, and we abbreviate this procedure as SF-KS-TDA. SF-KS-TDA can be applied either with the original collinear kernel of Krylov and co-workers or with a noncollinear kernel, as suggested by Wang and Ziegler. The SF-KS-TDA method does bring some new practical difficulties into play, but it can at least formally model doubly excited states and states with double-excitation character, so it might be more useful than conventional TDDFT (both KS-LR and KS-TDA) for photochemistry if these additional difficulties can be surmounted and if it is accurate with existing approximate exchange-correlation functionals. In the present work, we carried out calculations specifically designed to understand better the accuracy and limitations of the conventional TDDFT and SF-KS-TDA methods; we did this by studying closed-shell atoms and closed-shell monatomic cations because they provide a simple but challenging testing ground for what we might expect in studying the photochemistry of molecules with closed-shell ground states. To test their accuracy, we applied conventional KS-LR and KS-TDA and 18 versions of SF-KS-TDA (nine collinear and nine noncollinear) to the same set of vertical excitation energies (including both Rydberg and valence excitations) of Be, B(+), Ne, Na(+), Mg, and Al(+). We did this for 10 exchange-correlation functionals of various types, both local and nonlocal. We found that the GVWN5 and M06 functionals with nonlocal kernels in spin-flip calculations

  3. 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.

  4. 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)

  5. 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)

  6. Functional association prediction by community profiling.

    PubMed

    Jiao, Dazhi; Han, Wontack; Ye, Yuzhen

    2017-04-26

    Recent years have witnessed unprecedented accumulation of DNA sequences and therefore protein sequences (predicted from DNA sequences), due to the advances of sequencing technology. One of the major sources of the hypothetical proteins is the metagenomics research. Current annotation of metagenomes (collections of short metagenomic sequences or assemblies) relies on similarity searches against known gene/protein families, based on which functional profiles of microbial communities can be built. This practice, however, leaves out the hypothetical proteins, which may outnumber the known proteins for many microbial communities. On the other hand, we may ask: what can we gain from the large number of metagenomes made available by the metagenomic studies, for the annotation of metagenomic sequences as well as functional annotation of hypothetical proteins in general? Here we propose a community profiling approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. We tested different profile construction methods, the selection of reference metagenomes, and correlation metrics, among others, to optimize the performance of this new approach. We demonstrated that the community profiling approach alone slightly outperforms the phylogenetic profiling approach for associating proteins in species that are well represented by sequenced genomes, and combining phylogenetic and community profiling further improves (though only marginally) the prediction of functional association. Further we showed that community profiling method significantly outperforms phylogenetic profiling, revealing more functional associations, when applied to a more recently sequenced bacterial genome

  7. 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…

  8. Pulmonary Function Tests

    MedlinePlus

    ... common PFT’s are spirometry (spy-RAH-me-tree), diffusion studies and body plethysmography (ple-thiz-MA-gra- ... blowing and let the staff know. What are diffusion studies? Diffusion tests find out how well the ...

  9. Apollo quality through predictive testing.

    NASA Technical Reports Server (NTRS)

    White, G. C., Jr.

    1972-01-01

    Discussion of testing performed during the Apollo program and its relationship to the engineering, qualification, manufacturing, maintenance, and training aspects of the program. Illustrative examples of Apollo experience are used to highlight the discussion.

  10. The Functions of Testing.

    ERIC Educational Resources Information Center

    Tumin, Melvin M.

    1981-01-01

    Admissions testing and its consequences are looked upon as a reflection of the current debate occurring in Western capitalist democracies concerning the optimization of freedom, fairness, and wealth. In dealing with the competition and conflict of values and interests, there can be no factual but political resolution. (Author/AL)

  11. Predictable Losers in Testing Schemes.

    ERIC Educational Resources Information Center

    Sacks, Peter

    2000-01-01

    For 2 decades, policymakers have pretended that bureaucratic, state-imposed standards, testing, and sanctions will fundamentally raise all schoolchildren's academic achievement and create productive citizens. The losers have been children of the poor, working class, and undereducated. Policymakers are holding schools and children accountable for…

  12. Defining predictive values using three different platelet function tests for CYP2C19 phenotype status on maintenance dual antiplatelet therapy after PCI.

    PubMed

    Zhang, Hong-Zhe; Kim, Moo Hyun; Han, Jin-Yeong; Jeong, Young-Hoon

    2014-01-01

    Published data suggests that the presence of CYP2C19*2 or *3 loss of function (LOF) alleles is indicative of increased platelet aggregation and a higher risk of adverse cardiovascular events after clopidogrel administration. We sought to determine cut-off values using three different assays for prediction of the CYP2C19 phenotype in Korean percutaneous coronary intervention (PCI) patients. We enrolled 244 patients with drug-eluting stent implantation who were receiving clopidogrel and aspirin maintenance therapy for one month or more. Platelet reactivity was assessed with light transmittance aggregometry (LTA), multiple electrode aggregometry (MEA) and the VerifyNow P2Y12 assay (VN). The CYP2C19 genotype was analyzed by polymerase chain reaction (PCR) and snapshot method. The frequency of CYP2C19 LOF allele carriers was 58.6%. The cut-off values from LTA, MEA and VerifyNow for the identification of LOF allele carriers were as follows: 10 µM ADP-induced LTA ≥ 48 %, VN>242 PRU and MEA ≥ 37 U. Between the three tests, correlation was higher between LTA vs. VN assays (r=0.69) and LTA vs. MEA (r=0.56), with moderate agreement (κ=0.46 and κ=0.46), but between VN assay and MEA, both devices using whole blood showed a lower correlation (r=0.42) and agreement (κ=0.3). Our results provide guidance regarding cut-off levels for LTA, VerifyNow and MEA assays to detect the CYP2C19 LOF allele in patients during dual antiplatelet maintenance therapy.

  13. The prediction of above-average participation in volunteerism: a test of the theory of planned behavior and the volunteers functions inventory in older Australian adults.

    PubMed

    Greenslade, Jaimi H; White, Katherine M

    2005-04-01

    In the present prospective study of 81 older volunteers from a nonprofit organization in Australia, the authors compared the predictive utility of I. Ajzen's (1988) theory of planned behavior with that of E. G. Clary and M. Snyder's (1991) functional approach to volunteering. The authors mailed questionnaires to 385 volunteers in two waves of data collection. The first wave measured theory-of-planned-behavior variables and functional-approach variables. The second wave measured self-reported volunteering behavior for the previous month. Regression analyses supported both the theory of planned behavior and the functional approach; the theory of planned behavior accounted for a significantly larger proportion of variance in above-average participation in self-reported volunteerism. The findings of the present study provided some support for both the theory of planned behavior and the functional approach as models of self-reported volunteerism.

  14. 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

  15. Graph pyramids for protein function prediction.

    PubMed

    Sandhan, Tushar; Yoo, Youngjun; Choi, Jin; Kim, Sun

    2015-01-01

    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. 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. 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.

  16. Parental education predicts corticostriatal functionality in adulthood.

    PubMed

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

    2011-04-01

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

  17. Parental Education Predicts Corticostriatal Functionality in Adulthood

    PubMed Central

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

    2011-01-01

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

  18. Vibration Test Prediction for a Telecom Satellite

    NASA Astrophysics Data System (ADS)

    Asmolovskiy, Nikolay; Ruess, Florian; Segelke, Harald; Obst, Andreas; Rubio, Alberto

    2014-06-01

    The paper presents the process of a sinusoidal vibration test prediction analysis for a typical telecom satellite. This analysis has been performed in order to simulate the spacecraft behaviour during satellite PFM vibration test. The purposes of the prediction are:- confirmation of the adequacy of the chosen instrumentation,- consideration of the specific spacecraft test configuration as opposed to available flight configuration predictions,- derivation of a notching plan that considers all structure and equipment unit qualification limits and allows early consultation with the launch service provider and test facility.Number of parameters which have to be monitored during the test prediction is high, therefore an automated process has been developed which allows individual and simultaneous consideration of all secondary notching criteria and subsequent calculation of the resulting notched input profile.The automation resulted in a significantly increased robustness and speed of the process, reducing overall project risk and cost.

  19. An iterative approach of protein function prediction

    PubMed Central

    2011-01-01

    Background Current approaches of predicting protein functions from a protein-protein interaction (PPI) dataset are based on an assumption that the available functions of the proteins (a.k.a. annotated proteins) will determine the functions of the proteins whose functions are unknown yet at the moment (a.k.a. un-annotated proteins). Therefore, the protein function prediction is a mono-directed and one-off procedure, i.e. from annotated proteins to un-annotated proteins. However, the interactions between proteins are mutual rather than static and mono-directed, although functions of some proteins are unknown for some reasons at present. That means when we use the similarity-based approach to predict functions of un-annotated proteins, the un-annotated proteins, once their functions are predicted, will affect the similarities between proteins, which in turn will affect the prediction results. In other words, the function prediction is a dynamic and mutual procedure. This dynamic feature of protein interactions, however, was not considered in the existing prediction algorithms. Results In this paper, we propose a new prediction approach that predicts protein functions iteratively. This iterative approach incorporates the dynamic and mutual features of PPI interactions, as well as the local and global semantic influence of protein functions, into the prediction. To guarantee predicting functions iteratively, we propose a new protein similarity from protein functions. We adapt new evaluation metrics to evaluate the prediction quality of our algorithm and other similar algorithms. Experiments on real PPI datasets were conducted to evaluate the effectiveness of the proposed approach in predicting unknown protein functions. Conclusions The iterative approach is more likely to reflect the real biological nature between proteins when predicting functions. A proper definition of protein similarity from protein functions is the key to predicting functions iteratively. The

  20. Differential Prediction Generalization in College Admissions Testing

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  1. Differential Prediction Generalization in College Admissions Testing

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  2. In vitro T cell function, delayed-type hypersensitivity skin testing, and CD4+ T cell subset phenotyping independently predict survival time in patients infected with human immunodeficiency virus.

    PubMed

    Dolan, M J; Clerici, M; Blatt, S P; Hendrix, C W; Melcher, G P; Boswell, R N; Freeman, T M; Ward, W; Hensley, R; Shearer, G M

    1995-07-01

    Human immunodeficiency virus type 1 (HIV-1)-infected patients (n = 335) in the US Air Force HIV Natural History Program were followed for 3 years (mean) after skin testing, immunophenotyping of CD4+ cell subsets, and measurement of in vitro interleukin-2 production after stimulation by phytohemagglutinin, alloantigens, tetanus toxoid, and influenza A virus. The T cell functional assay predicted survival time (P < .001) and time for progression to AIDS (P = .014). Skin testing for tetanus, mumps, and Candida antigen and the total number of positive tests (P < .001 for each) stratified patients for survival time. In a multivariable proportional hazards model, the T cell functional assay (P = .008), the absolute number of CD4+ T cells (P = .001), the percentage of CD4+ CD29+ cells (P = .06), and the number of reactive skin tests (P < .001) predicted survival time. Thus, cellular immune functional tests have significant predictive value for survival time in HIV-1-infected patients independent of CD4+ cell count.

  3. 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. ...

  4. Protein Function Prediction: Problems and Pitfalls.

    PubMed

    Pearson, William R

    2015-09-03

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

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

    PubMed

    Delahunt, Eamonn; Fitzpatrick, Helen; Blake, Catherine

    2017-01-01

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

  6. Functional tests for myocardial ischemia

    SciTech Connect

    Levinson, J.R.; Guiney, T.E.; Boucher, C.A. )

    1991-01-01

    Functional tests for myocardial ischemia are numerous. Most depend upon a combination of either exercise or pharmacologic intervention with analysis of the electrocardiogram, of regional perfusion with radionuclide imaging, or of regional wall motion with radionuclide imaging or echocardiography. While each test has unique features, especially at the research level, they are generally quite similar in clinical practice, so the clinician is advised to concentrate on one or two in which local expertise is high.22 references.

  7. 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

  8. Hierarchical ensemble methods for protein function prediction.

    PubMed

    Valentini, Giorgio

    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.

  9. Identification of suitable combinations of in vitro sperm-function test for the prediction of fertility in buffalo bull.

    PubMed

    Singh, Raushan K; Kumaresan, A; Chhillar, Shivani; Rajak, Shailendra K; Tripathi, Utkarsh K; Nayak, Samiksha; Datta, T K; Mohanty, T K; Malhotra, R

    2016-12-01

    The present study assessed sperm functional characteristics in the frozen-thawed semen of buffalo bulls and estimated their relationship with field fertility. Frozen semen samples from three different freezing operations each from nine Murrah buffalo bulls were used for the assessment of different sperm functions related to fertilizing potential. Bulls were classified into high (n = 2), medium (n = 5), and low (n = 2) fertile based on adjusted field fertility. The sperm functions estimated included membrane integrity using carboxyfluorescein diacetate-propidium iodide, acrosome reaction status using fluorescein isothiocyanate peanut agglutinine, status of apoptosis using Annexin-V, protamine deficiency using Chromomycin A3, membrane stability using Merocyanine 540 and lipid peroxidation status using 4, 4-difluoro-4-bora-3a, 4a-diaza-s-indacene. The relationship between the proportion of live acrosome-intact spermatozoa and fertility was positive and significant (r = 0.59; P = 0.001). The proportion of moribund spermatozoa showed a significantly negative correlation with fertility (r = -0.50; P = 0.008). Similarly, the relationship of spermatozoa with unstable membrane (r = -0.51; P = 0.007), necrotic (r = - 0.42; P = 0.028), early necrotic (r = -0.42; P = 0.031), and apoptotic spermatozoa (r = -0.39; P = 0.046) with bull fertility was negative and significant. The correlation between the protamine-deficient spermatozoa and fertility was negative, but not significant. Among different combinations of tests, live acrosome-intact spermatozoa and lipid peroxidation status of spermatozoa revealed high positive correlation with buffalo bull fertility (adjusted R(2) = 0.73, C[p] = 0.80). These preliminary findings may help in developing tools for assessing fertility of buffalo bulls, once validated in more animals. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. 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.

  11. Predicting network functions with nested patterns

    NASA Astrophysics Data System (ADS)

    Ganter, Mathias; Kaltenbach, Hans-Michael; Stelling, Jörg

    2014-01-01

    Identifying suitable patterns in complex biological interaction networks helps understanding network functions and allows for predictions at the pattern level: by recognizing a known pattern, one can assign its previously established function. However, current approaches fail for previously unseen patterns, when patterns overlap and when they are embedded into a new network context. Here we show how to conceptually extend pattern-based approaches. We define metabolite patterns in metabolic networks that formalize co-occurrences of metabolites. Our probabilistic framework decodes the implicit information in the networks’ metabolite patterns to predict metabolic functions. We demonstrate the predictive power by identifying ‘indicator patterns’, for instance, for enzyme classification, by predicting directions of novel reactions and of known reactions in new network contexts, and by ranking candidate network extensions for gap filling. Beyond their use in improving genome annotations and metabolic network models, we expect that the concepts transfer to other network types.

  12. 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%.

  13. Optimal test selection for prediction uncertainty reduction

    DOE PAGES

    Mullins, Joshua; Mahadevan, Sankaran; Urbina, Angel

    2016-12-02

    Economic factors and experimental limitations often lead to sparse and/or imprecise data used for the calibration and validation of computational models. This paper addresses resource allocation for calibration and validation experiments, in order to maximize their effectiveness within given resource constraints. When observation data are used for model calibration, the quality of the inferred parameter descriptions is directly affected by the quality and quantity of the data. This paper characterizes parameter uncertainty within a probabilistic framework, which enables the uncertainty to be systematically reduced with additional data. The validation assessment is also uncertain in the presence of sparse and imprecisemore » data; therefore, this paper proposes an approach for quantifying the resulting validation uncertainty. Since calibration and validation uncertainty affect the prediction of interest, the proposed framework explores the decision of cost versus importance of data in terms of the impact on the prediction uncertainty. Often, calibration and validation tests may be performed for different input scenarios, and this paper shows how the calibration and validation results from different conditions may be integrated into the prediction. Then, a constrained discrete optimization formulation that selects the number of tests of each type (calibration or validation at given input conditions) is proposed. Furthermore, the proposed test selection methodology is demonstrated on a microelectromechanical system (MEMS) example.« less

  14. Optimal test selection for prediction uncertainty reduction

    SciTech Connect

    Mullins, Joshua; Mahadevan, Sankaran; Urbina, Angel

    2016-12-02

    Economic factors and experimental limitations often lead to sparse and/or imprecise data used for the calibration and validation of computational models. This paper addresses resource allocation for calibration and validation experiments, in order to maximize their effectiveness within given resource constraints. When observation data are used for model calibration, the quality of the inferred parameter descriptions is directly affected by the quality and quantity of the data. This paper characterizes parameter uncertainty within a probabilistic framework, which enables the uncertainty to be systematically reduced with additional data. The validation assessment is also uncertain in the presence of sparse and imprecise data; therefore, this paper proposes an approach for quantifying the resulting validation uncertainty. Since calibration and validation uncertainty affect the prediction of interest, the proposed framework explores the decision of cost versus importance of data in terms of the impact on the prediction uncertainty. Often, calibration and validation tests may be performed for different input scenarios, and this paper shows how the calibration and validation results from different conditions may be integrated into the prediction. Then, a constrained discrete optimization formulation that selects the number of tests of each type (calibration or validation at given input conditions) is proposed. Furthermore, the proposed test selection methodology is demonstrated on a microelectromechanical system (MEMS) example.

  15. Genetic Ancestry in Lung-Function Predictions

    PubMed Central

    Kumar, Rajesh; Seibold, Max A.; Aldrich, Melinda C.; Williams, L. Keoki; Reiner, Alex P.; Colangelo, Laura; Galanter, Joshua; Gignoux, Christopher; Hu, Donglei; Sen, Saunak; Choudhry, Shweta; Peterson, Edward L.; Rodriguez-Santana, Jose; Rodriguez-Cintron, William; Nalls, Michael A.; Leak, Tennille S.; O’Meara, Ellen; Meibohm, Bernd; Kritchevsky, Stephen B.; Li, Rongling; Harris, Tamara B.; Nickerson, Deborah A.; Fornage, Myriam; Enright, Paul; Ziv, Elad; Smith, Lewis J.; Liu, Kiang; Burchard, Esteban González

    2010-01-01

    BACKGROUND Self-identified race or ethnic group is used to determine normal reference standards in the prediction of pulmonary function. We conducted a study to determine whether the genetically determined percentage of African ancestry is associated with lung function and whether its use could improve predictions of lung function among persons who identified themselves as African American. METHODS We assessed the ancestry of 777 participants self-identified as African American in the Coronary Artery Risk Development in Young Adults (CARDIA) study and evaluated the relation between pulmonary function and ancestry by means of linear regression. We performed similar analyses of data for two independent cohorts of subjects identifying themselves as African American: 813 participants in the Health, Aging, and Body Composition (HABC) study and 579 participants in the Cardiovascular Health Study (CHS). We compared the fit of two types of models to lung-function measurements: models based on the covariates used in standard prediction equations and models incorporating ancestry. We also evaluated the effect of the ancestry-based models on the classification of disease severity in two asthma-study populations. RESULTS African ancestry was inversely related to forced expiratory volume in 1 second (FEV1) and forced vital capacity in the CARDIA cohort. These relations were also seen in the HABC and CHS cohorts. In predicting lung function, the ancestry-based model fit the data better than standard models. Ancestry-based models resulted in the reclassification of asthma severity (based on the percentage of the predicted FEV1) in 4 to 5% of participants. CONCLUSIONS Current predictive equations, which rely on self-identified race alone, may misestimate lung function among subjects who identify themselves as African American. Incorporating ancestry into normative equations may improve lung-function estimates and more accurately categorize disease severity. (Funded by the National

  16. Predictive and diagnostic genetic testing in psychiatry.

    PubMed

    Mitchell, Philip B; Meiser, Bettina; Wilde, Alex; Fullerton, Janice; Donald, Jennifer; Wilhelm, Kay; Schofield, Peter R

    2010-12-01

    The recent advent of commercially available genetic tests for the diagnosis of several mental illnesses has led to intense controversy amongst the psychiatric research community. In this article the authors review these developments, and contrast these with the growing evidence from genomewide association studies that highly heritable psychiatric conditions such as schizophrenia are due to the contributions and interaction of multiple allelic variants, each of small effect size. There is also evidence for the contribution of some highly penetrant rare de novo copy number variants, though the lack of disease specificity for these is of concern. This article outlines the prerequisites for predictive and diagnostic genetic tests, such as clinical validity and utility, and reviews the opportunity that genetic tests for mental illnesses present. As the scientific discourse on genetic tests for complex disorders is not limited to psychiatry, the authors outline current thoughts on the significance of genome-wide association studies across health, and the phenomenon of direct-to-consumer tests in medicine. The attitudes and understanding of patients, families, and clinicians about the future (currently hypothetical) scenario of psychiatric genetic tests are discussed, as is the potential for such testing to increase, rather than diminish stigma. Finally, recommendations on the future development and availability of genetic tests in psychiatry are provided. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. 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.

  18. 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).

  19. Clinical course and predictive value of liver function tests in patients hospitalized for worsening heart failure with reduced ejection fraction: an analysis of the EVEREST trial.

    PubMed

    Ambrosy, Andrew P; Vaduganathan, Muthiah; Huffman, Mark D; Khan, Sadiya; Kwasny, Mary J; Fought, Angela J; Maggioni, Aldo P; Swedberg, Karl; Konstam, Marvin A; Zannad, Faiez; Gheorghiade, Mihai

    2012-03-01

    Abnormal liver function tests (LFTs) are common in ambulatory heart failure (HF). The aim of this study was to characterize abnormal LFTs during index hospitalization. A post-hoc analysis was carried out of the placebo group of the EVEREST (Efficacy of Vasopressin Antagonism in Heart Failure Outcome Study with Tolvaptan) trial, which enrolled patients hospitalized for HF with an ejection fraction (EF) ≤40% and no history of primary significant liver disease or acute hepatic failure. LFTs (abbreviation, cut-offs for abnormal values) including serum albumin (ALB, <3.3 g/dL), aspartate transaminase (AST, >34 IU/L), alanine transaminase (ALT, >34 IU/L), alkaline phosphatase (AP, >123 IU/L),γ-glutamyl transferase (GGT, >50 IU/L), and total bilirubin (T Bili, >1.2 mg/dL) were measured at baseline, discharge/day 7, and post-discharge. Co-primary endpoints were all-cause mortality (ACM) and cardiovascular mortality or first HF hospitalization (CVM + HFH). Study participants had a mean age of 65.6 ±12.0 years, were mostly male, reported high prevalences of medical co-morbidities, and were well treated with evidence-based therapies. Baseline LFT abnormalities were common (ALB 17%, AST 21%, ALT 21%, AP 23%, GGT 62%, and T Bili 26%). Abnormal T Bili was the only marker to decrease substantially from baseline (26%) to discharge/day 7 (19%). All LFTs, except AP, improved post-discharge. Lower baseline ALB and elevated T Bili were associated with higher rates of ACM, and in-hospital decreases in ALB and increases in T Bili were associated with higher rates of both ACM and CVM + HFH. LFT abnormalities are common during hospitalization for HF in patients with reduced EF and were persistent at discharge. Baseline and in-hospital changes in ALB and T Bili provide additional prognostic value.

  20. 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.

  1. Binocular low-contrast letter acuity and the symbol digit modalities test improve the ability of the Multiple Sclerosis Functional Composite to predict disease in pediatric multiple sclerosis.

    PubMed

    Waldman, Amy T; Chahin, Salim; Lavery, Amy M; Liu, Geraldine; Banwell, Brenda L; Liu, Grant T; Balcer, Laura J

    2016-11-01

    Outcome measures to capture disability, such as the Multiple Sclerosis Functional Composite (MSFC), were developed to enhance outcome measurements for clinical trials in adults with multiple sclerosis (MS). The MSFC initially included three components: a timed 25-foot walk [T25FW], 9-hole peg test [9HPT], and the Paced Auditory Serial Addition Task [PASAT]. Modifications to the original MSFC, such as adding binocular low-contrast letter acuity (LCLA) or substituting the symbol digit modalities test (SDMT) for the PASAT, improved the capacity to capture neurologic impairment in adults. Similar outcome scales for pediatric MS have not yet been established. To determine whether the three-component MSFC or a modified MSFC with LCLA and the SDMT better identifies neurological deficits in pediatric MS. We evaluated 5 measures (T25FW, 9HPT, Children's PASAT [ChiPASAT], SDMT, and binocular LCLA [Sloan charts, 1.25% contrast]) in children with MS (disease onset <18 years) and healthy controls. To be able to compare measures whose scores have different scales, Z-scores were also created for each test based on the numbers of standard deviations from a control group mean, and these individual scale scores were combined to create composite scores. Logistic regression models, accounting for age, were used to determine whether the standard 3-component MSFC or modified versions (including 4 or 5 metrics) best distinguished children with MS from controls. Twenty pediatric-onset MS subjects, aged 6-21 years, and thirteen healthy controls, aged 6-19 years, were enrolled. MS subjects demonstrated worse scores on the 9HPT (p=0.004) and SDMT (p=0.001), but not the 25FTW (adjusted for height, p=0.63) or the ChiPASAT (p=0.10): all comparisons adjusted for age. Decreased (worse) binocular LCLA scores were associated with MS (vs. control status, p=0.03, logistic regression; p=0.08, accounting for age). The MSFC composite score for the traditional 3 components did not differ between the

  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. Executive function processes predict mobility outcomes in older adults.

    PubMed

    Gothe, Neha P; Fanning, Jason; Awick, Elizabeth; Chung, David; Wójcicki, Thomas R; Olson, Erin A; Mullen, Sean P; Voss, Michelle; Erickson, Kirk I; Kramer, Arthur F; McAuley, Edward

    2014-02-01

    To examine the relationship between performance on executive function measures and subsequent mobility outcomes in community-dwelling older adults. Randomized controlled clinical trial. Champaign-Urbana, Illinois. Community-dwelling older adults (N = 179; mean age 66.4). A 12-month exercise trial with two arms: an aerobic exercise group and a stretching and strengthening group. Established cognitive tests of executive function (flanker task, task switching, and a dual-task paradigm) and the Wisconsin card sort test. Mobility was assessed using the timed 8-foot up and go test and times to climb up and down a flight of stairs. Participants completed the cognitive tests at baseline and the mobility measures at baseline and after 12 months of the intervention. Multiple regression analyses were conducted to determine whether baseline executive function predicted postintervention functional performance after controlling for age, sex, education, cardiorespiratory fitness, and baseline mobility levels. Selective baseline executive function measurements, particularly performance on the flanker task (β = 0.15-0.17) and the Wisconsin card sort test (β = 0.11-0.16) consistently predicted mobility outcomes at 12 months. The estimates were in the expected direction, such that better baseline performance on the executive function measures predicted better performance on the timed mobility tests independent of intervention. Executive functions of inhibitory control, mental set shifting, and attentional flexibility were predictive of functional mobility. Given the literature associating mobility limitations with disability, morbidity, and mortality, these results are important for understanding the antecedents to poor mobility function that well-designed interventions to improve cognitive performance can attenuate. © 2014, Copyright the Authors Journal compilation © 2014, The American Geriatrics Society.

  4. Gene function prediction using labeled and unlabeled data

    PubMed Central

    Zhao, Xing-Ming; Wang, Yong; Chen, Luonan; Aihara, Kazuyuki

    2008-01-01

    Background In general, gene function prediction can be formalized as a classification problem based on machine learning technique. Usually, both labeled positive and negative samples are needed to train the classifier. For the problem of gene function prediction, however, the available information is only about positive samples. In other words, we know which genes have the function of interested, while it is generally unclear which genes do not have the function, i.e. the negative samples. If all the genes outside of the target functional family are seen as negative samples, the imbalanced problem will arise because there are only a relatively small number of genes annotated in each family. Furthermore, the classifier may be degraded by the false negatives in the heuristically generated negative samples. Results In this paper, we present a new technique, namely Annotating Genes with Positive Samples (AGPS), for defining negative samples in gene function prediction. With the defined negative samples, it is straightforward to predict the functions of unknown genes. In addition, the AGPS algorithm is able to integrate various kinds of data sources to predict gene functions in a reliable and accurate manner. With the one-class and two-class Support Vector Machines as the core learning algorithm, the AGPS algorithm shows good performances for function prediction on yeast genes. Conclusion We proposed a new method for defining negative samples in gene function prediction. Experimental results on yeast genes show that AGPS yields good performances on both training and test sets. In addition, the overlapping between prediction results and GO annotations on unknown genes also demonstrates the effectiveness of the proposed method. PMID:18221567

  5. Improved network community structure improves function prediction

    PubMed Central

    Lee, Juyong; Gross, Steven P.; Lee, Jooyoung

    2013-01-01

    We are overwhelmed by experimental data, and need better ways to understand large interaction datasets. While clustering related nodes in such networks—known as community detection—appears a promising approach, detecting such communities is computationally difficult. Further, how to best use such community information has not been determined. Here, within the context of protein function prediction, we address both issues. First, we apply a novel method that generates improved modularity solutions than the current state of the art. Second, we develop a better method to use this community information to predict proteins' functions. We discuss when and why this community information is important. Our results should be useful for two distinct scientific communities: first, those using various cost functions to detect community structure, where our new optimization approach will improve solutions, and second, those working to extract novel functional information about individual nodes from large interaction datasets. PMID:23852097

  6. Blind tests of RNA nearest-neighbor energy prediction

    PubMed Central

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

    2016-01-01

    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

  7. Prediction of Chemical Function: Model Development and ...

    EPA Pesticide Factsheets

    The United States Environmental Protection Agency’s Exposure Forecaster (ExpoCast) project is developing both statistical and mechanism-based computational models for predicting exposures to thousands of chemicals, including those in consumer products. The high-throughput (HT) screening-level exposures developed under ExpoCast can be combined with HT screening (HTS) bioactivity data for the risk-based prioritization of chemicals for further evaluation. The functional role (e.g. solvent, plasticizer, fragrance) that a chemical performs can drive both the types of products in which it is found and the concentration in which it is present and therefore impacting exposure potential. However, critical chemical use information (including functional role) is lacking for the majority of commercial chemicals for which exposure estimates are needed. A suite of machine-learning based models for classifying chemicals in terms of their likely functional roles in products based on structure were developed. This effort required collection, curation, and harmonization of publically-available data sources of chemical functional use information from government and industry bodies. Physicochemical and structure descriptor data were generated for chemicals with function data. Machine-learning classifier models for function were then built in a cross-validated manner from the descriptor/function data using the method of random forests. The models were applied to: 1) predict chemi

  8. Prediction of Chemical Function: Model Development and ...

    EPA Pesticide Factsheets

    The United States Environmental Protection Agency’s Exposure Forecaster (ExpoCast) project is developing both statistical and mechanism-based computational models for predicting exposures to thousands of chemicals, including those in consumer products. The high-throughput (HT) screening-level exposures developed under ExpoCast can be combined with HT screening (HTS) bioactivity data for the risk-based prioritization of chemicals for further evaluation. The functional role (e.g. solvent, plasticizer, fragrance) that a chemical performs can drive both the types of products in which it is found and the concentration in which it is present and therefore impacting exposure potential. However, critical chemical use information (including functional role) is lacking for the majority of commercial chemicals for which exposure estimates are needed. A suite of machine-learning based models for classifying chemicals in terms of their likely functional roles in products based on structure were developed. This effort required collection, curation, and harmonization of publically-available data sources of chemical functional use information from government and industry bodies. Physicochemical and structure descriptor data were generated for chemicals with function data. Machine-learning classifier models for function were then built in a cross-validated manner from the descriptor/function data using the method of random forests. The models were applied to: 1) predict chemi

  9. 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?

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

    PubMed

    Whitmal, Nathaniel A; DeRoy, Kristina

    2011-12-01

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

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

    PubMed Central

    Whitmal, Nathaniel A.; DeRoy, Kristina

    2011-01-01

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

  12. 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.

  13. Prediction of First Grade Social-Emotional and Intellectual Functioning.

    ERIC Educational Resources Information Center

    Kohn, Martin; And Others

    In order to determine the longitudinal persistence of two major personality dimensions, namely Apathy-Withdrawal versus Interest-Participation (Factor 1) and Anger-Defiance versus Conformity-Compliance (Factor 2), and to test the hypothesis that the social-emotional functioning of the preschool child is predictive of later intellectual-academic…

  14. 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.…

  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. 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.

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

    PubMed

    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.

  20. Benchmark notch test for life prediction

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

    Aircraft gas turbine engine components are subjected to severe stress, temperature, and environmental conditions. Economic and reliabilty demands have prompted inordinate effort in development of analytic methods to predict stresses and strains in aircraft engines. There remains, however, the need to check or verify these analytical methodologies against actual experimental data measurements. The laser interferometric strain displacement gage was recognized as having the potential to accomplish this task and was employed in this program. The actual strains incurred at the root of a discontinuity in cyclically loaded test samples subjected to inelastic deformation at high temperature where creep deformation readily occur were measured. The steady-state, cyclic stress-strain response at the root of the discontinuity in the tested samples was analyzed for comparison with the measured results. A comprehensive set of local notch root strain measurements for a variety of load patterns in an Inconel 718 notch specimen at 649 C (1200 F) was obtained and documented using the laser interferometric strain displacement gage.

  1. 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.

  2. Genetic predictive testing and private insurances.

    PubMed

    Abbing, H D

    1991-08-01

    Genetic information is a potential tool for selection of job applicants and of candidates for insurance. Social implications of genetic information may represent a threshold for the access to health care facilities. Some of the issues related to the use of predictive genetic information by private life and health insurance companies are discussed. They include the potential threat for the privacy of the individual and his relatives, the pressure to undergo genetic testing and the social consequences of the use of genetic information by private insurance companies. The justified financial interests of insurance companies and the interests of the individual to have his privacy protected and to be able to partake in social attainments have to be brought into balance. A ban on genetic testing in connection with access to insurances and a limitation to the use of existing genetic information have been suggested by the Dutch Health Council. This approach to the problem should be adopted throughout the European Communities, so that medical progress does not turn out to be against the interests of the consumer.

  3. Effort test failure: toward a predictive model.

    PubMed

    Webb, James W; Batchelor, Jennifer; Meares, Susanne; Taylor, Alan; Marsh, Nigel V

    2012-01-01

    Predictors of effort test failure were examined in an archival sample of 555 traumatically brain-injured (TBI) adults. Logistic regression models were used to examine whether compensation-seeking, injury-related, psychological, demographic, and cultural factors predicted effort test failure (ETF). ETF was significantly associated with compensation-seeking (OR = 3.51, 95% CI [1.25, 9.79]), low education (OR:. 83 [.74, . 94]), self-reported mood disorder (OR: 5.53 [3.10, 9.85]), exaggerated displays of behavior (OR: 5.84 [2.15, 15.84]), psychotic illness (OR: 12.86 [3.21, 51.44]), being foreign-born (OR: 5.10 [2.35, 11.06]), having sustained a workplace accident (OR: 4.60 [2.40, 8.81]), and mild traumatic brain injury severity compared with very severe traumatic brain injury severity (OR: 0.37 [0.13, 0.995]). ETF was associated with a broader range of statistical predictors than has previously been identified and the relative importance of psychological and behavioral predictors of ETF was evident in the logistic regression model. Variables that might potentially extend the model of ETF are identified for future research efforts.

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

    SciTech Connect

    Li, Shaohong L.; Truhlar, Donald G.

    2014-09-14

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

  5. Mining phenotypes for gene function prediction

    PubMed Central

    Groth, Philip; Weiss, Bertram; Pohlenz, Hans-Dieter; Leser, Ulf

    2008-01-01

    Background Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In the past years, many technologies to systematically generate phenotypes in a high-throughput manner, such as RNA interference or gene knock-out, have been developed and used to decipher functions for genes. However, there have been relatively few efforts to make use of phenotype data beyond the single genotype-phenotype relationships. Results We present results on a study where we use a large set of phenotype data – in textual form – to predict gene annotation. To this end, we use text clustering to group genes based on their phenotype descriptions. We show that these clusters correlate well with several indicators for biological coherence in gene groups, such as functional annotations from the Gene Ontology (GO) and protein-protein interactions. We exploit these clusters for predicting gene function by carrying over annotations from well-annotated genes to other, less-characterized genes in the same cluster. For a subset of groups selected by applying objective criteria, we can predict GO-term annotations from the biological process sub-ontology with up to 72.6% precision and 16.7% recall, as evaluated by cross-validation. We manually verified some of these clusters and found them to exhibit high biological coherence, e.g. a group containing all available antennal Drosophila odorant receptors despite inconsistent GO-annotations. Conclusion The intrinsic nature of phenotypes to visibly reflect genetic activity underlines their usefulness in inferring new gene functions. Thus, systematically analyzing these data on a large scale offers many possibilities for inferring functional annotation of genes. We show that text clustering can play an important role in this process. PMID:18315868

  6. Characterization and Prediction of Chemical Functions and ...

    EPA Pesticide Factsheets

    Assessing exposures from the thousands of chemicals in commerce requires quantitative information on the chemical constituents of consumer products. Unfortunately, gaps in available composition data prevent assessment of exposure to chemicals in many products. Here we propose filling these gaps via consideration of chemical functional role. We obtained function information for thousands of chemicals from public sources and used a clustering algorithm to assign chemicals into 35 harmonized function categories (e.g., plasticizers, antimicrobials, solvents). We combined these functions with weight fraction data for 4115 personal care products (PCPs) to characterize the composition of 66 different product categories (e.g., shampoos). We analyzed the combined weight fraction/function dataset using machine learning techniques to develop quantitative structure property relationship (QSPR) classifier models for 22 functions and for weight fraction, based on chemical-specific descriptors (including chemical properties). We applied these classifier models to a library of 10196 data-poor chemicals. Our predictions of chemical function and composition will inform exposure-based screening of chemicals in PCPs for combination with hazard data in risk-based evaluation frameworks. As new information becomes available, this approach can be applied to other classes of products and the chemicals they contain in order to provide essential consumer product data for use in exposure-b

  7. Predicting individual brain functional connectivity using a Bayesian hierarchical model.

    PubMed

    Dai, Tian; Guo, Ying

    2017-02-15

    Network-oriented analysis of functional magnetic resonance imaging (fMRI), especially resting-state fMRI, has revealed important association between abnormal connectivity and brain disorders such as schizophrenia, major depression and Alzheimer's disease. Imaging-based brain connectivity measures have become a useful tool for investigating the pathophysiology, progression and treatment response of psychiatric disorders and neurodegenerative diseases. Recent studies have started to explore the possibility of using functional neuroimaging to help predict disease progression and guide treatment selection for individual patients. These studies provide the impetus to develop statistical methodology that would help provide predictive information on disease progression-related or treatment-related changes in neural connectivity. To this end, we propose a prediction method based on Bayesian hierarchical model that uses individual's baseline fMRI scans, coupled with relevant subject characteristics, to predict the individual's future functional connectivity. A key advantage of the proposed method is that it can improve the accuracy of individualized prediction of connectivity by combining information from both group-level connectivity patterns that are common to subjects with similar characteristics as well as individual-level connectivity features that are particular to the specific subject. Furthermore, our method also offers statistical inference tools such as predictive intervals that help quantify the uncertainty or variability of the predicted outcomes. The proposed prediction method could be a useful approach to predict the changes in individual patient's brain connectivity with the progression of a disease. It can also be used to predict a patient's post-treatment brain connectivity after a specified treatment regimen. Another utility of the proposed method is that it can be applied to test-retest imaging data to develop a more reliable estimator for individual

  8. Data modeling for predictive behavior hypothesis formation and testing

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.; Barnett, Marvin H.; Esslinger, Richard; Grover, David A.; Faucheux, Jeffrey P.; Lamkin, Kenneth

    2006-04-01

    This paper presents a novel hypothesis analysis tool building on QUEST and DANCER. Unique is the ability to convert cause/effect relationships into analytical equation transfer functions for exploitation. In this the third phase of our work, we derive Data Models for each unique word and its ontological associated unique words. We form a classical control theory transfer function using the associated words as the input vector and the assigned unique word as the output vector. Each transfer function model can be tested against new evidence to yield new output. Additionally, conjectured output can be passed through the inverse model to predict the requisite case observations required to yield the conjectured output. Hypotheses are tested using circumstantial evidence, notional similarity, evidential strength, and plausibility to determine if they are supported or rejected. Examples of solving for evidence links are provided from tool execution.

  9. Blind Test of Physics-Based Prediction of Protein Structures

    PubMed Central

    Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.

    2009-01-01

    We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130

  10. Blind test of physics-based prediction of protein structures.

    PubMed

    Shell, M Scott; Ozkan, S Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A

    2009-02-01

    We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences.

  11. Classical Testing in Functional Linear Models

    PubMed Central

    Kong, Dehan; Staicu, Ana-Maria; Maity, Arnab

    2016-01-01

    We extend four tests common in classical regression - Wald, score, likelihood ratio and F tests - to functional linear regression, for testing the null hypothesis, that there is no association between a scalar response and a functional covariate. Using functional principal component analysis, we re-express the functional linear model as a standard linear model, where the effect of the functional covariate can be approximated by a finite linear combination of the functional principal component scores. In this setting, we consider application of the four traditional tests. The proposed testing procedures are investigated theoretically for densely observed functional covariates when the number of principal components diverges. Using the theoretical distribution of the tests under the alternative hypothesis, we develop a procedure for sample size calculation in the context of functional linear regression. The four tests are further compared numerically for both densely and sparsely observed noisy functional data in simulation experiments and using two real data applications. PMID:28955155

  12. Biochemical testing of thyroid function.

    PubMed

    Klee, G G; Hay, I D

    1997-12-01

    Various published guidelines recommending serum thyrotropin (TSH)-first thyroid testing are outlined. The entities called "subclinical hypothyroidism" and "subclinical hyperthyroidism" are defined on the basis of abnormal TSH concentrations and normal values of other biochemical thyroid tests. The controversies about follow-up and treatment of these disorders are discussed. The laboratory experience of Mayo Clinic Rochester in using TSH-first thyroid testing and the subsequent implementation of a thyroid test ordering cascade are presented. Finally, recommendations are given for further optimizing laboratory testing for thyroid disorders.

  13. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.

    PubMed

    Kankainen, Matti; Ojala, Teija; Holm, Liisa

    2012-02-15

    Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacterial genomics because it is one of the few methods that is practical for large datasets and because it does not require additional functional genomics experiments. However, the existing solutions produce erroneous predictions in many cases, especially when query sequences have low levels of identity with the annotated source protein. This problem has created a pressing need for improvements in homology-based annotation. We present an automated method for the functional annotation of bacterial protein sequences. Based on sequence similarity searches, BLANNOTATOR accurately annotates query sequences with one-line summary descriptions of protein function. It groups sequences identified by BLAST into subsets according to their annotation and bases its prediction on a set of sequences with consistent functional information. We show the results of BLANNOTATOR's performance in sets of bacterial proteins with known functions. We simulated the annotation process for 3090 SWISS-PROT proteins using a database in its state preceding the functional characterisation of the query protein. For this dataset, our method outperformed the five others that we tested, and the improved performance was maintained even in the absence of highly related sequence hits. We further demonstrate the value of our tool by analysing the putative proteome of Lactobacillus crispatus strain ST1. BLANNOTATOR is an accurate method for bacterial protein function prediction. It is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs of bacterial genome and metagenome researchers. The method and a web-server are available at http://ekhidna.biocenter.helsinki.fi/poxo/blannotator/.

  14. 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

  15. 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.

  16. 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 ...

  17. 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 ...

  18. 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 ...

  19. 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 ...

  20. What Are Lung Function Tests?

    MedlinePlus

    ... COPD How the Lungs Work Idiopathic Pulmonary Fibrosis Sarcoidosis Send a link to NHLBI to someone by ... the Lungs Work Idiopathic Pulmonary Fibrosis Oxygen Therapy Sarcoidosis Stress Testing Rate This Content: Updated: December 9, ...

  1. Predictability of Genetic Interactions from Functional Gene Modules

    PubMed Central

    Young, Jonathan H.; Marcotte, Edward M.

    2016-01-01

    Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal. PMID:28007839

  2. Testing Properties of Boolean Functions

    DTIC Science & Technology

    2012-01-01

    think of Pno as forming the argument multiset Sno by choosing ` = k − e random columns from Q 103 without replacement, and including an additional e...Rno) ≤ dTV(Syes, Sno ). (10.2) This inequality can be extremely lossy, depending on the function gcore. However, since Theorem 10.1 applies for an...absence of additional restrictions on the class of functions considered, there is no obvious way to bound dTV(Ryes, Rno) except by dTV(Syes, Sno

  3. Predicting species establishment using absent species and functional neighborhoods.

    PubMed

    Bennett, Jonathan A; Pärtel, Meelis

    2017-04-01

    Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat-specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat-specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance-based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community's trait structure depended on the type of filtering considered, selecting these functional

  4. Interspecies gene function prediction using semantic similarity.

    PubMed

    Yu, Guoxian; Luo, Wei; Fu, Guangyuan; Wang, Jun

    2016-12-23

    Gene Ontology (GO) is a collaborative project that maintains and develops controlled vocabulary (or terms) to describe the molecular function, biological roles and cellular location of gene products in a hierarchical ontology. GO also provides GO annotations that associate genes with GO terms. GO consortium independently and collaboratively annotate terms to gene products, mainly from model organisms (or species) they are interested in. Due to experiment ethics, research interests of biologists and resources limitations, homologous genes from different species currently are annotated with different terms. These differences can be more attributed to incomplete annotations of genes than to functional difference between them. Semantic similarity between genes is derived from GO hierarchy and annotations of genes. It is positively correlated with the similarity derived from various types of biological data and has been applied to predict gene function. In this paper, we investigate whether it is possible to replenish annotations of incompletely annotated genes by using semantic similarity between genes from two species with homology. For this investigation, we utilize three representative semantic similarity metrics to compute similarity between genes from two species. Next, we determine the k nearest neighborhood genes from the two species based on the chosen metric and then use terms annotated to k neighbors of a gene to replenish annotations of that gene. We perform experiments on archived (from Jan-2014 to Jan-2016) GO annotations of four species (Human, Mouse, Danio rerio and Arabidopsis thaliana) to assess the contribution of semantic similarity between genes from different species. The experimental results demonstrate that: (1) semantic similarity between genes from homologous species contributes much more on the improved accuracy (by 53.22%) than genes from single species alone, and genes from two species with low homology; (2) GO annotations of genes from

  5. Ontology-Based Prediction and Prioritization of Gene Functional Annotations.

    PubMed

    Chicco, Davide; Masseroli, Marco

    2016-01-01

    Genes and their protein products are essential molecular units of a living organism. The knowledge of their functions is key for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. The association of a gene or protein with its functions, described by controlled terms of biomolecular terminologies or ontologies, is named gene functional annotation. Very many and valuable gene annotations expressed through terminologies and ontologies are available. Nevertheless, they might include some erroneous information, since only a subset of annotations are reviewed by curators. Furthermore, they are incomplete by definition, given the rapidly evolving pace of biomolecular knowledge. In this scenario, computational methods that are able to quicken the annotation curation process and reliably suggest new annotations are very important. Here, we first propose a computational pipeline that uses different semantic and machine learning methods to predict novel ontology-based gene functional annotations; then, we introduce a new semantic prioritization rule to categorize the predicted annotations by their likelihood of being correct. Our tests and validations proved the effectiveness of our pipeline and prioritization of predicted annotations, by selecting as most likely manifold predicted annotations that were later confirmed.

  6. Predicting functional decline and survival in amyotrophic lateral sclerosis.

    PubMed

    Ong, Mei-Lyn; Tan, Pei Fang; Holbrook, Joanna D

    2017-01-01

    Better predictors of amyotrophic lateral sclerosis disease course could enable smaller and more targeted clinical trials. Partially to address this aim, the Prize for Life foundation collected de-identified records from amyotrophic lateral sclerosis sufferers who participated in clinical trials of investigational drugs and made them available to researchers in the PRO-ACT database. In this study, time series data from PRO-ACT subjects were fitted to exponential models. Binary classes for decline in the total score of amyotrophic lateral sclerosis functional rating scale revised (ALSFRS-R) (fast/slow progression) and survival (high/low death risk) were derived. Data was segregated into training and test sets via cross validation. Learning algorithms were applied to the demographic, clinical and laboratory parameters in the training set to predict ALSFRS-R decline and the derived fast/slow progression and high/low death risk categories. The performance of predictive models was assessed by cross-validation in the test set using Receiver Operator Curves and root mean squared errors. A model created using a boosting algorithm containing the decline in four parameters (weight, alkaline phosphatase, albumin and creatine kinase) post baseline, was able to predict functional decline class (fast or slow) with fair accuracy (AUC = 0.82). However similar approaches to build a predictive model for decline class by baseline subject characteristics were not successful. In contrast, baseline values of total bilirubin, gamma glutamyltransferase, urine specific gravity and ALSFRS-R item score-climbing stairs were sufficient to predict survival class. Using combinations of small numbers of variables it was possible to predict classes of functional decline and survival across the 1-2 year timeframe available in PRO-ACT. These findings may have utility for design of future ALS clinical trials.

  7. Predicting functional decline and survival in amyotrophic lateral sclerosis

    PubMed Central

    Ong, Mei-Lyn; Tan, Pei Fang

    2017-01-01

    Background Better predictors of amyotrophic lateral sclerosis disease course could enable smaller and more targeted clinical trials. Partially to address this aim, the Prize for Life foundation collected de-identified records from amyotrophic lateral sclerosis sufferers who participated in clinical trials of investigational drugs and made them available to researchers in the PRO-ACT database. Methods In this study, time series data from PRO-ACT subjects were fitted to exponential models. Binary classes for decline in the total score of amyotrophic lateral sclerosis functional rating scale revised (ALSFRS-R) (fast/slow progression) and survival (high/low death risk) were derived. Data was segregated into training and test sets via cross validation. Learning algorithms were applied to the demographic, clinical and laboratory parameters in the training set to predict ALSFRS-R decline and the derived fast/slow progression and high/low death risk categories. The performance of predictive models was assessed by cross-validation in the test set using Receiver Operator Curves and root mean squared errors. Results A model created using a boosting algorithm containing the decline in four parameters (weight, alkaline phosphatase, albumin and creatine kinase) post baseline, was able to predict functional decline class (fast or slow) with fair accuracy (AUC = 0.82). However similar approaches to build a predictive model for decline class by baseline subject characteristics were not successful. In contrast, baseline values of total bilirubin, gamma glutamyltransferase, urine specific gravity and ALSFRS-R item score—climbing stairs were sufficient to predict survival class. Conclusions Using combinations of small numbers of variables it was possible to predict classes of functional decline and survival across the 1–2 year timeframe available in PRO-ACT. These findings may have utility for design of future ALS clinical trials. PMID:28406915

  8. 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.

  9. Predicting transfer performance: a comparison of competing function learning models.

    PubMed

    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 values with their paired output values. Transfer incorporates a linear rule-based response mechanism (McDaniel & Busemeyer, 2005). Learners were trained on a functional relationship defined by 2 linear-function segments with mirror slopes. In Experiment 1, 1 segment was densely trained and 1 was sparsely trained; in Experiment 2, both segments were trained equally, but the 2 segments were widely separated. Transfer to new input values was tested. For each model, training performance for each individual participant was fit, and transfer predictions were generated. POLE generally better fit the training data than did EXAM, but EXAM was more accurate at predicting (and fitting) transfer behaviors. It was especially telling that in Experiment 2 the transfer pattern was more consistent with EXAM's but not POLE's predictions, even though the presentation of salient linear segments during training dovetailed with POLE's approach.

  10. Test-Wiseness: A Cognitive Function?

    ERIC Educational Resources Information Center

    Woodley, Katheryn K.

    This paper reports the findings of an attempt to improve test-wiseness (TW) through direct instruction in selected test-taking strategies. TW was defined as "a cognitive function, subject to improvement through both general exposure to a wide variety of test items, and specific training in test-taking skills." The total investigation included:…

  11. 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

  12. Accurate sperm morphology assessment predicts sperm function.

    PubMed

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

    2012-05-01

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

  13. ADEQUACY OF TEST VALIDITIES FOR INDIVIDUAL PREDICTION.

    ERIC Educational Resources Information Center

    WEITZ, HENRY

    COUNSELORS OFTEN ADMINISTER TESTS OF QUESTIONABLE VALIDITY. IN RELIABILITY STUDIES, EVERY PRECAUTION IS TAKEN TO STABILIZE THE STIMULUS SITUATION. IN ASSESSING VALIDITY, CONCERN CENTERS ON BEHAVIOR UNDER DIFFERENT STIMULUS CONDITIONS. CRONBACH'S THEORETICAL LIMIT FOR A VALIDITY COEFFICIENT OF A TEST IS THE SQUARE ROOT OF THE RELIABILITY…

  14. 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.

  15. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    PubMed Central

    Wong, Aloysius; Gehring, Chris; Irving, Helen R.

    2015-01-01

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers. PMID:26106597

  16. Predicting Attrition: A Test of Alternative Approaches

    DTIC Science & Technology

    1977-03-01

    entry to the poorer riskEs. There are two bases for screening. The first one is actuarial . With a sufficiently large recruit cohort, actual loss rates...predicting attrition overcome the drawbacks of the actuarial approach. They let us know what the significant combinations of characteristics are that...terms of their character- istics and average first-year attrition rate, which was about 17.5 percent. Then, each of the four approaches or models was

  17. Predicted and tested performance of durable TPS

    NASA Technical Reports Server (NTRS)

    Shideler, John L.

    1992-01-01

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

  18. Prediction of Metropolitan Readiness Test Scores

    ERIC Educational Resources Information Center

    Blowers, E. A.

    1977-01-01

    The efficiency of several visual and auditory predictors of the Metropolitan Readiness Test was examined utilizing 106 grade 1 subjects considered by their teachers to show learning difficulties. (Author/JC)

  19. 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...

  20. 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...

  1. Resting state functional connectivity predicts neurofeedback response

    PubMed Central

    Scheinost, Dustin; Stoica, Teodora; Wasylink, Suzanne; Gruner, Patricia; Saksa, John; Pittenger, Christopher; Hampson, Michelle

    2014-01-01

    Tailoring treatments to the specific needs and biology of individual patients—personalized medicine—requires delineation of reliable predictors of response. Unfortunately, these have been slow to emerge, especially in neuropsychiatric disorders. We have recently described a real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback protocol that can reduce contamination-related anxiety, a prominent symptom of many cases of obsessive-compulsive disorder (OCD). Individual response to this intervention is variable. Here we used patterns of brain functional connectivity, as measured by baseline resting-state fMRI (rs-fMRI), to predict improvements in contamination anxiety after neurofeedback training. Activity of a region of the orbitofrontal cortex (OFC) and anterior prefrontal cortex, Brodmann area (BA) 10, associated with contamination anxiety in each subject was measured in real time and presented as a neurofeedback signal, permitting subjects to learn to modulate this target brain region. We have previously reported both enhanced OFC/BA 10 control and improved anxiety in a group of subclinically anxious subjects after neurofeedback. Five individuals with contamination-related OCD who underwent the same protocol also showed improved clinical symptomatology. In both groups, these behavioral improvements were strongly correlated with baseline whole-brain connectivity in the OFC/BA 10, computed from rs-fMRI collected several days prior to neurofeedback training. These pilot data suggest that rs-fMRI can be used to identify individuals likely to benefit from rt-fMRI neurofeedback training to control contamination anxiety. PMID:25309375

  2. Slash prediction: a test in commercial thinnings in northeasrern California

    Treesearch

    C. Phillip Weatherspoon; Gary O. Fiddler

    1984-01-01

    Two slash prediction handbooks commonly used in California do not use data from California. To test predictions of the handbooks in northeastern California, logging residues from commercially thinned young-growth stands were surveyed. Measured residues were compared to handbook predictions. Species represented were ponderosa pine, California white fir, California red...

  3. Predicting Cognitive Function from Clinical Measures of Physical Function and Health Status in Older Adults

    PubMed Central

    Bolandzadeh, Niousha; Kording, Konrad; Salowitz, Nicole; Davis, Jennifer C.; Hsu, Liang; Chan, Alison; Sharma, Devika; Blohm, Gunnar; Liu-Ambrose, Teresa

    2015-01-01

    Introduction Current research suggests that the neuropathology of dementia—including brain changes leading to memory impairment and cognitive decline—is evident years before the onset of this disease. Older adults with cognitive decline have reduced functional independence and quality of life, and are at greater risk for developing dementia. Therefore, identifying biomarkers that can be easily assessed within the clinical setting and predict cognitive decline is important. Early recognition of cognitive decline could promote timely implementation of preventive strategies. Methods We included 89 community-dwelling adults aged 70 years and older in our study, and collected 32 measures of physical function, health status and cognitive function at baseline. We utilized an L1–L2 regularized regression model (elastic net) to identify which of the 32 baseline measures were strongly predictive of cognitive function after one year. We built three linear regression models: 1) based on baseline cognitive function, 2) based on variables consistently selected in every cross-validation loop, and 3) a full model based on all the 32 variables. Each of these models was carefully tested with nested cross-validation. Results Our model with the six variables consistently selected in every cross-validation loop had a mean squared prediction error of 7.47. This number was smaller than that of the full model (115.33) and the model with baseline cognitive function (7.98). Our model explained 47% of the variance in cognitive function after one year. Discussion We built a parsimonious model based on a selected set of six physical function and health status measures strongly predictive of cognitive function after one year. In addition to reducing the complexity of the model without changing the model significantly, our model with the top variables improved the mean prediction error and R-squared. These six physical function and health status measures can be easily implemented in a

  4. Nonparametric predictive inference for combining diagnostic tests with parametric copula

    NASA Astrophysics Data System (ADS)

    Muhammad, Noryanti; Coolen, F. P. A.; Coolen-Maturi, T.

    2017-09-01

    Measuring the accuracy of diagnostic tests is crucial in many application areas including medicine and health care. The Receiver Operating Characteristic (ROC) curve is a popular statistical tool for describing the performance of diagnostic tests. The area under the ROC curve (AUC) is often used as a measure of the overall performance of the diagnostic test. In this paper, we interest in developing strategies for combining test results in order to increase the diagnostic accuracy. We introduce nonparametric predictive inference (NPI) for combining two diagnostic test results with considering dependence structure using parametric copula. NPI is a frequentist statistical framework for inference on a future observation based on past data observations. NPI uses lower and upper probabilities to quantify uncertainty and is based on only a few modelling assumptions. While copula is a well-known statistical concept for modelling dependence of random variables. A copula is a joint distribution function whose marginals are all uniformly distributed and it can be used to model the dependence separately from the marginal distributions. In this research, we estimate the copula density using a parametric method which is maximum likelihood estimator (MLE). We investigate the performance of this proposed method via data sets from the literature and discuss results to show how our method performs for different family of copulas. Finally, we briefly outline related challenges and opportunities for future research.

  5. Predictive Validity of the Gesell School Readiness Tests.

    ERIC Educational Resources Information Center

    Graue, M. Elizabeth; Shepard, Lorrie A.

    1989-01-01

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

  6. Predicting Leadership Potential through Psychological Testing

    DTIC Science & Technology

    1992-06-01

    impotent; and without craft they are dreamers . Successful senior leaders and commanders establish a clear personal vision or concept of what needs to...Military Personnel File composition be augmented through the inclusion of psychological test results designed to measure these psychological traits. 39

  7. 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.

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

    PubMed

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

    2013-01-01

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

  9. 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

  10. Predictive computation of genomic logic processing functions in embryonic development

    PubMed Central

    Peter, Isabelle S.; Faure, Emmanuel; Davidson, Eric H.

    2012-01-01

    Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations. PMID:22927416

  11. FSM test: A functional test generation system for sequential circuits

    NASA Astrophysics Data System (ADS)

    Fummi, Franco

    1993-03-01

    An approach to test pattern generation for Finite State Machines (FSM's) and the relationships with their gate level implementation is presented. The algorithm is based on a functional fault model. A restricted set of transitions of the FSM is analyzed and particular state distinguishing sequences (EUIO's) are adopted to observe their final state. Overlapping and concatenation of test sequences is performed in order to reduce test length. Test length obtained is in most cases shorter than previously published functional approaches and the CPU (Central Processing Unit) time requirements are very low in comparison with the gate level ATPG's. Some polynomial complexity preserving techniques are introduced in order to improve the final fault coverage. A number of experiments on MCNC benchmarks have shown the effectiveness of the test algorithm both at the functional level and at the gate level, where the coverage of single stuck-at faults in most cases achieves 100.

  12. Using liver enzymes as screening tests to predict mortality risk.

    PubMed

    Fulks, Michael; Stout, Robert L; Dolan, Vera F

    2008-01-01

    Determine the relationship between liver function test results (GGT, alkaline phosphatase, AST, and ALT) and all-cause mortality in life insurance applicants. By use of the Social Security Master Death File, mortality was examined in 1,905,664 insurance applicants for whom blood samples were submitted to the Clinical Reference Laboratory. There were 50,174 deaths observed in this study population. Results were stratified by 3 age/sex groups: females, age <60; males, age <60; and all, age 60+. Liver function test values were grouped using percentiles of their distribution in these 3 age/sex groups, as well as ranges of actual values. Using the risk of the middle 50% of the population by distribution as a reference, relative mortality observed for GGT and alkaline phosphatase was linear with a steep slope from very low to relatively high values. Relative mortality was increased at lower values for both AST and ALT. ALT did not predict mortality for values above the middle 50% of its distribution. GGT and alkaline phosphatase are significant predictors of mortality risk for all values. ALT is still useful for triggering further testing for hepatitis, but AST should be used instead to assess mortality risk linked with transaminases.

  13. Predictive Validity of the ACT Tests at Selective Colleges.

    ERIC Educational Resources Information Center

    Lenning, Oscar T.

    Included are three studies, each dealing with an aspect of comparative validity of the American College Test (ACT) and the Scholastic Aptitude Test (SAT) at selective colleges. The first study considered the predictive efficiency of the ACT test scores and ACT test scores plus high school grades at 120 colleges, separated into three groups…

  14. Maturity of judgement in decision making for predictive testing for nontreatable adult-onset neurogenetic conditions: a case against predictive testing of minors.

    PubMed

    Richards, F H

    2006-11-01

    International guidelines developed to minimize harm from predictive testing for adult-onset, nontreatable neurogenetic conditions such as Huntington disease (HD) state that such testing should not be available to minors. Some authors have proposed that predictive testing for these conditions should be available to minors at the request of parents and/or of younger adolescents themselves. They highlight the lack of empirical evidence that predictive testing of minors causes harm and suggest that refusing to test minors may be detrimental. The current study focuses on the context of predictive test requests by adolescents younger than 18 years, and presents arguments and evidence that the risk of potential harm from testing such young people is sufficiently high to justify continued caution in this area. A study based on a model of psychosocial maturity found that the 3 factors involved in maturity of judgement in decision making - responsibility, temperance and perspective - continue to develop into late adolescence. There is also evidence that the prefrontal areas of the brain, which are involved in executive functions such as decision making, are not fully developed until early adulthood. Combined with evidence of adverse long-term effects, from research with adults who have undergone predictive testing, these findings constitute grounds for retaining a minimum age of 18 years for predictive testing for nontreatable conditions. Further research on assessment of maturity will assist with reaching a consensus on this issue.

  15. 22 Years of predictive testing for Huntington's disease: the experience of the UK Huntington's Prediction Consortium.

    PubMed

    Baig, Sheharyar S; Strong, Mark; Rosser, Elisabeth; Taverner, Nicola V; Glew, Ruth; Miedzybrodzka, Zosia; Clarke, Angus; Craufurd, David; Quarrell, Oliver W

    2016-10-01

    Huntington's disease (HD) is a progressive neurodegenerative condition. At-risk individuals have accessed predictive testing via direct mutation testing since 1993. The UK Huntington's Prediction Consortium has collected anonymised data on UK predictive tests, annually, from 1993 to 2014: 9407 predictive tests were performed across 23 UK centres. Where gender was recorded, 4077 participants were male (44.3%) and 5122 were female (55.7%). The median age of participants was 37 years. The most common reason for predictive testing was to reduce uncertainty (70.5%). Of the 8441 predictive tests on individuals at 50% prior risk, 4629 (54.8%) were reported as mutation negative and 3790 (44.9%) were mutation positive, with 22 (0.3%) in the database being uninterpretable. Using a prevalence figure of 12.3 × 10(-5), the cumulative uptake of predictive testing in the 50% at-risk UK population from 1994 to 2014 was estimated at 17.4% (95% CI: 16.9-18.0%). We present the largest study conducted on predictive testing in HD. Our findings indicate that the vast majority of individuals at risk of HD (>80%) have not undergone predictive testing. Future therapies in HD will likely target presymptomatic individuals; therefore, identifying the at-risk population whose gene status is unknown is of significant public health value.

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  17. 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.

  18. 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

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

    USDA-ARS?s Scientific Manuscript database

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

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

    PubMed Central

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

    2016-01-01

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

  1. Marijuana Use Predicts Cognitive Performance on Tasks of Executive Function

    PubMed Central

    Dahlgren, Mary Kathryn; Sagar, Kelly A.; Racine, Megan T.; Dreman, Meredith W.; Gruber, Staci A.

    2016-01-01

    Objective: Despite growing evidence that chronic marijuana use is associated with cognitive impairment, particularly when use is initiated at an early age, national trends demonstrate significant decreases in the perceived risk of marijuana corresponding with increased use, especially among youth. The current study assessed the impact of marijuana use on executive function and whether patterns of marijuana use, including earlier age at onset, higher frequency, and increased magnitude of use, predict impairment. Method: Forty-four chronic, heavy marijuana smokers (37 male, 7 female) and 32 healthy, nonsmoking control participants (20 male, 12 female) recruited from the Greater Boston area completed two assessments of executive function: the Stroop Color Word Test and Wisconsin Card Sorting Test (WCST). Results: Marijuana smokers had poorer executive function relative to control participants, a between-group difference that was primarily driven by individuals with early onset of marijuana use (before age 16; n = 21); significance remained even when controlling for frequency and magnitude of use. Further, earlier age at marijuana onset and increased marijuana use predicted poorer neurocognitive performance, and perseverative errors on the WCST significantly predicted marijuana group membership. Conclusions: These findings underscore the impact of early onset of marijuana use on executive function impairment independent of increased frequency and magnitude of use. In addition, poorer performance on the WCST may serve as a neuropsychological marker for heavy marijuana users. These results highlight the need for additional research to identify predictors associated with early marijuana use, as exposure to marijuana during a period of developmental vulnerability may result in negative cognitive consequences. PMID:26997188

  2. A test to evaluate the earthquake prediction algorithm, M8

    USGS Publications Warehouse

    Healy, John H.; Kossobokov, Vladimir G.; Dewey, James W.

    1992-01-01

    A test of the algorithm M8 is described. The test is constructed to meet four rules, which we propose to be applicable to the test of any method for earthquake prediction:  1. An earthquake prediction technique should be presented as a well documented, logical algorithm that can be used by  investigators without restrictions. 2. The algorithm should be coded in a common programming language and implementable on widely available computer systems. 3. A test of the earthquake prediction technique should involve future predictions with a black box version of the algorithm in which potentially adjustable parameters are fixed in advance. The source of the input data must be defined and ambiguities in these data must be resolved automatically by the algorithm. 4. At least one reasonable null hypothesis should be stated in advance of testing the earthquake prediction method, and it should be stated how this null hypothesis will be used to estimate the statistical significance of the earthquake predictions. The M8 algorithm has successfully predicted several destructive earthquakes, in the sense that the earthquakes occurred inside regions with linear dimensions from 384 to 854 km that the algorithm had identified as being in times of increased probability for strong earthquakes. In addition, M8 has successfully "post predicted" high percentages of strong earthquakes in regions to which it has been applied in retroactive studies. The statistical significance of previous predictions has not been established, however, and post-prediction studies in general are notoriously subject to success-enhancement through hindsight. Nor has it been determined how much more precise an M8 prediction might be than forecasts and probability-of-occurrence estimates made by other techniques. We view our test of M8 both as a means to better determine the effectiveness of M8 and as an experimental structure within which to make observations that might lead to improvements in the algorithm

  3. New statistical PDFs: Predictions and tests up to LHC energies

    NASA Astrophysics Data System (ADS)

    Soffer, Jacques; Bourrely, Claude

    2017-03-01

    The quantum statistical parton distributions approach proposed more than one decade ago is revisited by considering a larger set of recent and accurate Deep Inelastic Scattering experimental results. It enables us to improve the description of the data by means of a new determination of the parton distributions. This global next-to-leading order QCD analysis leads to a good description of several structure functions, involving unpolarized parton distributions and helicity distributions, in a broad range of x and Q2 and in terms of a rather small number of free parameters. There are several challenging issues, in particular the behavior of d ¯(x )/u ¯(x ) at large x, a possible large positive gluon helicity distribution, etc.. The predictions of this theoretical approach will be tested for single-jet production and charge asymmetry in W± production in p ¯p and pp collisions up to LHC energies, using recent data and also for forthcoming experimental results.

  4. 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.

  5. A PREDICTIVE SCREENING TEST FOR CHILDREN WITH ARTICULATORY SPEECH DEFECTS.

    ERIC Educational Resources Information Center

    VAN RIPER, CHARLES

    THE CONSTRUCTION OF A TEST TO IDENTIFY DEFECTIVE ARTICULATION IN FIRST-GRADE CHILDREN WAS REPORTED. THE "EMPIRICAL SCALE DERIVATION METHOD" WAS SELECTED AS THE MOST APPROPRIATE TECHNIQUE TO SEEK TEST ITEMS FOR THE PREDICTION OF ARTICULATORY MATUARATION. AFTER SELECTION AND REDUCTION TO 135 TEST ITEMS, AN EXPERIMENTAL ITEM POOL WAS…

  6. Predictive Validity of the Gesell School Readiness Tests.

    ERIC Educational Resources Information Center

    Graue, M. Elizabeth; Shepard, Lorrie A.

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

  7. CombFunc: predicting protein function using heterogeneous data sources.

    PubMed

    Wass, Mark N; Barton, Geraint; Sternberg, Michael J E

    2012-07-01

    Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at http://www.sbg.bio.ic.ac.uk/combfunc.

  8. An empirical propellant response function for combustion stability predictions

    NASA Technical Reports Server (NTRS)

    Hessler, R. O.

    1980-01-01

    An empirical response function model was developed for ammonium perchlorate propellants to supplant T-burner testing at the preliminary design stage. The model was developed by fitting a limited T-burner data base, in terms of oxidizer size and concentration, to an analytical two parameter response function expression. Multiple peaks are predicted, but the primary effect is of a single peak for most formulations, with notable bulges for the various AP size fractions. The model was extended to velocity coupling with the assumption that dynamic response was controlled primarily by the solid phase described by the two parameter model. The magnitude of velocity coupling was then scaled using an erosive burning law. Routine use of the model for stability predictions on a number of propulsion units indicates that the model tends to overpredict propellant response. It is concluded that the model represents a generally conservative prediction tool, suited especially for the preliminary design stage when T-burner data may not be readily available. The model work included development of a rigorous summation technique for pseudopropellant properties and of a concept for modeling ordered packing of particulates.

  9. 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

  10. The Full Function Test Explosive Generator

    SciTech Connect

    Reisman, D B; Javedani, J B; Griffith, L V; Ellsworth, G F; Kuklo, R M; Goerz, D A; White, A D; Tallerico, L J; Gidding, D A; Murphy, M J; Chase, J B

    2009-12-13

    We have conducted three tests of a new pulsed power device called the Full Function Test (FFT). These tests represented the culmination of an effort to establish a high energy pulsed power capability based on high explosive pulsed power (HEPP) technology. This involved an extensive computational modeling, engineering, fabrication, and fielding effort. The experiments were highly successful and a new US record for magnetic energy was obtained.

  11. Withdrawing Divorce Petitions: A Predictive Test of the Exchange Model of Divorce.

    ERIC Educational Resources Information Center

    Kitson, Gay C.; And Others

    1983-01-01

    Tested the utility of an exchange model for predicting divorce or withdrawal of divorce petitions, using court records and interviews of men and women who were divorced or subsequently withdrew their divorce petitions. Discriminant function analyses indicated that an exchange model can predict divorce versus petition withdrawal. (JAC)

  12. Psychosocial impact of predictive testing for myotonic dystrophy type 1.

    PubMed

    Prévost, Claude; Veillette, Suzanne; Perron, Michel; Laberge, Claude; Tremblay, Carmen; Auclair, Julie; Villeneuve, Josée; Tremblay, Marc; Mathieu, Jean

    2004-04-01

    In the Saguenay-Lac-Saint-Jean region (Quebec, Canada), a predictive DNA-testing program for myotonic dystrophy type 1 (DM1) has been available as a clinical service since 1988. From 1 to 12 years (median, 5 years) after receiving predictive testing, a total of 308 participants (44 carriers and 264 non-carriers) answered a questionnaire to determine the psychosocial impact of this genetic testing. The main reasons for wanting to be tested were to learn if children are at risk for DM1 or for reproductive decision making (75%) and to relieve the uncertainty for themselves (17%). The majority of participants (96.1%) remembered correctly their test result. At the time of the survey, the perception of the general well-being, the psychological distress (Psychiatric Symptom Index), and the self-esteem (Rosenberg Self-Esteem Scale) were similar in carriers, in non-carriers, and in the reference (Quebec) population. When participants indicated a change in different aspects of their lives following predictive testing, it was perceived as a change for the better by non-carriers and as a change for the worse by carriers. Nevertheless, for a majority of carriers and of non-carriers, the test result did not bring changes in their lives. All respondents believed that predictive testing should be available for the at-risk population and the vast majority of carrier and of non-carriers would recommend the use of predictive testing to their family members. Predictive testing for individuals at-risk of DM1 can be offered safely within a well-organized clinical and genetic counseling program that includes careful pre-test counseling, pre-test clinical assessment, post-test psychological support, and follow-up for those identified as carriers. Copyright 2003 Wiley-Liss, Inc.

  13. Evaluating the Predictive Validity of Graduate Management Admission Test Scores

    ERIC Educational Resources Information Center

    Sireci, Stephen G.; Talento-Miller, Eileen

    2006-01-01

    Admissions data and first-year grade point average (GPA) data from 11 graduate management schools were analyzed to evaluate the predictive validity of Graduate Management Admission Test[R] (GMAT[R]) scores and the extent to which predictive validity held across sex and race/ethnicity. The results indicated GMAT verbal and quantitative scores had…

  14. Evaluating the Predictive Validity of Graduate Management Admission Test Scores

    ERIC Educational Resources Information Center

    Sireci, Stephen G.; Talento-Miller, Eileen

    2006-01-01

    Admissions data and first-year grade point average (GPA) data from 11 graduate management schools were analyzed to evaluate the predictive validity of Graduate Management Admission Test[R] (GMAT[R]) scores and the extent to which predictive validity held across sex and race/ethnicity. The results indicated GMAT verbal and quantitative scores had…

  15. Ebola Blood Test May Help Predict Survival Chances

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_163165.html Ebola Blood Test May Help Predict Survival Chances Findings ... help determine a person's chance of surviving an Ebola infection, researchers say. "It is not just defining ...

  16. Test Predicting Alzheimer's Would Be Welcome, Survey Finds

    MedlinePlus

    ... medlineplus.gov/news/fullstory_162525.html Test Predicting Alzheimer's Would Be Welcome, Survey Finds 3 out of ... could tell them they were going to develop Alzheimer's disease, most American seniors would take it, a ...

  17. Brain Scan Test Predicts Fall Risk in Elderly

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_162417.html Brain Scan Test Predicts Fall Risk in Elderly Such ... research suggests that measurements of healthy older adults' brain activity may help determine their future risk. "Our ...

  18. Possibility of quantitative prediction of cavitation erosion without model test

    SciTech Connect

    Kato, Hiroharu; Konno, Akihisa; Maeda, Masatsugu; Yamaguchi, Hajime

    1996-09-01

    A scenario for quantitative prediction of cavitation erosion was proposed. The key value is the impact force/pressure spectrum on a solid surface caused by cavitation bubble collapse. As the first step of prediction, the authors constructed the scenario from an estimation of the cavity generation rate to the prediction of impact force spectrum, including the estimations of collapsing cavity number and impact pressure. The prediction was compared with measurements of impact force spectra on a partially cavitating hydrofoil. A good quantitative agreement was obtained between the prediction and the experiment. However, the present method predicted a larger effect of main flow velocity than that observed. The present scenario is promising as a method of predicting erosion without using a model test.

  19. Which Working Memory Functions Predict Intelligence?

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  20. Protein Function Prediction: Towards Integration of Similarity Metrics

    PubMed Central

    Erdin, Serkan; Lisewski, Andreas Martin; Lichtarge, Olivier

    2011-01-01

    Summary Genomics centers discover increasingly many protein sequences and structures, but not necessarily their full biological functions. Thus, currently, fewer than one percent of proteins have experimentally verified biochemical activities. To fill this gap, function prediction algorithms apply metrics of similarity between proteins on the premise that those sufficiently alike in sequence, or structure, will perform identical functions. Although high sensitivity is elusive, network analyses that integrate these metrics together hold the promise of rapid gains in function prediction specificity. PMID:21353529

  1. Using Machine Learning to Predict Laboratory Test Results.

    PubMed

    Luo, Yuan; Szolovits, Peter; Dighe, Anand S; Baron, Jason M

    2016-06-01

    While clinical laboratories report most test results as individual numbers, findings, or observations, clinical diagnosis usually relies on the results of multiple tests. Clinical decision support that integrates multiple elements of laboratory data could be highly useful in enhancing laboratory diagnosis. Using the analyte ferritin in a proof of concept, we extracted clinical laboratory data from patient testing and applied a variety of machine-learning algorithms to predict ferritin test results using the results from other tests. We compared predicted with measured results and reviewed selected cases to assess the clinical value of predicted ferritin. We show that patient demographics and results of other laboratory tests can discriminate normal from abnormal ferritin results with a high degree of accuracy (area under the curve as high as 0.97, held-out test data). Case review indicated that predicted ferritin results may sometimes better reflect underlying iron status than measured ferritin. These findings highlight the substantial informational redundancy present in patient test results and offer a potential foundation for a novel type of clinical decision support aimed at integrating, interpreting, and enhancing the diagnostic value of multianalyte sets of clinical laboratory test results. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Functional brain network efficiency predicts intelligence.

    PubMed

    Langer, Nicolas; Pedroni, Andreas; Gianotti, Lorena R R; Hänggi, Jürgen; Knoch, Daria; Jäncke, Lutz

    2012-06-01

    The neuronal causes of individual differences in mental abilities such as intelligence are complex and profoundly important. Understanding these abilities has the potential to facilitate their enhancement. The purpose of this study was to identify the functional brain network characteristics and their relation to psychometric intelligence. In particular, we examined whether the functional network exhibits efficient small-world network attributes (high clustering and short path length) and whether these small-world network parameters are associated with intellectual performance. High-density resting state electroencephalography (EEG) was recorded in 74 healthy subjects to analyze graph-theoretical functional network characteristics at an intracortical level. Ravens advanced progressive matrices were used to assess intelligence. We found that the clustering coefficient and path length of the functional network are strongly related to intelligence. Thus, the more intelligent the subjects are the more the functional brain network resembles a small-world network. We further identified the parietal cortex as a main hub of this resting state network as indicated by increased degree centrality that is associated with higher intelligence. Taken together, this is the first study that substantiates the neural efficiency hypothesis as well as the Parieto-Frontal Integration Theory (P-FIT) of intelligence in the context of functional brain network characteristics. These theories are currently the most established intelligence theories in neuroscience. Our findings revealed robust evidence of an efficiently organized resting state functional brain network for highly productive cognitions.

  3. 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.

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

    SciTech Connect

    Silverman, D.C.

    1994-12-31

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

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

    PubMed

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

    2016-02-01

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

  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. 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.

  8. 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)

  9. 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)

  10. 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…

  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…

  12. 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.

  13. 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…

  14. 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.

  15. 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.

  16. Predicting Tests Ordered in Hospital Laboratories using Generalized Linear Modeling.

    PubMed

    Leaven, Laquanda T

    2016-01-01

    Laboratory services in healthcare systems play a vital role in inpatient care. Most hospital laboratories are facing the challenge of reducing cost and improving service quality. The author focuses on identifying test order patterns in a laboratory for a large urban hospital. The data collected from this facility consists of all tests ordered over a three-month time frame and contains test orders for approximately 17,500 patients. Poisson and negative binomial regression models are used to determine how well patient characteristics (patient length of stay and the medical units in which patients are placed) will predict the number of tests being ordered. The test order prediction model developed in this study will aid the management and phlebotomists in the hospital laboratory in securing methods to satisfy the test order demand. By implementing the recommendations of this study, hospital laboratories should see significant improvements in phlebotomist productivity and resource utilization, implementation of which could result in cost savings.

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

    PubMed

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

    2012-01-01

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

  18. Testing the Link between Functional Diversity and Ecosystem Functioning in a Minnesota Grassland Experiment

    PubMed Central

    Butterfield, Bradley J.; Reich, Peter B.

    2012-01-01

    The functional diversity of a community can influence ecosystem functioning and reflects assembly processes. The large number of disparate metrics used to quantify functional diversity reflects the range of attributes underlying this concept, generally summarized as functional richness, functional evenness, and functional divergence. However, in practice, we know very little about which attributes drive which ecosystem functions, due to a lack of field-based tests. Here we test the association between eight leading functional diversity metrics (Rao’s Q, FD, FDis, FEve, FDiv, convex hull volume, and species and functional group richness) that emphasize different attributes of functional diversity, plus 11 extensions of these existing metrics that incorporate heterogeneous species abundances and trait variation. We assess the relationships among these metrics and compare their performances for predicting three key ecosystem functions (above- and belowground biomass and light capture) within a long-term grassland biodiversity experiment. Many metrics were highly correlated, although unique information was captured in FEve, FDiv, and dendrogram-based measures (FD) that were adjusted by abundance. FD adjusted by abundance outperformed all other metrics in predicting both above- and belowground biomass, although several others also performed well (e.g. Rao’s Q, FDis, FDiv). More generally, trait-based richness metrics and hybrid metrics incorporating multiple diversity attributes outperformed evenness metrics and single-attribute metrics, results that were not changed when combinations of metrics were explored. For light capture, species richness alone was the best predictor, suggesting that traits for canopy architecture would be necessary to improve predictions. Our study provides a comprehensive test linking different attributes of functional diversity with ecosystem function for a grassland system. PMID:23300787

  19. Sixth blind test of organic crystal-structure prediction methods.

    PubMed

    Groom, Colin R; Reilly, Anthony M

    2014-08-01

    Over the past 15 years progress in predicting crystal structures of small organic molecules has been charted by a series of blind tests hosted by the Cambridge Crystallographic Data Centre. This letter announces a sixth blind test to take place between September 2014 and August 2015, giving details of the target systems and the revised procedure. We hope that as many methods as possible will be assessed and benchmarked in this new blind test.

  20. 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.

  1. PPT-DB: the protein property prediction and testing database

    PubMed Central

    Wishart, David S.; Arndt, David; Berjanskii, Mark; Guo, An Chi; Shi, Yi; Shrivastava, Savita; Zhou, Jianjun; Zhou, You; Lin, Guohui

    2008-01-01

    The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. order parameters, B-factors, folding rates) features that have been measured, derived or tabulated from a variety of sources. PPT-DB is designed to serve two purposes. First it is intended to serve as a centralized, up-to-date, freely downloadable and easily queried repository of predictable or ‘derived’ protein property data. In this role, PPT-DB can serve as a one-stop, fully standardized repository for developers to obtain the required training, testing and validation data needed for almost any kind of protein property prediction program they may wish to create. The second role that PPT-DB can play is as a tool for homology-based protein property prediction. Users may query PPT-DB with a sequence of interest and have a specific property predicted using a sequence similarity search against PPT-DB's extensive collection of proteins with known properties. PPT-DB exploits the well-known fact that protein structure and dynamic properties are highly conserved between homologous proteins. Predictions derived from PPT-DB's similarity searches are typically 85–95% correct (for categorical predictions, such as secondary structure) or exhibit correlations of >0.80 (for numeric predictions, such as accessible surface area). This performance is 10–20% better than what is typically obtained from standard ‘ab initio’ predictions. PPT-DB, its prediction utilities and all of its contents are available at http://www.pptdb.ca PMID:17916570

  2. PPT-DB: the protein property prediction and testing database.

    PubMed

    Wishart, David S; Arndt, David; Berjanskii, Mark; Guo, An Chi; Shi, Yi; Shrivastava, Savita; Zhou, Jianjun; Zhou, You; Lin, Guohui

    2008-01-01

    The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. order parameters, B-factors, folding rates) features that have been measured, derived or tabulated from a variety of sources. PPT-DB is designed to serve two purposes. First it is intended to serve as a centralized, up-to-date, freely downloadable and easily queried repository of predictable or 'derived' protein property data. In this role, PPT-DB can serve as a one-stop, fully standardized repository for developers to obtain the required training, testing and validation data needed for almost any kind of protein property prediction program they may wish to create. The second role that PPT-DB can play is as a tool for homology-based protein property prediction. Users may query PPT-DB with a sequence of interest and have a specific property predicted using a sequence similarity search against PPT-DB's extensive collection of proteins with known properties. PPT-DB exploits the well-known fact that protein structure and dynamic properties are highly conserved between homologous proteins. Predictions derived from PPT-DB's similarity searches are typically 85-95% correct (for categorical predictions, such as secondary structure) or exhibit correlations of >0.80 (for numeric predictions, such as accessible surface area). This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions. PPT-DB, its prediction utilities and all of its contents are available at http://www.pptdb.ca.

  3. Modifications of the Test Information Function.

    ERIC Educational Resources Information Center

    Samejima, Fumiko

    Two modification formulas are presented for the test information function in order to provide better measures of local accuracies of the estimation of "theta" when maximum likelihood estimation is used to provide the estimate of ability "theta." A minimum bound of any estimator, biased or unbiased, is considered; and Formula 1…

  4. Structure analysis, fatigue testing, and lifetime prediction of composite steels

    NASA Astrophysics Data System (ADS)

    Sokolkin, Yu. V.; Chekalkin, A. A.; Babushkin, A. V.

    1998-05-01

    Composite steels prepared by technology of powder metallurgy are widely used as low cost parts with good resistance to wear, fracture, and corrosion. The development of powder composite steels is directly related to strength under vibration, fatigue stabilizing, and accurate lifetime prediction for actual composite topology. The fatigue behavior of powder steels was studied by experimental and numerical methods of composite mechanics and materials sciences. The chemical composition of composite steel is a pure iron powder as the base material and a handful of carbon, chromium, nickel, or phosphorus powders. The powder multi-component mixture is compacted by cold isostatic pressing to a rectangular form. The compactants are sintered in protective atmosphere. The microscale examination of the composite structure included an METAM-RV-21 metallographic optic microscope with a high-resolution ScanNexIIc scanner and an image processing package on the PC platform. The phase composition of powder steels has complex disordered topology with irregular ferrite/austenite grains, iron carbide inclusions, and pores. The microstructure images are treated according to the theory of stochastic processes as ergodic probability functions; statistical moments and a structural covariance function of the composite steels are given. The microscale stress-strain state of the composite steel is analyzed by finite element methods. The stiffness matrix of the composite steel is also presented together with stiffness matrices of ferrite/austenite grains, iron carbide inclusions, and pores as zero matrices. Endurance limits of the microstructural components are described by the Basquin or Coffin-Manson laws, respectively, as high and low cycle fatigue; cumulative microdamage in loading with a variable amplitude is taken from the Palmgren-Miner rule. Planar specimens were tested by console bending. Symmetric fatigue cycling was performed at a stable frequency of 20 Hz with endurance limits up

  5. Do optimism and pessimism predict physical functioning?

    PubMed

    Brenes, Gretchen A; Rapp, Stephen R; Rejeski, W Jack; Miller, Michael E

    2002-06-01

    Dispositional optimism has been shown to be related to self-report measures of health and well-being, yet little research has examined the relationship between optimism and more objective measures of functioning. The purpose of this study was to examine the relationship between optimism and pessimism and objective physical functioning. Four hundred eighty community-dwelling older adults with knee pain completed a measure of optimism and pessimism and were observed performing four daily activities (walking, lifting an object, climbing stairs, and getting into and out of a car). Results indicated that pessimism was significantly related to performance on all four tasks (p < .001), while optimism was related to performance only on the walking task (p < .05), after controlling for demographic and health variables.

  6. Improving structure-based function prediction using molecular dynamics

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2001-01-01

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

  8. Link prediction boosted psychiatry disorder classification for functional connectivity network

    NASA Astrophysics Data System (ADS)

    Li, Weiwei; Mei, Xue; Wang, Hao; Zhou, Yu; Huang, Jiashuang

    2017-02-01

    Functional connectivity network (FCN) is an effective tool in psychiatry disorders classification, and represents cross-correlation of the regional blood oxygenation level dependent signal. However, FCN is often incomplete for suffering from missing and spurious edges. To accurate classify psychiatry disorders and health control with the incomplete FCN, we first `repair' the FCN with link prediction, and then exact the clustering coefficients as features to build a weak classifier for every FCN. Finally, we apply a boosting algorithm to combine these weak classifiers for improving classification accuracy. Our method tested by three datasets of psychiatry disorder, including Alzheimer's Disease, Schizophrenia and Attention Deficit Hyperactivity Disorder. The experimental results show our method not only significantly improves the classification accuracy, but also efficiently reconstructs the incomplete FCN.

  9. Taper Functions for Predicting Product Volumes in Natural Shortleaf Pines

    Treesearch

    Robert M. Farrar; Paul A. Murphy

    1987-01-01

    Taper (stem-profile) functions are presented for natural shortleaf pine (Pinus echinata Mill.) trees growing in the West Gulf area. These functions, when integrated, permit the prediction of volume between any two heights on a stem and, conversely by iteration, the volume between any two diameters on a stem. Examples are given of use of the functions...

  10. Platelet function tests: a comparative review.

    PubMed

    Paniccia, Rita; Priora, Raffaella; Liotta, Agatina Alessandrello; 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.

  11. Platelet function tests: a comparative review

    PubMed Central

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

    2015-01-01

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

  12. Platelet function tests in clinical cardiology: unfulfilled expectations.

    PubMed

    Gorog, Diana A; Fuster, Valentin

    2013-05-28

    This review is a critical evaluation of publications in the past decade on the usefulness of platelet function tests (PFTs) in clinical cardiology, in aiding diagnosis, predicting risk, and monitoring therapy. The ideal PFT should: 1) detect baseline platelet hyperreactivity; 2) allow individualization of antiplatelet medication; 3) predict thrombotic risk; and 4) predict bleeding risk. The practicalities of clinical cardiology demand rapid, accurate, and reliable tests that are simple to operate at the bedside and available 24 h a day, 7 days a week. Point-of-care PFTs most widely evaluated clinically include PFA-100 and VerifyNow. None of these tests can reliably detect platelet hyperreactivity and thus identify a prothrombotic state. Identification of antiplatelet nonresponsiveness or hyporesponsiveness is highly test specific, and does not allow individualization of therapy. The power of PFTs in predicting thrombotic events for a given individual is variable and often modest, and alteration of antithrombotic treatment on the basis of the results of PFTs has not been shown to alter clinical outcome. PFTs in current mainstream use cannot reliably assess bleeding risk. These tests have been in use for over a decade, but the hopes raised by PFTs in clinical practice remain unfulfilled. Although physiologically relevant measurement of platelet function now is more important than ever, a critical reappraisal of available techniques in light of clinical requirements is needed. The use of native blood, global stimulus instead of individual agonists, contribution of thrombin generation by activated platelets to the test results, and establishment of a PFT therapeutic range for each antiplatelet drug should be considered and is discussed.

  13. 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

  14. Submaximal treadmill test predicts VO2max in overweight children.

    PubMed

    Nemeth, Blaise A; Carrel, Aaron L; Eickhoff, Jens; Clark, R Randall; Peterson, Susan E; Allen, David B

    2009-05-01

    To demonstrate the ability of a submaximal test to predict VO(2max) in overweight children. A total of 130 children, 11 to 14 years old, with body mass index >85 percentile for age and sex performed a submaximal walking test. VO(2max) was measured by using open circuit spirometry during a graded exercise test to volitional fatigue. An equation to predict VO(2max) was modeled by using the variables of sex, weight (kg), height (cm), heart rate (HR) after 4 minutes during the submaximal test (4minHR), HR difference (4minHR - resting HR), and submaximal treadmill speed (miles per hour [mph]) in 75% of the subjects. Validation was performed by using the remaining 25% of subjects. A total of 113 subjects achieved a maximal effort and was used in the statistical analysis. Development and validation groups were similar in all aspects. On validation, the mean square error was 241.06 with the predicted VO(2max) within 10% of the observed value in 67% of subjects. VO(2max) was accurately predicted in this cohort of overweight children by using a submaximal, treadmill-based testing protocol.

  15. Functional Performance Testing for Power and Return to Sports

    PubMed Central

    Manske, Robert; Reiman, Michael

    2013-01-01

    Context: Functional performance testing of athletes can determine physical limitations that may affect sporting activities. Optimal functional performance testing simulates the athlete’s activity. Evidence Acquisition: A Medline search from 1960 to 2012 was implemented with the keywords functional testing, functional impairment testing, and functional performance testing in the English language. Each author also undertook independent searches of article references. Conclusion: Functional performance tests can bridge the gap between general physical tests and full, unrestricted athletic activity. PMID:24427396

  16. [Cardiology. Platelet function testing for clinicians].

    PubMed

    Pellaton, Cyril; Eeckhout, Eric; Silvain, Johanne; Montalescot, Gilles; Collet, Jean-Phillipe

    2014-01-15

    Platelet P2YI2 receptor inhibition with clopidogrel, prasugrel or ticagrelor plays a key role to prevent recurrent ischaemic events after percutaneous coronary intervention in acute coronary syndromes or elective settings. The degree of platelet inhibition depends on the antiplatelet medication used and is influenced by clinical and genetic factors. A concept of therapeutic window exists. On one side, efficient anti-aggregation is required in order to reduce cardio-vascular events. On the other side, an excessive platelet inhibition represents a risk of bleeding complications. This article describes the current knowledge about some platelet function tests and genetic tests and summarises their role in the clinical practice.

  17. 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

  18. Pulmonary function testing in asthma: nursing applications.

    PubMed

    Conner, Brenda; Meng, Anne

    2003-12-01

    Spirometry has become the most widely used assessment of pulmonary function for diagnostic and prognostic purposes. This article reviews the indications for spirometry in persons who have asthma, the parameters measured, acceptable testing techniques, acceptability, quality assurance criteria, and basic interpretation of results in evaluating the person who has asthma. Understanding basic spirometry is an invaluable aid to the nurse and nurse practitioner who provide care to children and adults who have asthma.

  19. Predictive values for cardiopulmonary exercise testing in sedentary Chinese adults.

    PubMed

    Ong, Kian Chung; Loo, Chian Min; Ong, Yong Yau; Chan, Siew Pang; Earnest, Arul; Saw, Seang Mei

    2002-09-01

    Normative data for cardiopulmonary exercise testing (CPET) may vary among subjects of different races. The objectives of the present study were to: (i) establish normal standards for cardiopulmonary responses during incremental cycle ergometer testing in order to derive predictive equations for clinically useful variables during CPET of Chinese subjects; and (ii) determine the validity of existing prediction equations of maximal exercise performance for use in our local Chinese population. The maximal and submaximal cardiopulmonary responses were analysed for 95 healthy sedentary adult Chinese subjects (48 men and 47 women; aged 20-70 years) who underwent CPET using a cycle ergometer and an incremental work-rate protocol until symptom limitation. Measurements, at maximal exercise, of oxygen uptake (VO2(max)), power output and heart rate were regressed on age, height, weight and gender. The predictive equations for these exercise parameters performed better than those published previously in out-sample predictive accuracy. Comparison with previous studies also showed that prediction equations of VO2(max) derived from studies based predominantly or exclusively on Caucasian populations overestimated the actual values for our subjects. Previously established prediction equations for maximal exercise performance during CPET based on non-Chinese populations may not be applicable to Chinese subjects in our population.

  20. Predicting Chemical Reactivity from the Charge Density through Gradient Bundle Analysis: Moving beyond Fukui Functions.

    PubMed

    Morgenstern, Amanda; Wilson, Timothy R; Eberhart, M E

    2017-06-08

    Predicting chemical reactivity is a major goal of chemistry. Toward this end, atom condensed Fukui functions of conceptual density functional theory have been used to predict which atom is most likely to undergo electrophilic or nucleophilic attack, providing regioselectivity information. We show that the most probable regions for electrophilic attack within each atom can be predicted through analysis of gradient bundle volumes, a property that depends only on the charge density of the neutral molecules. We also introduce gradient bundle condensed Fukui functions to compare the stereoselectivity information obtained from gradient bundle volume analysis. We demonstrate this method using the test set of molecular fluorine, oxygen, nitrogen, carbon monoxide, and hydrogen cyanide.

  1. A Prediction for the 4-Loop beta Function in QCD

    SciTech Connect

    Samuel, Mark A.

    2003-05-14

    We predict that the four-loop contribution {beta}{sub 3} to the QCD {beta} function in the {ovr MS} prescription is given by {beta}{sub 3} {approx_equal} 23,600(900) - 6,400(200) N{sub f} + 350(70)N{sub f}{sup 2} + 1.5 N{sub f}{sup 3}, where N{sub f} is the number of flavours and the coefficient of N{sub f}{sup 3} is an exact result from large-N{sub f} expansion. In the phenomenologically-interesting case N{sub f} = 3, we estimate {beta}{sub 3} = (7.6 {+-} 0.1) x 10{sup 3}. We discuss our estimates of the errors in these QCD predictions, basing them on the demonstrated accuracy of our method in test applications to the O(N) {Phi}{sup 4} theory, and on variations in the details of our estimation method, which goes beyond conventional Pade approximants by estimating and correcting for subasymptotic deviations from exact results.

  2. 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.

  3. An Automated Preschool Pulmonary Function Test

    PubMed Central

    Budd, Jeffrey R.; Finkelstein, Stanley M.; Warwick, Warren J.

    1981-01-01

    A non-invasive, non-effort dependent pulmonary function test has been created which can be used on preschool subjects. The integration of a mini-computer system with the test procedure allows extensive analysis of flow and gas concentration data. This analysis not only supplies lung volume measurements but also gas mixing efficiency which quantifies the evenness of gas distribution and alveolar efficiency which indicates the extent of ventilation-perfusion inequalities and diffusion abnormalities. The test has been performed on a sample of control subjects and cystic fibrosis patients aged 1 to 23 years old. The results indicate that the measurements are not only sensitive and specific to lung disease but also that they should prove useful for following the extent of lung disease over time.

  4. 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.

  5. The microcomputer scientific software series 4: testing prediction accuracy.

    Treesearch

    H. Michael Rauscher

    1986-01-01

    A computer program, ATEST, is described in this combination user's guide / programmer's manual. ATEST provides users with an efficient and convenient tool to test the accuracy of predictors. As input ATEST requires observed-predicted data pairs. The output reports the two components of accuracy, bias and precision.

  6. 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,…

  7. 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)

  8. 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)

  9. 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…

  10. 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

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2015-02-22

    Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  13. 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

  14. Error estimates for density-functional theory predictions of surface energy and work function

    NASA Astrophysics Data System (ADS)

    De Waele, Sam; Lejaeghere, Kurt; Sluydts, Michael; Cottenier, Stefaan

    2016-12-01

    Density-functional theory (DFT) predictions of materials properties are becoming ever more widespread. With increased use comes the demand for estimates of the accuracy of DFT results. In view of the importance of reliable surface properties, this work calculates surface energies and work functions for a large and diverse test set of crystalline solids. They are compared to experimental values by performing a linear regression, which results in a measure of the predictable and material-specific error of the theoretical result. Two of the most prevalent functionals, the local density approximation (LDA) and the Perdew-Burke-Ernzerhof parametrization of the generalized gradient approximation (PBE-GGA), are evaluated and compared. Both LDA and GGA-PBE are found to yield accurate work functions with error bars below 0.3 eV, rivaling the experimental precision. LDA also provides satisfactory estimates for the surface energy with error bars smaller than 10%, but GGA-PBE significantly underestimates the surface energy for materials with a large correlation energy.

  15. Testing galaxy formation models with galaxy stellar mass functions

    NASA Astrophysics Data System (ADS)

    Lim, S. H.; Mo, H. J.; Lan, T.-W.; Ménard, B.

    2017-01-01

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

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

    PubMed

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

    2006-08-01

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

  17. 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

  18. A survey of computational intelligence techniques in protein function prediction.

    PubMed

    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.

  19. 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. © 2014 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

  20. 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.

  1. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  3. 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

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

    SciTech Connect

    Silverman, D.C. )

    1994-06-01

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

  5. 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

  6. 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…

  7. A Unitary Executive Function Predicts Intelligence in Children

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  9. 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.

  10. Community monitoring for youth violence surveillance: testing a prediction model.

    PubMed

    Henry, David B; Dymnicki, Allison; Kane, Candice; Quintana, Elena; Cartland, Jenifer; Bromann, Kimberly; Bhatia, Shaun; Wisnieski, Elise

    2014-08-01

    Predictive epidemiology is an embryonic field that involves developing informative signatures for disorder and tracking them using surveillance methods. Through such efforts assistance can be provided to the planning and implementation of preventive interventions. Believing that certain minor crimes indicative of gang activity are informative signatures for the emergence of serious youth violence in communities, in this study we aim to predict outbreaks of violence in neighborhoods from pre-existing levels and changes in reports of minor offenses. We develop a prediction equation that uses publicly available neighborhood-level data on disorderly conduct, vandalism, and weapons violations to predict neighborhoods likely to have increases in serious violent crime. Data for this study were taken from the Chicago Police Department ClearMap reporting system, which provided data on index and non-index crimes for each of the 844 Chicago census tracts. Data were available in three month segments for a single year (fall 2009, winter, spring, and summer 2010). Predicted change in aggravated battery and overall violent crime correlated significantly with actual change. The model was evaluated by comparing alternative models using randomly selected training and test samples, producing favorable results with reference to overfitting, seasonal variation, and spatial autocorrelation. A prediction equation based on winter and spring levels of the predictors had area under the curve ranging from .65 to .71 for aggravated battery, and .58 to .69 for overall violent crime. We discuss future development of such a model and its potential usefulness in violence prevention and community policing.

  11. 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.

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

    PubMed

    Yang, Jianyi; Zhang, Yang

    2015-12-17

    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. Copyright © 2015 John Wiley & Sons, Inc.

  13. 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

  14. Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks.

    PubMed

    Cao, Renzhi; Cheng, Jianlin

    2016-01-15

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

  15. Prediction of sprint triathlon performance from laboratory tests.

    PubMed

    Van Schuylenbergh, R; Eynde, B Vanden; Hespel, P

    2004-01-01

    This study investigated whether sprint triathlon performance can be adequately predicted from laboratory tests. Ten triathletes [mean (SEM), age 21.8 (0.3) years, height 179 (2) cm, body mass 67.5 (2.5) kg] performed two graded maximal exercise test in random order, either on their own bicycle which was mounted on an ergometer or on a treadmill, to determine their peak oxygen consumption ( VO(2)peak). Furthermore, they participated in two to three 30-min constant-load tests in both swimming, cycling and running to establish their maximal lactate steady state (MLSS) in each exercise mode. Swim tests were performed in a 25-m swimming pool (water temperature 27 degrees C). During each test heart rate (HR), power output (PO) or running/swimming speed and blood lactate concentration (BLC) were recorded at regular intervals. Oxygen uptake ( VO(2)) was continuously measured during the graded tests. Two weeks after the laboratory tests all subjects competed in a triathlon race (500 m swim, 20-km bike, 5-km run) [1 h 4 min 45 s (1 min 38 s)]. Peak HR was 7 beats.min(-1) lower in the graded cycle test than in the treadmill test ( p<0.05) at similar peak BLC (approximately 10 mmol.l(-1)) and VO(2)peak (approximately 5 L.min(-1)). High correlations were found between VO(2)peak during cycling ( r=-0.71, p<0.05) or running ( r=-0.69, p<0.05) and triathlon performance. Stepwise multiple regression analysis showed that running speed and swimming speed at MLSS, together with BLC in running at MLSS, yielded the best prediction of performance [1 h 5 min 18 s (1 min 49 s)]. Thus, our data indicate that exercise tests aimed to determine MLSS in running and swimming allow for a precise estimation of sprint triathlon performance.

  16. Testing visual function in the clinical setting.

    PubMed

    Westheimer, Gerald

    2010-07-01

    The explosive growth of automatic examination of the eye, in particular for determining refractive corrections, invites an analysis of the strengths and limitations of these devices and their role in clinical decisions. Subjective refraction procedures are based on a patient's visual responses and these embrace many levels of additional optical and neural processing and factors involving the higher-order nervous system and perception. Because the ultimate mission is the maintenance and improvement of a patient's visual experiences, the optometric examination necessarily extends beyond the employment of automatic devices and therefore, should include engaging the patients in tests of their visual functions.

  17. 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.

  18. Can simple clinical tests predict walking ability after prosthetic rehabilitation?

    PubMed

    Sansam, Kate; O'Connor, Rory J; Neumann, Vera; Bhakta, Bipin

    2012-11-01

    To investigate whether simple clinical measures can predict walking ability after lower limb prosthetic rehabilitation. Prospective observational study. Ninety five adults who were assessed as suitable for lower limb prosthetic rehabilitation by the multidisciplinary team. Information regarding baseline clinical factors (amputation details, comorbidities, physical ability, mood and cognitive ability) was collected prior to provision of the prosthesis. Backward step linear regression was used to identify factors predictive of performance on the Timed Up and Go test following rehabilitation. Seventy one participants were able to complete this walking test and were included in the final analysis. The backward step regression model had an adjusted R2 of 0.588 and comprised 6 factors: age (p = 0.002), gender (p = 0.027), level of amputation (p = 0.000), presence of contracture (p = 0.088), ability to stand on one leg (p = 0.062) and Trail Making Tests A + B (p = 0.047), a test of cognitive flexibility. Cause of amputation (dysvascular or non-dysvascular) was not an independent predictor of walking outcome. These results indicate that simple clinical assessments completed prior to prosthetic provision can be used to predict mobility outcome. These findings need to be validated in a larger population across other amputee rehabilitation services and if confirmed could easily be incorporated into routine clinical practice.

  19. 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.

  20. Triple test as predictive screen for unilateral weakness on caloric testing in routine practice.

    PubMed

    Rohrmeier, Christian; Richter, Otto; Schneider, Michael; Wirsching, Kornelia; Fiedler, Isabella; Haubner, Frank; Strutz, Jürgen; Kühnel, Thomas S

    2013-02-01

    To investigate in vertigo patients in routine practice to what extent a rapid and straightforward triple bedside test (spontaneous nystagmus, head-shaking nystagmus, and the head impulse test) can predict a normal result on caloric testing. Prospective, single-blind, diagnostic study. Tertiary referral center. 151 patients (78 male and 73 female subjects; mean age, 52.5 +/- 16.4 yr) presenting with acute or recent symptoms of vertigo. Diagnostic evaluation. The negative predictive value (NPV) of the triple test in relation to a normal caloric test response. In unilateral weakness (UW) on caloric testing (UW, >=25%), the triple test had sensitivity of 63.6%, specificity of 85.4%, a positive predictive value (PPV) of 71.4%, and an NPV of 80.4%. In other words, 80.4% of patients with a negative triple test also had a normal response on caloric testing. In pronounced canal paresis (UW, >=50%), the triple test had sensitivity of 81.8%, specificity of 81.4%, a PPV of 55.1%, and an NPV of 94.1%. Significant differences were found between 2 subgroups assessed by examiners with differing levels of experience (p < 0.05). The triple test represents a good screening tool that quickly and reliably excludes unilateral weakness and in particular pronounced canal paresis on caloric testing. (C) 2013 Otology & Neurotology, Inc.

  1. Predictive Value of Screening Tests for Visually Significant Eye Disease

    PubMed Central

    Kopplin, Laura J.; Mansberger, Steven L.

    2017-01-01

    Purpose To determine the predictive value of ophthalmic screening tests with visually significant eye disease in a cohort of American Indian/Alaskan Natives from the Pacific Northwest. Design Validity assessment of a possible screening protocol. Methods Ophthalmic technicians performed a screening examination including medical and ocular history, best-corrected visual acuity, limbal anterior chamber depth assessment, frequency doubling technology perimetry (FDT, C-20-5), confocal scanning laser ophthalmoscopy, nonmydriatic digital photography, and tonometry on 429 participants. An ophthalmologist performed a comprehensive eye exam on subjects with one or more abnormal screening tests and a random selection of those with normal screening tests. We used univariate and multivariate logistic regression to determine the association between abnormal screening test results and visually significant eye disease. We also determined the predictive value of screening tests with ocular disease. Results Univariate analysis identified history of eye disease or diabetes mellitus (p<.001), visual acuity <20/40 (p<.001), abnormal/poor quality confocal scanning laser ophthalmoscopy (p<.001), abnormal FDT (p<.001), and abnormal/poor quality non-mydriatic imaging (p<.001) as associated with visually significant eye disease. A multivariate analysis found visually significant eye disease to be associated (p<.001; receiver operating curve area= .827, negative predictive value=84%) with four screening tests: visual acuity <20/40, abnormal/poor quality non-mydriatic imaging, abnormal FDT and abnormal/poor quality confocal scanning laser ophthalmoscopy. Conclusions Ophthalmic technicians performing a subset of screening tests may provide an accurate and efficient means of screening for eye disease in an American Indian/Alaskan Native population. Confirmation of these results in other populations, particularly those with a different profile of disease prevalence is needed. PMID:26052087

  2. Predictive value of screening tests for visually significant eye disease.

    PubMed

    Kopplin, Laura J; Mansberger, Steven L

    2015-09-01

    To determine the predictive value of ophthalmic screening tests with visually significant eye disease in a cohort of American Indian/Alaskan Natives from the Pacific Northwest. Validity assessment of a possible screening protocol. Ophthalmic technicians performed a screening examination including medical and ocular history, best-corrected visual acuity, limbal anterior chamber depth assessment, frequency-doubling technology perimetry (FDT, C-20-5), confocal scanning laser ophthalmoscopy, nonmydriatic digital photography, and tonometry on 429 participants. An ophthalmologist performed a comprehensive eye examination on subjects with 1 or more abnormal screening tests and a random selection of those with normal screening tests. We used univariate and multivariate logistic regression to determine the association between abnormal screening test results and visually significant eye disease. We also determined the predictive value of screening tests with ocular disease. Univariate analysis identified history of eye disease or diabetes mellitus (P < .001), visual acuity <20/40 (P < .001), abnormal/poor-quality confocal scanning laser ophthalmoscopy (P < .001), abnormal FDT (P < .001), and abnormal/poor-quality nonmydriatic imaging (P < .001) as associated with visually significant eye disease. A multivariate analysis found visually significant eye disease to be associated (P < .001; receiver operating characteristic curve area = 0.827, negative predictive value = 84%) with 4 screening tests: visual acuity <20/40, abnormal/poor-quality nonmydriatic imaging, abnormal FDT, and abnormal/poor-quality confocal scanning laser ophthalmoscopy. Ophthalmic technicians performing a subset of screening tests may provide an accurate and efficient means of screening for eye disease in an American Indian/Alaskan Native population. Confirmation of these results in other populations, particularly those with a different profile of disease prevalence, is needed. Copyright © 2015 Elsevier

  3. Roles for text mining in protein function prediction.

    PubMed

    Verspoor, Karin M

    2014-01-01

    The Human Genome Project has provided science with a hugely valuable resource: the blueprints for life; the specification of all of the genes that make up a human. While the genes have all been identified and deciphered, it is proteins that are the workhorses of the human body: they are essential to virtually all cell functions and are the primary mechanism through which biological function is carried out. Hence in order to fully understand what happens at a molecular level in biological organisms, and eventually to enable development of treatments for diseases where some aspect of a biological system goes awry, we must understand the functions of proteins. However, experimental characterization of protein function cannot scale to the vast amount of DNA sequence data now available. Computational protein function prediction has therefore emerged as a problem at the forefront of modern biology (Radivojac et al., Nat Methods 10(13):221-227, 2013).Within the varied approaches to computational protein function prediction that have been explored, there are several that make use of biomedical literature mining. These methods take advantage of information in the published literature to associate specific proteins with specific protein functions. In this chapter, we introduce two main strategies for doing this: association of function terms, represented as Gene Ontology terms (Ashburner et al., Nat Genet 25(1):25-29, 2000), to proteins based on information in published articles, and a paradigm called LEAP-FS (Literature-Enhanced Automated Prediction of Functional Sites) in which literature mining is used to validate the predictions of an orthogonal computational protein function prediction method.

  4. 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

  5. The Wada test might predict postoperative fine finger motor deficit after hemispherotomy.

    PubMed

    Fujimoto, Ayataka; Okanishi, Tohru; Nishimura, Mitsuyo; Kanai, Sotaro; Sato, Keishiro; Enoki, Hideo

    2017-09-07

    Cerebral hemispherotomy is a surgical method with a high rate of seizure reduction in patients with intractable epilepsy. However, there is a probability of postoperative motor deficits. The objective of this study was to investigate whether the Wada test can help predict motor function outcomes after hemispherotomy and, therefore, may be useful in decision-making and patient selection. A total of 13 patients with hemispherical intractable epilepsy underwent hemispherical disconnection surgeries. Six of them underwent the Wada test to evaluate motor function and language function followed by peri-insula hemispherotomy. The patients' age ranged from 11 to 45years (mean 27years). Three of six patients had reduced dexterity on the Wada test. The finger motor function in the other patients did not change on the Wada test. Postoperatively, all patients who had decreased fine motor movement on the Wada test showed postoperative clumsiness of their hands and fingers. The Wada test might predict postoperative fine finger motor deficit after hemispherotomy. This study showed that gross motor function was compensated in the ipsilateral hemisphere, whereas fine finger motor movement function remained in the contralateral frontal cortex. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Narcissism and childhood recollections: a quantitative test of psychoanalytic predictions.

    PubMed

    Otway, Lorna J; Vignoles, Vivian L

    2006-01-01

    Different psychotherapeutic theories provide contradictory accounts of adult narcissism as the product of either parental coldness or excessive parental admiration during childhood. Yet, none of these theories has been tested systematically in a nonclinical sample. The authors compared four structural equation models predicting overt and covert narcissism among 120 United Kingdom adults. Both forms of narcissism were predicted by both recollections of parental coldness and recollections of excessive parental admiration. Moreover, a suppression relationship was detected between these predictors: The effects of each were stronger when modeled together than separately. These effects were found after controlling for working models of attachment; covert narcissism was predicted also by attachment anxiety. This combination of childhood experiences may help to explain the paradoxical combination of grandiosity and fragility in adult narcissism.

  7. [Preoperative lung function tests using impulse oscillometry].

    PubMed

    Fujiwara, Kumiko

    2010-02-01

    Preoperative lung function tests are useful to evaluate the preoperative pulmonary condition and to detect a high risk of postoperative pulmonary complications. However, maximum expiratory effort by patients is necessary to determine lung function using spirometry and flow-volume curve measurements. When patients are not able to expire completely during the measurement, incorrect data regarding their respiratory system is obtained. On the other hand, respiratory system impedance using an impulse oscillatory system (IOS) can evaluate total airway resistance (R5), large airway resistance (R20), small airway resistance (R5-20) and reactance (X5) under breathing at rest within a few minutes. There are few reports that indicate the standard values for IOS. In addition, the effects of age on IOS value are not clear. In this study preoperative lung functions using IOS were studied to examine the standard value and effect of aging. Subjects were 420 patients aged from 20 to 89 years with normal pulmonary function (%VC > or = 80%, %FEV(1.0) > or = 70%), and scheduled for an elective surgery. Lung function measurements such as IOS, spirometry, maximum expiratory flow-volume curve and single N2 washout were done preoperatively. Subjects were divided into seven groups in decades from 20 to 80. Although there was no statistical change in R5, R20, R5-R20, Z5 and X5 in the decades from 20 to 60, there were statistically significant changes during the 70s and 80s. There were significant differences in IOS parameters between the adult group and the aged group. Changes due to aging were stronger on V25/Ht than those of IOS. This study indicates that there are differences between V25/Ht and IOS values because of the difference in breathing conditions during measurements.

  8. 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.

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

    PubMed

    Tassicker, Roslyn J

    2005-04-01

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

  10. 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.

  11. 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

  12. The Development of MST Test Information for the Prediction of Test Performances

    ERIC Educational Resources Information Center

    Park, Ryoungsun; Kim, Jiseon; Chung, Hyewon; Dodd, Barbara G.

    2017-01-01

    The current study proposes novel methods to predict multistage testing (MST) performance without conducting simulations. This method, called MST test information, is based on analytic derivation of standard errors of ability estimates across theta levels. We compared standard errors derived analytically to the simulation results to demonstrate the…

  13. Electrical test prediction using hybrid metrology and machine learning

    NASA Astrophysics Data System (ADS)

    Breton, Mary; Chao, Robin; Muthinti, Gangadhara Raja; de la Peña, Abraham A.; Simon, Jacques; Cepler, Aron J.; Sendelbach, Matthew; Gaudiello, John; Emans, Susan; Shifrin, Michael; Etzioni, Yoav; Urenski, Ronen; Lee, Wei Ti

    2017-03-01

    Electrical test measurement in the back-end of line (BEOL) is crucial for wafer and die sorting as well as comparing intended process splits. Any in-line, nondestructive technique in the process flow to accurately predict these measurements can significantly improve mean-time-to-detect (MTTD) of defects and improve cycle times for yield and process learning. Measuring after BEOL metallization is commonly done for process control and learning, particularly with scatterometry (also called OCD (Optical Critical Dimension)), which can solve for multiple profile parameters such as metal line height or sidewall angle and does so within patterned regions. This gives scatterometry an advantage over inline microscopy-based techniques, which provide top-down information, since such techniques can be insensitive to sidewall variations hidden under the metal fill of the trench. But when faced with correlation to electrical test measurements that are specific to the BEOL processing, both techniques face the additional challenge of sampling. Microscopy-based techniques are sampling-limited by their small probe size, while scatterometry is traditionally limited (for microprocessors) to scribe targets that mimic device ground rules but are not necessarily designed to be electrically testable. A solution to this sampling challenge lies in a fast reference-based machine learning capability that allows for OCD measurement directly of the electrically-testable structures, even when they are not OCD-compatible. By incorporating such direct OCD measurements, correlation to, and therefore prediction of, resistance of BEOL electrical test structures is significantly improved. Improvements in prediction capability for multiple types of in-die electrically-testable device structures is demonstrated. To further improve the quality of the prediction of the electrical resistance measurements, hybrid metrology using the OCD measurements as well as X-ray metrology (XRF) is used. Hybrid metrology

  14. Predictive gene testing for Huntington disease and other neurodegenerative disorders.

    PubMed

    Wedderburn, S; Panegyres, P K; Andrew, S; Goldblatt, J; Liebeck, T; McGrath, F; Wiltshire, M; Pestell, C; Lee, J; Beilby, J

    2013-12-01

    Controversies exist around predictive testing (PT) programmes in neurodegenerative disorders. This study sets out to answer the following questions relating to Huntington disease (HD) and other neurodegenerative disorders: differences between these patients in their PT journeys, why and when individuals withdraw from PT, and decision-making processes regarding reproductive genetic testing. A case series analysis of patients having PT from the multidisciplinary Western Australian centre for PT over the past 20 years was performed using internationally recognised guidelines for predictive gene testing in neurodegenerative disorders. Of 740 at-risk patients, 518 applied for PT: 466 at risk of HD, 52 at risk of other neurodegenerative disorders - spinocerebellar ataxias, hereditary prion disease and familial Alzheimer disease. Thirteen percent withdrew from PT - 80.32% of withdrawals occurred during counselling stages. Major withdrawal reasons related to timing in the patients' lives or unknown as the patient did not disclose the reason. Thirty-eight HD individuals had reproductive genetic testing: 34 initiated prenatal testing (of which eight withdrew from the process) and four initiated pre-implantation genetic diagnosis. There was no recorded or other evidence of major psychological reactions or suicides during PT. People withdrew from PT in relation to life stages and reasons that are unknown. Our findings emphasise the importance of: (i) adherence to internationally recommended guidelines for PT; (ii) the role of the multidisciplinary team in risk minimisation; and (iii) patient selection. © 2013 The Authors; Internal Medicine Journal © 2013 Royal Australasian College of Physicians.

  15. Prediction of Erectile Function Following Treatment for Prostate Cancer

    PubMed Central

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

    2013-01-01

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

  16. Liver Function Tests Following Open Cardiac Surgery

    PubMed Central

    Sabzi, Feridoun; Faraji, Reza

    2015-01-01

    Introduction: The cardiopulmonary bypass may have multiple systemic effects on the body organs as liver. This prospective study was planned to explore further the incidence and significance of this change. Methods: Two hundred patients with coronary artery bypass grafting (CABG), were randomly selected for the study. Total and indirect bilirubin, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase were measured preoperatively and at 24, 48 and 72 hours, following coronary artery bypass grafting. Postoperative value of the liver function tests with respect to hypothermia or hypotension were compared by one way analysis of variance for repeated measure and compared with t test. Patient’s characteristics with bilirubin value (≤1.5 mg or >1.5 mg) were compared with t test. Results: A significant increase of total bilirubin, aspartate aminotransferase, and alkaline phosphatase were noted in the third postoperative day. Significant relation was seen between hypotension and alkaline phosphatase, and aspartate aminotransferase change but hypothermia had not affected alanine aminotransferase, total bilirubin and indirect bilirubin change. Pump time, alanine aminotransferase in third postoperative day and direct bilirubin in first and second day of postoperative period had significant relation with pre and post-operative bilirubin change. Conclusion: Transient but not permanent alterations of hepatic enzymes after coronary artery bypass grafting presumably attributed to the decreased hepatic flow, hypoxia, or pump-induced inflammation. PMID:26191391

  17. Diabetic rat testes: morphological and functional alterations.

    PubMed

    Ricci, G; Catizone, A; Esposito, R; Pisanti, F A; Vietri, M T; Galdieri, M

    2009-12-01

    Reproductive dysfunction is a consequence of diabetes, but the underlying mechanisms are poorly understood. This study investigated the histological and molecular alterations in the testes of rats injected with streptozotocin at prepuperal (SPI rats) and adult age (SAI rats) to understand whether diabetes affects testicular tissue with different severity depending on the age in which this pathological condition starts. The testes of diabetic animals showed frequent abnormal histology, and seminiferous epithelium cytoarchitecture appeared altered as well as the occludin distribution pattern. The early occurrence of diabetes increased the percentage of animals with high number of damaged tubules. The interstitial compartment of the testes was clearly hypertrophic in several portions of the organs both in SPI and SAI rats. Interestingly, fully developed Leydig cells were present in all the treated animals although abnormally distributed. Besides the above-described damages, we found a similar decrease in plasma testosterone levels both in SPI and SAI rats. Oxidative stress (OS) is involved in the pathogenesis of various diabetic complications, and in our experimental models we found that manganese superoxide dismutase was reduced in diabetic animals. We conclude that in STZ-induced diabetes, the altered spermatogenesis, more severe in SPI animals, is possibly due to the effect of OS on Leydig cell function which could cause the testosterone decrease responsible for the alterations found in the seminiferous epithelium of diabetic animals.

  18. An overview of in silico protein function prediction.

    PubMed

    Sleator, Roy D; Walsh, Paul

    2010-03-01

    As the protein databases continue to expand at an exponential rate, fed by daily uploads from multiple large scale genomic and metagenomic projects, the problem of assigning a function to each new protein has become the focus of significant research interest in recent times. Herein, we review the most recent advances in the field of automated function prediction (AFP). We begin by defining what is meant by biological "function" and the means of describing such functions using standardised machine readable ontologies. We then focus on the various function-prediction programs available, both sequence and structure based, and outline their associated strengths and weaknesses. Finally, we conclude with a brief overview of the future challenges and outstanding questions in the field, which still remain unanswered.

  19. Prediction of protein function from protein sequence and structure.

    PubMed

    Whisstock, James C; Lesk, Arthur M

    2003-08-01

    The sequence of a genome contains the plans of the possible life of an organism, but implementation of genetic information depends on the functions of the proteins and nucleic acids that it encodes. Many individual proteins of known sequence and structure present challenges to the understanding of their function. In particular, a number of genes responsible for diseases have been identified but their specific functions are unknown. Whole-genome sequencing projects are a major source of proteins of unknown function. Annotation of a genome involves assignment of functions to gene products, in most cases on the basis of amino-acid sequence alone. 3D structure can aid the assignment of function, motivating the challenge of structural genomics projects to make structural information available for novel uncharacterized proteins. Structure-based identification of homologues often succeeds where sequence-alone-based methods fail, because in many cases evolution retains the folding pattern long after sequence similarity becomes undetectable. Nevertheless, prediction of protein function from sequence and structure is a difficult problem, because homologous proteins often have different functions. Many methods of function prediction rely on identifying similarity in sequence and/or structure between a protein of unknown function and one or more well-understood proteins. Alternative methods include inferring conservation patterns in members of a functionally uncharacterized family for which many sequences and structures are known. However, these inferences are tenuous. Such methods provide reasonable guesses at function, but are far from foolproof. It is therefore fortunate that the development of whole-organism approaches and comparative genomics permits other approaches to function prediction when the data are available. These include the use of protein-protein interaction patterns, and correlations between occurrences of related proteins in different organisms, as

  20. Pulmonary function testing in children with the airflometer.

    PubMed

    Lowdon, B J; Pateman, N A

    1984-01-01

    Use of the airflometer (AFM) as an inexpensive apparatus for routine screening of pulmonary function has been hindered by the lack of established norms of AFM readings for young children. Using both the airflometer and the vitalograph, lung function was measured in 828 children, aged five to 11 years, randomly selected from six schools. Results indicate that girls aged five, 8-11 years have lower Forced Vital Capacity (FVC), Forced Expiratory Volume in one second (FEV1, and AFM scores than boys. High correlations were observed between AFM units and FEV1 (0.93), between height and FEV1 (0.88), and between FVC (0.89) and AFM units (0.84). Regression equations are given to enable prediction of AFM from height and from age for boys and girls. Tables indicate scores that should be followed with further pulmonary function testing. A protocol is outlined to enable the airflometer to be used as a first level screening device.

  1. Predicting protein function by frequent functional association pattern mining in protein interaction networks.

    PubMed

    Cho, Young-Rae; Zhang, Aidong

    2010-01-01

    Predicting protein function from protein interaction networks has been challenging because of the complexity of functional relationships among proteins. Most previous function prediction methods depend on the neighborhood of or the connected paths to known proteins. However, their accuracy has been limited due to the functional inconsistency of interacting proteins. In this paper, we propose a novel approach for function prediction by identifying frequent patterns of functional associations in a protein interaction network. A set of functions that a protein performs is assigned into the corresponding node as a label. A functional association pattern is then represented as a labeled subgraph. Our frequent labeled subgraph mining algorithm efficiently searches the functional association patterns that occur frequently in the network. It iteratively increases the size of frequent patterns by one node at a time by selective joining, and simplifies the network by a priori pruning. Using the yeast protein interaction network, our algorithm found more than 1400 frequent functional association patterns. The function prediction is performed by matching the subgraph, including the unknown protein, with the frequent patterns analogous to it. By leave-one-out cross validation, we show that our approach has better performance than previous link-based methods in terms of prediction accuracy. The frequent functional association patterns generated in this study might become the foundations of advanced analysis for functional behaviors of proteins in a system level.

  2. Postoperative testing to predict recurrent Cushing disease in children.

    PubMed

    Batista, Dalia L; Oldfield, Edward H; Keil, Margaret F; Stratakis, Constantine A

    2009-08-01

    Postoperative testing after transsphenoidal surgery (TSS) for Cushing disease (CD) in children and its usefulness in predicting residual disease or recurrence are not well studied. The objective of the study was to identify which one of three tests that are routinely performed in our institution after TSS performs better in the identification of noncured patients or predict relapse for CD. This was a retrospective review of clinical data of 72 children who received surgery for CD (age range 5.8-18.3 yr). The study was conducted at a tertiary care center. After TSS, plasma ACTH and serum cortisol (at 0800 h), urinary free cortisol (UFC) values and an ovine CRH (oCRH) stimulation test were obtained. Patients were followed up for 24-120 months by a formal protocol. Of 72 children with CD, 66 (94%) achieved sustained remission after TSS. Two children had persistent disease after TSS, whereas four children appeared cured at first but relapsed later. All four had low or undetectable UFCs that were not different from cured patients (P > 0.0.1). Children who remained in remission had significantly lower morning ACTH and cortisol levels after TSS compared with those who relapsed (P < 0.001). During an oCRH stimulation test, ACTH and cortisol values were higher in patients who relapsed vs. those in remission (P <0.001). Lack of histological confirmation of an adenoma, normal serum cortisol or ACTH, a normal response to oCRH, and glucocorticoid replacement for less than 6 months after surgery were associated with relapse. In pediatric patients with CD, low UFCs after TSS are not good predictors of sustained remission; morning ACTH and cortisol values and/or an oCRH test after TSS predicted patients that recurred.

  3. Predicting functional brain ROIs via fiber shape models.

    PubMed

    Zhang, Tuo; Guo, Lei; Li, Kaiming; Zhu, Dajing; Cui, Guangbin; Liu, Tianming

    2011-01-01

    Study of structural and functional connectivities of the human brain has received significant interest and effort recently. A fundamental question arises when attempting to measure the structural and/or functional connectivities of specific brain networks: how to best identify possible Regions of Interests (ROIs)? In this paper, we present a novel ROI prediction framework that localizes ROIs in individual brains based on learned fiber shape models from multimodal task-based fMRI and diffusion tensor imaging (DTI) data. In the training stage, ROIs are identified as activation peaks in task-based fMRI data. Then, shape models of white matter fibers emanating from these functional ROIs are learned. In addition, ROIs' location distribution model is learned to be used as an anatomical constraint. In the prediction stage, functional ROIs are predicted in individual brains based on DTI data. The ROI prediction is formulated and solved as an energy minimization problem, in which the two learned models are used as energy terms. Our experiment results show that the average ROI prediction error is 3.45 mm, in comparison with the benchmark data provided by working memory task-based fMRI. Promising results were also obtained on the ADNI-2 longitudinal DTI dataset.

  4. A Test for Measuring Gustatory Function

    PubMed Central

    Smutzer, Gregory; Lam, Si; Hastings, Lloyd; Desai, Hetvi; Abarintos, Ray A.; Sobel, Marc; Sayed, Nabil

    2010-01-01

    Objectives The purpose of this study is to determine the usefulness of edible taste strips for measuring human gustatory function. Research Design The physical properties of edible taste strips were examined in order to determine their potential for delivering threshold and suprathreshold amounts of taste stimuli to the oral cavity. Taste strips were then assayed by fluorescence to analyze the uniformity and distribution of bitter tastant in the strips. Finally, taste recognition thresholds for sweet taste were examined in order to determine whether or not taste strips would produce recognition thresholds that were equal to or better than those obtained from aqueous tests. Methodology Edible strips were prepared from pullulan-hydroxypropyl methylcellulose solutions that were dried to a thin film. The maximal amount of a tastant that could be incorporated in a 2.54 × 2.54 cm taste strip was identified by including representative taste stimuli for each class of tastant (sweet, sour, salty, bitter, and umami) during strip formation. Distribution of the bitter tastant quinine hydrochloride in taste strips was assayed by fluorescence emission spectroscopy. The efficacy of taste strips for evaluating human gustatory function was examined by using a single series ascending method of limits protocol. Sucrose taste recognition threshold data from edible strips was then compared to results that were obtained from a standard “sip and spit” recognition threshold test. Results Edible films that formed from a pullulan-hydroxypropyl methylcellulose polymer mixture can be used to prepare clear, thin strips that have essentially no background taste and leave no physical presence after release of tastant. Edible taste strips could uniformly incorporate up to five percent of their composition as tastant. Taste recognition thresholds for sweet taste were over one order of magnitude lower with edible taste strips when compared to an aqueous taste test. Conclusion Edible taste

  5. PredictProtein--an open resource for online prediction of protein structural and functional features.

    PubMed

    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

    2014-07-01

    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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Validity of an Interactive Functional Reach Test.

    PubMed

    Galen, Sujay S; Pardo, Vicky; Wyatt, Douglas; Diamond, Andrew; Brodith, Victor; Pavlov, Alex

    2015-08-01

    Videogaming platforms such as the Microsoft (Redmond, WA) Kinect(®) are increasingly being used in rehabilitation to improve balance performance and mobility. These gaming platforms do not have built-in clinical measures that offer clinically meaningful data. We have now developed software that will enable the Kinect sensor to assess a patient's balance using an interactive functional reach test (I-FRT). The aim of the study was to test the concurrent validity of the I-FRT and to establish the feasibility of implementing the I-FRT in a clinical setting. The concurrent validity of the I-FRT was tested among 20 healthy adults (mean age, 25.8±3.4 years; 14 women). The Functional Reach Test (FRT) was measured simultaneously by both the Kinect sensor using the I-FRT software and the Optotrak Certus(®) 3D motion-capture system (Northern Digital Inc., Waterloo, ON, Canada). The feasibility of implementing the I-FRT in a clinical setting was assessed by performing the I-FRT in 10 participants with mild balance impairments recruited from the outpatient physical therapy clinic (mean age, 55.8±13.5 years; four women) and obtaining their feedback using a NASA Task Load Index (NASA-TLX) questionnaire. There was moderate to good agreement between FRT measures made by the two measurement systems. The greatest agreement between the two measurement system was found with the Kinect sensor placed at a distance of 2.5 m [intraclass correlation coefficient (2,k)=0.786; P<0.001] from the participant. Participants with mild balance impairments whose balance was assessed using the I-FRT software scored their experience favorably by assigning lower scores for the Frustration, Mental Demand, and Temporal Demand subscales on the NASA/TLX questionnaire. FRT measures made using the Kinect sensor I-FRT software provides a valid clinical measure that can be used with the gaming platforms.

  7. White matter predicts functional connectivity in premanifest Huntington's disease.

    PubMed

    McColgan, Peter; Gregory, Sarah; Razi, Adeel; Seunarine, Kiran K; Gargouri, Fatma; Durr, Alexandra; Roos, Raymund A C; Leavitt, Blair R; Scahill, Rachael I; Clark, Chris A; Tabrizi, Sarah J; Rees, Geraint; Coleman, A; Decolongon, J; Fan, M; Petkau, T; Jauffret, C; Justo, D; Lehericy, S; Nigaud, K; Valabrègue, R; Choonderbeek, A; Hart, E P T; Hensman Moss, D J; Crawford, H; Johnson, E; Papoutsi, M; Berna, C; Reilmann, R; Weber, N; Stout, J; Labuschagne, I; Landwehrmeyer, B; Orth, M; Johnson, H

    2017-02-01

    The distribution of pathology in neurodegenerative disease can be predicted by the organizational characteristics of white matter in healthy brains. However, we have very little evidence for the impact these pathological changes have on brain function. Understanding any such link between structure and function is critical for understanding how underlying brain pathology influences the progressive behavioral changes associated with neurodegeneration. Here, we demonstrate such a link between structure and function in individuals with premanifest Huntington's. Using diffusion tractography and resting state functional magnetic resonance imaging to characterize white matter organization and functional connectivity, we investigate whether characteristic patterns of white matter organization in the healthy human brain shape the changes in functional coupling between brain regions in premanifest Huntington's disease. We find changes in functional connectivity in premanifest Huntington's disease that link directly to underlying patterns of white matter organization in healthy brains. Specifically, brain areas with strong structural connectivity show decreases in functional connectivity in premanifest Huntington's disease relative to controls, while regions with weak structural connectivity show increases in functional connectivity. Furthermore, we identify a pattern of dissociation in the strongest functional connections between anterior and posterior brain regions such that anterior functional connectivity increases in strength in premanifest Huntington's disease, while posterior functional connectivity decreases. Our findings demonstrate that organizational principles of white matter underlie changes in functional connectivity in premanifest Huntington's disease. Furthermore, we demonstrate functional antero-posterior dissociation that is in keeping with the caudo-rostral gradient of striatal pathology in HD.

  8. SitesIdentify: a protein functional site prediction tool

    PubMed Central

    2009-01-01

    Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify), based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/ PMID:19922660

  9. Controlled test for predictive power of Lyapunov exponents: their inability to predict epileptic seizures.

    PubMed

    Lai, Ying-Cheng; Harrison, Mary Ann F; Frei, Mark G; Osorio, Ivan

    2004-09-01

    Lyapunov exponents are a set of fundamental dynamical invariants characterizing a system's sensitive dependence on initial conditions. For more than a decade, it has been claimed that the exponents computed from electroencephalogram (EEG) or electrocorticogram (ECoG) signals can be used for prediction of epileptic seizures minutes or even tens of minutes in advance. The purpose of this paper is to examine the predictive power of Lyapunov exponents. Three approaches are employed. (1) We present qualitative arguments suggesting that the Lyapunov exponents generally are not useful for seizure prediction. (2) We construct a two-dimensional, nonstationary chaotic map with a parameter slowly varying in a range containing a crisis, and test whether this critical event can be predicted by monitoring the evolution of finite-time Lyapunov exponents. This can thus be regarded as a "control test" for the claimed predictive power of the exponents for seizure. We find that two major obstacles arise in this application: statistical fluctuations of the Lyapunov exponents due to finite time computation and noise from the time series. We show that increasing the amount of data in a moving window will not improve the exponents' detective power for characteristic system changes, and that the presence of small noise can ruin completely the predictive power of the exponents. (3) We report negative results obtained from ECoG signals recorded from patients with epilepsy. All these indicate firmly that, the use of Lyapunov exponents for seizure prediction is practically impossible as the brain dynamical system generating the ECoG signals is more complicated than low-dimensional chaotic systems, and is noisy. Copyright 2004 American Institute of Physics

  10. Controlled test for predictive power of Lyapunov exponents: Their inability to predict epileptic seizures

    NASA Astrophysics Data System (ADS)

    Lai, Ying-Cheng; Harrison, Mary Ann F.; Frei, Mark G.; Osorio, Ivan

    2004-09-01

    Lyapunov exponents are a set of fundamental dynamical invariants characterizing a system's sensitive dependence on initial conditions. For more than a decade, it has been claimed that the exponents computed from electroencephalogram (EEG) or electrocorticogram (ECoG) signals can be used for prediction of epileptic seizures minutes or even tens of minutes in advance. The purpose of this paper is to examine the predictive power of Lyapunov exponents. Three approaches are employed. (1) We present qualitative arguments suggesting that the Lyapunov exponents generally are not useful for seizure prediction. (2) We construct a two-dimensional, nonstationary chaotic map with a parameter slowly varying in a range containing a crisis, and test whether this critical event can be predicted by monitoring the evolution of finite-time Lyapunov exponents. This can thus be regarded as a "control test" for the claimed predictive power of the exponents for seizure. We find that two major obstacles arise in this application: statistical fluctuations of the Lyapunov exponents due to finite time computation and noise from the time series. We show that increasing the amount of data in a moving window will not improve the exponents' detective power for characteristic system changes, and that the presence of small noise can ruin completely the predictive power of the exponents. (3) We report negative results obtained from ECoG signals recorded from patients with epilepsy. All these indicate firmly that, the use of Lyapunov exponents for seizure prediction is practically impossible as the brain dynamical system generating the ECoG signals is more complicated than low-dimensional chaotic systems, and is noisy.

  11. Plasma metabolite levels predict bird growth rates: A field test of model predictive ability.

    PubMed

    Albano, Noelia; Masero, José A; Villegas, Auxiliadora; Abad-Gómez, José María; Sánchez-Guzmán, Juan M

    2011-09-01

    Bird growth rates are usually derived from nonlinear relationships between age and some morphological structure, but this procedure may be limited by several factors. To date, nothing is known about the capacity of plasma metabolite profiling to predict chick growth rates. Based on laboratory-trials, we here develop predictive logistic models of body mass, and tarsus and wing length growth rates in Gull-billed Tern Gelochelidon nilotica chicks from measurements of plasma metabolite levels at different developmental stages. The predictive model obtained during the fastest growth period (at the age of 12 days) explained 65-68% of the chicks' growth rates, with fasting triglyceride level explaining most of the variation in growth rate. At the end of pre-fledging period, β-hydroxybutyrate level was also a good predictor of growth rates. Finally, we carried out a field test to check the predictive capacity of the models in two colonies of wild Gull-billed Tern, comparing field-measured and model-predicted growth rates between groups. Both, measured and predicted growth rates, matched statistically. Plasma metabolite levels can thus be applied in comparative studies of chick growth rates when semi-precocial birds can be captured only once.

  12. Improved prediction of accessible surface area results in efficient energy function application.

    PubMed

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

    2015-09-07

    An accurate prediction of real value accessible surface area (ASA) from protein sequence alone has wide application in the field of bioinformatics and computational biology. ASA has been helpful in understanding the 3-dimensional structure and function of a protein, acting as high impact feature in secondary structure prediction, disorder prediction, binding region identification and fold recognition applications. To enhance and support broad applications of ASA, we have made an attempt to improve the prediction accuracy of absolute accessible surface area by developing a new predictor paradigm, namely REGAd(3)p, for real value prediction through classical Exact Regression with Regularization and polynomial kernel of degree 3 which was further optimized using Genetic Algorithm. ASA assisting effective energy function, motivated us to enhance the accuracy of predicted ASA for better energy function application. Our ASA prediction paradigm was trained and tested using a new benchmark dataset, proposed in this work, consisting of 1001 and 298 protein chains, respectively. We achieved maximum Pearson Correlation Coefficient (PCC) of 0.76 and 1.45% improved PCC when compared with existing top performing predictor, SPINE-X, in ASA prediction on independent test set. Furthermore, we modeled the error between actual and predicted ASA in terms of energy and combined this energy linearly with the energy function 3DIGARS which resulted in an effective energy function, namely 3DIGARS2.0, outperforming all the state-of-the-art energy functions. Based on Rosetta and Tasser decoy-sets 3DIGARS2.0 resulted 80.78%, 73.77%, 141.24%, 16.52%, and 32.32% improvement over DFIRE, RWplus, dDFIRE, GOAP and 3DIGARS respectively.

  13. X-29 flight - Acid test for design predictions

    NASA Technical Reports Server (NTRS)

    Putnam, T. W.; Petersen, K. L.; Ishmael, S. D.; Sefic, W. J.

    1986-01-01

    The X-29 flight test data are being disseminated to interested industrial and military users as fast as it becomes available. The aircraft is extensively instrumented with accelerometers and pressure sensors and optical sensors for measuring wing deflection. The thoroughness of preflight preparations permitted a rapid advance through initial test checkpoints, which have both confirmed many predictions and revealed several discrepancies. The flight envelope had been expanded to Mach 1.1 and an altitude of 40,000 ft by December 1985. Notably, the X-29 has provided in-flight data which could not be faithfully depicted in a simulator, e.g., flare procedures during landing, and has shown that the stability adjustments, although adequate for controlling the aircraft, are not rapid enough to offer a satisfactory margin of harmony. The tests are now being performed in the transonic regime, where supercritical airfoil and forward swept wing drag reduction become significant factors.

  14. Which Neuropsychological Tests Predict Progression to Alzheimer’s Disease in Hispanics?

    PubMed Central

    Weissberger, Gali H.; Salmon, David P.; Bondi, Mark W.; Gollan, Tamar H.

    2013-01-01

    Objective To investigate which neuropsychological tests predict eventual progression to Alzheimer’s disease (AD) in both Hispanic and non-Hispanic individuals. Although our approach was exploratory, we predicted that tests that underestimate cognitive ability in healthy aging Hispanics might not be sensitive to future cognitive decline in this cultural group. Method We compared first-year data of 22 older adults (11 Hispanic) who were diagnosed as cognitively normal but eventually developed AD (decliners), to 60 age- and education-matched controls (27 Hispanic) who remained cognitively normal. To identify tests that may be culturally biased in our sample, we compared Hispanic with non-Hispanic controls on all tests and asked which tests were sensitive to future decline in each cultural group. Results Compared to age-, education-, and gender-matched non-Hispanic controls, Hispanic controls obtained lower scores on tests of language, executive function, and some measures of global cognition. Consistent with our predictions, some tests identified non-Hispanic, but not Hispanic, decliners (vocabulary, semantic fluency). Contrary to our predictions, a number of tests on which Hispanics obtained lower scores than non-Hispanics nevertheless predicted eventual progression to AD in both cultural groups (e.g., Boston Naming Test [BNT], Trails A and B). Conclusions Cross-cultural variation in test sensitivity to decline may reflect greater resistance of medium difficulty items to decline and bilingual advantages that initially protect Hispanics against some aspects of cognitive decline commonly observed in non-Hispanics with preclinical AD. These findings highlight a need for further consideration of cross-cultural differences in neuropsychological test performance and development of culturally unbiased measures. PMID:23688216

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

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2004-04-02

    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.

  18. Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

    PubMed

    Martelotto, Luciano G; Ng, Charlotte Ky; De Filippo, Maria R; Zhang, Yan; Piscuoglio, Salvatore; Lim, Raymond S; Shen, Ronglai; Norton, Larry; Reis-Filho, Jorge S; Weigelt, Britta

    2014-10-28

    Massively parallel sequencing studies have led to the identification of a large number of mutations present in a minority of cancers of a given site. Hence, methods to identify the likely pathogenic mutations that are worth exploring experimentally and clinically are required. We sought to compare the performance of 15 mutation effect prediction algorithms and their agreement. As a hypothesis-generating aim, we sought to define whether combinations of prediction algorithms would improve the functional effect predictions of specific mutations. Literature and database mining of single nucleotide variants (SNVs) affecting 15 cancer genes was performed to identify mutations supported by functional evidence or hereditary disease association to be classified either as non-neutral (n = 849) or neutral (n = 140) with respect to their impact on protein function. These SNVs were employed to test the performance of 15 mutation effect prediction algorithms. The accuracy of the prediction algorithms varies considerably. Although all algorithms perform consistently well in terms of positive predictive value, their negative predictive value varies substantially. Cancer-specific mutation effect predictors display no-to-almost perfect agreement in their predictions of these SNVs, whereas the non-cancer-specific predictors showed no-to-moderate agreement. Combinations of predictors modestly improve accuracy and significantly improve negative predictive values. The information provided by mutation effect predictors is not equivalent. No algorithm is able to predict sufficiently accurately SNVs that should be taken forward for experimental or clinical testing. Combining algorithms aggregates orthogonal information and may result in improvements in the negative predictive value of mutation effect predictions.

  19. 3D-Fun: predicting enzyme function from structure.

    PubMed

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

    2008-07-01

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

  20. Lung function indices for predicting mortality in COPD

    PubMed Central

    Boutou, Afroditi K.; Shrikrishna, Dinesh; Tanner, Rebecca J.; Smith, Cayley; Kelly, Julia L.; Ward, Simon P.; Polkey, Michael I.; Hopkinson, Nicholas S.

    2013-01-01

    Chronic obstructive pulmonary disease (COPD) is characterised by high morbidity and mortality. It remains unknown which aspect of lung function carries the most prognostic information and if simple spirometry is sufficient. Survival was assessed in COPD outpatients whose data had been added prospectively to a clinical audit database from the point of first full lung function testing including spirometry, lung volumes, gas transfer and arterial blood gases. Variables univariately associated with survival were entered into a multivariate Cox proportional hazard model. 604 patients were included (mean±sd age 61.9±9.7 years; forced expiratory volume in 1 s 37±18.1% predicted; 62.9% males); 229 (37.9%) died during a median follow-up of 83 months. Median survival was 91.9 (95% CI 80.8–103) months with survival rates at 3 and 5 years 0.83 and 0.66, respectively. Carbon monoxide transfer factor % pred quartiles (best quartile (>51%): HR 0.33, 95% CI 0.172–0.639; and second quartile (51–37.3%): HR 0.52, 95% CI 0.322–0.825; versus lowest quartile (<27.9%)), age (HR 1.04, 95% CI 1.02–1.06) and arterial oxygen partial pressure (HR 0.85, 95% CI 0.77–0.94) were the only parameters independently associated with mortality. Measurement of gas transfer provides additional prognostic information compared to spirometry in patients under hospital follow-up and could be considered routinely. PMID:23349449

  1. Beyond genotype: serotonin transporter epigenetic modification predicts human brain function.

    PubMed

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

    2014-09-01

    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.

  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. 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.

  4. 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.

  5. 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.

  6. Predictive value and construct validity of the work functioning screener-healthcare (WFS-H)

    PubMed Central

    Boezeman, Edwin J.; Nieuwenhuijsen, Karen; Sluiter, Judith K.

    2016-01-01

    Objectives: To test the predictive value and convergent construct validity of a 6-item work functioning screener (WFS-H). Methods: Healthcare workers (249 nurses) completed a questionnaire containing the work functioning screener (WFS-H) and a work functioning instrument (NWFQ) measuring the following: cognitive aspects of task execution and general incidents, avoidance behavior, conflicts and irritation with colleagues, impaired contact with patients and their family, and level of energy and motivation. Productivity and mental health were also measured. Negative and positive predictive values, AUC values, and sensitivity and specificity were calculated to examine the predictive value of the screener. Correlation analysis was used to examine the construct validity. Results: The screener had good predictive value, since the results showed that a negative screener score is a strong indicator of work functioning not hindered by mental health problems (negative predictive values: 94%-98%; positive predictive values: 21%-36%; AUC:.64-.82; sensitivity: 42%-76%; and specificity 85%-87%). The screener has good construct validity due to moderate, but significant (p<.001), associations with productivity (r=.51), mental health (r=.48), and distress (r=.47). Conclusions: The screener (WFS-H) had good predictive value and good construct validity. Its score offers occupational health professionals a helpful preliminary insight into the work functioning of healthcare workers. PMID:27010085

  7. Predicting enzymatic function from global binding site descriptors.

    PubMed

    Volkamer, Andrea; Kuhn, Daniel; Rippmann, Friedrich; Rarey, Matthias

    2013-03-01

    Due to the rising number of solved protein structures, computer-based techniques for automatic protein functional annotation and classification into families are of high scientific interest. DoGSiteScorer automatically calculates global descriptors for self-predicted pockets based on the 3D structure of a protein. Protein function predictors on three levels with increasing granularity are built by use of a support vector machine (SVM), based on descriptors of 26632 pockets from enzymes with known structure and enzyme classification. The SVM models represent a generalization of the available descriptor space for each enzyme class, subclass, and substrate-specific sub-subclass. Cross-validation studies show accuracies of 68.2% for predicting the correct main class and accuracies between 62.8% and 80.9% for the six subclasses. Substrate-specific recall rates for a kinase subset are 53.8%. Furthermore, application studies show the ability of the method for predicting the function of unknown proteins and gaining valuable information for the function prediction field. Copyright © 2012 Wiley Periodicals, Inc.

  8. 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

  9. STRING: a database of predicted functional associations between proteins.

    PubMed

    von Mering, Christian; Huynen, Martijn; Jaeggi, Daniel; Schmidt, Steffen; Bork, Peer; Snel, Berend

    2003-01-01

    Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar species coverage, are often located in close proximity on the genome (in prokaryotes), and tend to be involved in gene-fusion events. The database STRING is a precomputed global resource for the exploration and analysis of these associations. Since the three types of evidence differ conceptually, and the number of predicted interactions is very large, it is essential to be able to assess and compare the significance of individual predictions. Thus, STRING contains a unique scoring-framework based on benchmarks of the different types of associations against a common reference set, integrated in a single confidence score per prediction. The graphical representation of the network of inferred, weighted protein interactions provides a high-level view of functional linkage, facilitating the analysis of modularity in biological processes. STRING is updated continuously, and currently contains 261 033 orthologs in 89 fully sequenced genomes. The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/.

  10. 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.

  11. 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.

  12. firestar—advances in the prediction of functionally important residues

    PubMed Central

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

    2011-01-01

    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

  13. 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.

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

    PubMed

    Hoehn, Amanda M; Mullenbach, Megan J; Fountaine, Charles J

    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.

  15. The predictive value of the height ratio and thyromental distance: four predictive tests for difficult laryngoscopy.

    PubMed

    Krobbuaban, Banjong; Diregpoke, Siriwan; Kumkeaw, Sujarit; Tanomsat, Malin

    2005-11-01

    Preoperative evaluation of anatomical landmarks and clinical factors help identify potentially difficult laryngoscopies; however, predictive reliability is unclear. Because the ratio of height to thyromental distance (RHTMD) has a demonstrably better predictive value than the thyromental distance (TMD), we evaluated the predictive value and odds ratios of RHTMD versus mouth opening, TMD, neck movement, and oropharyngeal view (modified Mallampati). We collected data on 550 consecutive patients scheduled for elective-surgery general anesthesia requiring endotracheal intubation and then assessed all five factors before surgery. An experienced anesthesiologist, not apprised of the recorded preoperative airway assessment, performed the laryngoscopy and grading (as per Cormack and Lehane's classification). Difficult laryngoscopy (Grade 3 or 4) occurred in 69 patients (12.5%). RHTMD had a higher sensitivity, positive predictive value, and fewer false negatives than the other variables tested. In the multivariate analysis, three criteria were found independent for difficult laryngoscopy (neck movement < or =80 degrees; Mallampati Class 3 or 4, and RHTMD > or =23.5). The odds ratio (95% confidence interval) of the RHTMD, Mallampati class, and neck movement were 6.72 (3.29-13.72), 2.96 (1.63-5.35), and 2.73 (1.14-6.51), respectively. The odds ratio for RHTMD was the largest and thus may prove a useful screening test for difficult laryngoscopy.

  16. Predicting and testing continental vertical motion histories since the Paleozoic

    NASA Astrophysics Data System (ADS)

    Zhang, N.; Zhong, S.; Flowers, R. M.

    2011-12-01

    Dynamic topography at the Earth's surface caused by mantle convection can affect a range of geophysical and geological observations including bathymetry, sea-level change, continental flooding, sedimentation and erosion. These observations provide important constraints on and test of mantle dynamic models. Based on global mantle convection models coupled with the surface plate motion history, we compute dynamic topography and its history for the last 400 Ma associated with Pangea assembly and breakup, with particular focus on continental cratonic regions. We propose that burial-unroofing histories of continental cratons inferred from thermochronology data can be used as a new diagnostic to test dynamic topography and mantle dynamic models. Our models show that there are currently two broad dynamic topography highs in the Pacific and Africa for the present-day Earth that are associated with the broad, warm structures (i.e., superplumes) in the deep mantle, consistent with previous proposals of dynamical support for the Pacific and African superswells. Our models reveal that Pangea assembly and breakup, by affecting subduction and mantle upwelling processes, have significant effects on continental vertical motions. Our models predict that the Slave craton in North America subsides before Pangea assembly at 330 Ma but uplifts significantly from 330 Ma to 240 Ma in response to pre-Pangea subduction and post-assembly mantle warming. The Kaapvaal craton of Africa is predicted to undergo uplift from ~180 Ma to 90 Ma after Pangea breakup, but its dynamic topography remains stable for the last 90 Ma. The predicted histories of elevation change for the Slave and Kaapvaal cratons compare well with the burial-unroofing histories inferred from thermochronology studies, thus supporting our dynamic models including the development of the African superplume mantle structure. The vertical motion histories for other cratons can provide further tests and constraints on our mantle

  17. Predicting and testing continental vertical motion histories since the Paleozoic

    NASA Astrophysics Data System (ADS)

    Zhang, Nan; Zhong, Shijie; Flowers, Rebecca M.

    2012-02-01

    Dynamic topography at the Earth's surface caused by mantle convection can affect a range of geophysical and geological observations including bathymetry, sea-level change, continental flooding, sedimentation and erosion. These observations provide important constraints on and test of mantle dynamic models. Based on global mantle convection models coupled with the surface plate motion history, we compute dynamic topography and its history for the last 400 Ma associated with Pangea assembly and breakup, with particular focus on cratonic regions. We propose that burial-unroofing histories of cratons inferred from thermochronology data can be used as a new diagnostic to test dynamic topography and mantle dynamic models. Our models show that there are currently two broad dynamic topography highs in the Pacific and Africa for the present-day Earth that are associated with the broad, warm structures (i.e., superplumes) in the deep mantle, consistent with previous proposals of dynamical support for the Pacific and African superswells. Our models reveal that Pangea assembly and breakup, by affecting subduction and mantle upwelling processes, have significant effects on continental vertical motions. Our models predict that the Slave craton in North America subsides before Pangea assembly at 330 Ma but uplifts significantly from 330 Ma to 240 Ma in response to pre-Pangea subduction and post-assembly mantle warming. The Kaapvaal craton of Africa is predicted to undergo uplift from ~180 Ma to 90 Ma after Pangea breakup, but its dynamic topography remains stable for the last 90 Ma. The predicted histories of elevation change for the Slave and Kaapvaal cratons compare well with the burial-unroofing histories inferred from thermochronology studies, thus supporting our dynamic models including the development of the African superplume mantle structure. The vertical motion histories for other cratons can provide further tests of and constraints on our mantle dynamic models.

  18. Fine-motor skills testing and prediction of endovascular performance.

    PubMed

    Bech, Bo; Lönn, Lars; Schroeder, Torben V; Ringsted, Charlotte

    2013-12-01

    Performing endovascular procedures requires good control of fine-motor digital movements and hand-eye coordination. Objective assessment of such skills is difficult. Trainees acquire control of catheter/wire movements at various paces. However, little is known to what extent talent plays for novice candidates at entry to practice. To study the association between performance in a novel aptitude test of fine-motor skills and performance in simulated procedures. The test was based on manual course-tracking using a proprietary hand-operated roller-bar device coupled to a personal computer with monitor view rotation. A total of 40 test repetitions were conducted separately with each hand. Test scores were correlated with simulator performance. Group A (n = 14), clinicians with various levels of endovascular experience, performed a simulated procedure of contralateral iliac artery stenting. Group B (n = 19), medical students, performed 10 repetitions of crossing a challenging aortic bifurcation in a simulator. The test score differed markedly between the individuals in both groups, in particular with the non-dominant hand. Group A: the test score with the non-dominant hand correlated significantly with simulator performance assessed with the global rating scale SAVE (R = -0.69, P = 0.007). There was no association observed from performances with the dominant hand. Group B: there was no significant association between the test score and endovascular skills acquisition neither with the dominant nor with the non-dominant hand. Clinicians with increasing levels of endovascular technical experience had developed good fine-motor control of the non-dominant hand, in particular, that was associated with good procedural performance in the simulator. The aptitude test did not predict endovascular skills acquisition among medical students, thus, cannot be suggested for selection of novice candidates. Procedural experience and practice probably supplant the influence of innate

  19. PRISM offers a comprehensive genomic approach to transcription factor function prediction.

    PubMed

    Wenger, Aaron M; Clarke, Shoa L; Guturu, Harendra; Chen, Jenny; Schaar, Bruce T; McLean, Cory Y; Bejerano, Gill

    2013-05-01

    The human genome encodes 1500-2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.

  20. PRISM offers a comprehensive genomic approach to transcription factor function prediction

    PubMed Central

    Wenger, Aaron M.; Clarke, Shoa L.; Guturu, Harendra; Chen, Jenny; Schaar, Bruce T.; McLean, Cory Y.; Bejerano, Gill

    2013-01-01

    The human genome encodes 1500–2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells. PMID:23382538

  1. Tests of Substorm Models' Predictions Using ISTP Observations

    NASA Technical Reports Server (NTRS)

    Sanchez, Ennio R.

    1998-01-01

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

  2. IR Materials Rain Damage Prediction And Tests Results

    NASA Astrophysics Data System (ADS)

    Cassaing, Joseph J.; Deom, Alain A.; Bouveret, Andre M.; Balageas, Daniel L.

    1989-09-01

    A comparison between G.S. Springer's theory, that predicts rain optical and rain mass degradations for different kinds of infrared materials, and the experimental results obtained by ONERA on the SAAB rain rotating arm on IR homogeneous samples is presented. The agreement between theory and experiment is rather poor. A very simple correlation between optical degradation and V, C, p (respectively : droplet impact velocity, longitudinal wave velocity and density of infrared materials) is proposed, which is in good agreement with all data obtained in the range of 200 to 300 m/s for the 9 tested materials.

  3. Predicting protein dynamic binding capacity from batch adsorption tests.

    PubMed

    Carta, Giorgio

    2012-10-01

    The dynamic binding capacity (DBC) and its dependence on residence time influence the design and productivity of adsorption columns used in protein capture applications. This paper offers a very simple approach to predict the DBC of an adsorption column based on a measurement of the equilibrium binding capacity (EBC) and of the time needed to achieve one-half of the EBC in a batch adsorption test. The approach is based on a mass transfer kinetics model that assumes pore diffusion with a rectangular isotherm; however, the same approach is also shown to work for other systems where solute transport inside the particle occurs through other transport mechanisms.

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

    PubMed

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

    2011-01-01

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

  5. In vitro cytotoxicity testing for prediction of acute human toxicity.

    PubMed

    Barile, F A; Dierickx, P J; Kristen, U

    1994-06-01

    This study was designed to compare the cytotoxic concentrations of chemicals, determined with three independent in vitro cytotoxicity testing protocols, with each other and with established animal LD50 values, and against human toxic concentrations for the same chemicals. Ultimately, these comparisons allow us to evaluate the potential of in vitro cell culture methods for the ability to screen a variety of chemicals for prediction of human toxicity. Each laboratory independently tested 50 chemicals with known human lethal plasma concentrations and LD50 values. Two of the methods used monolayer cell cultures to measure the incorporation of radiolabeled amino acids into newly synthesized proteins and cellular protein content, while the third technique used the pollen tube growth test. The latter is based on the photometric quantification of pollen tube mass production in suspension culture. Experiments were performed in the absence or presence of increasing doses of the test chemical, during an 18- to 24-h incubation. Inhibitory concentrations were extrapolated from concentration-effect curves after linear regression analysis. Comparison of the cytotoxic concentrations confirms previous independent findings that the experimental IC50 values are more accurate predictors of human toxicity than equivalent toxic blood concentrations (HETC values) derived from rodent LD50s. In addition, there were no conclusive statistical differences among the methods. It is anticipated that, together, these procedures can be used as a battery of tests to supplement or replace currently used animal protocols for human risk assessment.

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

    PubMed

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

    2015-12-01

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

  7. 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 integrate 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.

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

    SciTech Connect

    Collin, Blaise P.

    2014-09-01

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

  9. Structure-based Methods for Computational Protein Functional Site Prediction

    PubMed Central

    Dukka, B KC

    2013-01-01

    Due to the advent of high throughput sequencing techniques and structural genomic projects, the number of gene and protein sequences has been ever increasing. Computational methods to annotate these genes and proteins are even more indispensable. Proteins are important macromolecules and study of the function of proteins is an important problem in structural bioinformatics. This paper discusses a number of methods to predict protein functional site especially focusing on protein ligand binding site prediction. Initially, a short overview is presented on recent advances in methods for selection of homologous sequences. Furthermore, a few recent structural based approaches and sequence-and-structure based approaches for protein functional sites are discussed in details. PMID:24688745

  10. Protein Function Prediction Using Deep Restricted Boltzmann Machines

    PubMed Central

    Zou, Xianchun; Wang, Guijun

    2017-01-01

    Accurately annotating biological functions of proteins is one of the key tasks in the postgenome era. Many machine learning based methods have been applied to predict functional annotations of proteins, but this task is rarely solved by deep learning techniques. Deep learning techniques recently have been successfully applied to a wide range of problems, such as video, images, and nature language processing. Inspired by these successful applications, we investigate deep restricted Boltzmann machines (DRBM), a representative deep learning technique, to predict the missing functional annotations of partially annotated proteins. Experimental results on Homo sapiens, Saccharomyces cerevisiae, Mus musculus, and Drosophila show that DRBM achieves better performance than other related methods across different evaluation metrics, and it also runs faster than these comparing methods. PMID:28744460

  11. 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.

  12. Pain on Functional Movement Screen Tests and Injury Risk.

    PubMed

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

    2015-11-01

    The Functional Movement Screen (FMS) is a tool intended to evaluate limitations or asymmetries of movement to detect individuals at risk for exercise- and sports-related injury. The purpose was to determine the association and predictive value of specific FMS tests with injury risk in physically active men. Soldiers aged 18-57 years completed the FMS (n = 2,476). Demographic and fitness data were collected by survey. Medical record data for any, overuse, and traumatic injury 6 months after the assessment were obtained. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value were calculated along with receiver operator characteristics to determine area under the curve (AUC). Risks, risk ratios, odds ratios (ORs), and 95% confidence intervals were calculated to assess injury risks. Multivariate logistic regression identified that pain on 5 of the 7 tests was associated with greater risk for any injury (OR = 1.50-3.51): deep squat, hurdle step, in-line lunge, trunk stability push-up, and rotary stability. However, FMS registered low sensitivity, PPV, and AUC for all 7 tests for the 3 injury types (2-24% sensitivity, 16-74% PPV, and 50-58% AUC). Although the presence of pain was associated with a higher risk of injury on 5 tests, a low sensitivity, PPV, and AUC were displayed. Therefore, caution is advised when implementing the FMS as a screening tool in an Army or similarly active population as it could lead to prevention and treatment resources being directed toward individuals who are not at greater risk for injury.

  13. Testing Visual Functions in Patients with Visual Prostheses

    NASA Astrophysics Data System (ADS)

    Wilke, Robert; Bach, Michael; Wilhelm, Barbara; Durst, Wilhelm; Trauzettel-Klosinski, Susanne; Zrenner, Eberhart

    A number of different technical devices for restoring vision in blind patients have been proposed to date. They employ different strategies for the acquisition of optical information, image processing, and electrical stimulation. Devices with external cameras or with integrated components for light detection have been developed and are designed to stimulate such different sites as the retina, optic nerve, and cortex. First clinical trials for these devices are being planned or already underway. As vision with these artificial vision devices (AVDs) may differ considerably from natural vision and as it may not be possible to predict visual functions provided by such devices on the basis of technical specifications alone, novel test strategies are needed to comprehensively describe visual performance. We propose a battery of tests for standardized well-controlled investigations in these patients that allow for objective assessment of efficacy of these devices.

  14. A review of protein function prediction under machine learning perspective.

    PubMed

    Bernardes, Juliana S; Pedreira, Carlos E

    2013-08-01

    Protein function prediction is one of the most challenging problems in the post-genomic era. The number of newly identified proteins has been exponentially increasing with the advances of the high-throughput techniques. However, the functional characterization of these new proteins was not incremented in the same proportion. To fill this gap, a large number of computational methods have been proposed in the literature. Early approaches have explored homology relationships to associate known functions to the newly discovered proteins. Nevertheless, these approaches tend to fail when a new protein is considerably different (divergent) from previously known ones. Accordingly, more accurate approaches, that use expressive data representation and explore sophisticate computational techniques are required. Regarding these points, this review provides a comprehensible description of machine learning approaches that are currently applied to protein function prediction problems. We start by defining several problems enrolled in understanding protein function aspects, and describing how machine learning can be applied to these problems. We aim to expose, in a systematical framework, the role of these techniques in protein function inference, sometimes difficult to follow up due to the rapid evolvement of the field. With this purpose in mind, we highlight the most representative contributions, the recent advancements, and provide an insightful categorization and classification of machine learning methods in functional proteomics.

  15. Automated protein function prediction--the genomic challenge.

    PubMed

    Friedberg, Iddo

    2006-09-01

    Overwhelmed with genomic data, biologists are facing the first big post-genomic question--what do all genes do? First, not only is the volume of pure sequence and structure data growing, but its diversity is growing as well, leading to a disproportionate growth in the number of uncharacterized gene products. Consequently, established methods of gene and protein annotation, such as homology-based transfer, are annotating less data and in many cases are amplifying existing erroneous annotation. Second, there is a need for a functional annotation which is standardized and machine readable so that function prediction programs could be incorporated into larger workflows. This is problematic due to the subjective and contextual definition of protein function. Third, there is a need to assess the quality of function predictors. Again, the subjectivity of the term 'function' and the various aspects of biological function make this a challenging effort. This article briefly outlines the history of automated protein function prediction and surveys the latest innovations in all three topics.

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

    NASA Astrophysics Data System (ADS)

    Franklin, Oskar

    2016-04-01

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

  17. 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.

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

    PubMed

    Huang, Sheng-You; Zou, Xiaoqin

    2006-11-30

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

  20. Developmental Delays in Executive Function from 3 to 5 Years of Age Predict Kindergarten Academic Readiness

    ERIC Educational Resources Information Center

    Willoughby, Michael T.; Magnus, Brooke; Vernon-Feagans, Lynne; Blair, Clancy B.

    2017-01-01

    Substantial evidence has established that individual differences in executive function (EF) in early childhood are uniquely predictive of children's academic readiness at school entry. The current study tested whether growth trajectories of EF across the early childhood period could be used to identify a subset of children who were at pronounced…

  1. 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…

  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…

  3. 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.

  4. Predicting protein function and other biomedical characteristics with heterogeneous ensembles

    PubMed Central

    Whalen, Sean; Pandey, Om Prakash

    2015-01-01

    Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the variables and measurements used for prediction, as well as a lack of consensus regarding the ideal predictor for specific problems. In such scenarios, a powerful approach to improving prediction performance is to construct heterogeneous ensemble predictors that combine the output of diverse individual predictors that capture complementary aspects of the problems and/or datasets. In this paper, we demonstrate the potential of such heterogeneous ensembles, derived from stacking and ensemble selection methods, for addressing PFP and other similar biomedical prediction problems. Deeper analysis of these results shows that the superior predictive ability of these methods, especially stacking, can be attributed to their attention to the following aspects of the ensemble learning process: (i) better balance of diversity and performance, (ii) more effective calibration of outputs and (iii) more robust incorporation of additional base predictors. Finally, to make the effective application of heterogeneous ensembles to large complex datasets (big data) feasible, we present DataSink, a distributed ensemble learning framework, and demonstrate its sound scalability using the examined datasets. DataSink is publicly available from https://github.com/shwhalen/datasink. PMID:26342255

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

    PubMed

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

    2015-08-01

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

  6. Consumer preferences for the predictive genetic test for Alzheimer disease.

    PubMed

    Huang, Ming-Yi; Huston, Sally A; Perri, Matthew

    2014-04-01

    The purpose of this study was to assess consumer preferences for predictive genetic testing for Alzheimer disease in the United States. A rating conjoint analysis was conducted using an anonymous online survey distributed by Qualtrics to a general population panel in April 2011 in the United States. The study design included three attributes: Accuracy (40%, 80%, and 100%), Treatment Availability (Cure is available/Drug for symptom relief but no cure), and Anonymity (Anonymous/Not anonymous). A total of 12 scenarios were used to elicit people's preference, assessed by an 11-point scale. The respondents also indicated their highest willingness-to-pay (WTP) for each scenario through open-ended questions. A total of 295 responses were collected over 4 days. The most important attribute for the aggregate model was Accuracy, contributing 64.73% to the preference rating. Treatment Availability and Anonymity contributed 20.72% and 14.59%, respectively, to the preference rating. The median WTP for the highest-rating scenario (Accuracy 100%, a cure is available, test result is anonymous) was $100 (mean = $276). The median WTP for the lowest-rating scenario (40% accuracy, no cure but drugs for symptom relief, not anonymous) was zero (mean = $34). The results of this study highlight attributes people find important when making the hypothetical decision to obtain an AD genetic test. These results should be of interests to policy makers, genetic test developers and health care providers.

  7. Protein function prediction using local 3D templates.

    PubMed

    Laskowski, Roman A; Watson, James D; Thornton, Janet M

    2005-08-19

    The prediction of a protein's function from its 3D structure is becoming more and more important as the worldwide structural genomics initiatives gather pace and continue to solve 3D structures, many of which are of proteins of unknown function. Here, we present a methodology for predicting function from structure that shows great promise. It is based on 3D templates that are defined as specific 3D conformations of small numbers of residues. We use four types of template, covering enzyme active sites, ligand-binding residues, DNA-binding residues and reverse templates. The latter are templates generated from the target structure itself and scanned against a representative subset of all known protein structures. Together, the templates provide a fairly thorough coverage of the known structures and ensure that if there is a match to a known structure it is unlikely to be missed. A new scoring scheme provides a highly sensitive means of discriminating between true positive and false positive template matches. In all, the methodology provides a powerful new tool for function prediction to complement those already in use.

  8. Quantitative assessment of protein function prediction from metagenomics shotgun sequences.

    PubMed

    Harrington, E D; Singh, A H; Doerks, T; Letunic, I; von Mering, C; Jensen, L J; Raes, J; Bork, P

    2007-08-28

    To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associated with the well characterized heme biosynthesis operon and a potential transcription factor that might regulate a coupling between fatty acid biosynthesis and degradation. Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families.

  9. Postpartum Sexual Functioning and Its Predicting Factors among Iranian Women

    PubMed Central

    Rezaei, Nazanin; Azadi, Arman; Sayehmiri, Kourosh; Valizadeh, Reza

    2017-01-01

    Background Many women experience sexual dysfunction following childbirth but this has not been well investigated in Iran. The aim of this study was to evaluate women’s sexual function in the postpartum period in Iran. It also sought to determine predicting factors associated with their sexual function. Methods This was a cross-sectional study among 380 postpartum women attending 10 urban health centers in Ilam province in southwestern Iran. Participants were selected using random cluster sampling. Data was collected using the female sexual function index (FSFI) and a checklist of socio-demographic and maternal status for each of the women. Sexual dysfunction was classified according to an FSFI score of ≤ 28. Data were analysed using SPSS version 22. Results The majority of participants (76.3%) had sexual dysfunction. Primiparity (adjusted odds ratio (aOR): 1.78 (95% Confidence Interval (CI): 1.11, 2.94); P = 0.006) and exclusive breastfeeding (aOR: 2.47 (95% CI: 1.21, 5.03); P = 0.012) were associated with increased odds of experiencing sexual dysfunction in the postpartum period. Other factors such as age, type of delivery, education, time since delivery and family income did not predict women’s postpartum sexual function. Conclusion This study confirmed findings of previous studies on factors that may have an adverse effect on new mothers’ sexual function in the postpartum period. However the effect of type of delivery on postpartum sexual function remains unclear. PMID:28381932

  10. Incremental fuzzy mining of gene expression data for gene function prediction.

    PubMed

    Ma, Patrick C H; Chan, Keith C C

    2011-05-01

    Due to the complexity of the underlying biological processes, gene expression data obtained from DNA microarray technologies are typically noisy and have very high dimensionality and these make the mining of such data for gene function prediction very difficult. To tackle these difficulties, we propose to use an incremental fuzzy mining technique called incremental fuzzy mining (IFM). By transforming quantitative expression values into linguistic terms, such as highly or lowly expressed, IFM can effectively capture heterogeneity in expression data for pattern discovery. It does so using a fuzzy measure to determine if interesting association patterns exist between the linguistic gene expression levels. Based on these patterns, IFM can make accurate gene function predictions and these predictions can be made in such a way that each gene can be allowed to belong to more than one functional class with different degrees of membership. Gene function prediction problem can be formulated both as classification and clustering problems, and IFM can be used either as a classification technique or together with existing clustering algorithms to improve the cluster groupings discovered for greater prediction accuracies. IFM is characterized also by its being an incremental data mining technique so that the discovered patterns can be continually refined based only on newly collected data without the need for retraining using the whole dataset. For performance evaluation, IFM has been tested with real expression datasets for both classification and clustering tasks. Experimental results show that it can effectively uncover hidden patterns for accurate gene function predictions. © 2011 IEEE

  11. Diffusion kernel-based logistic regression models for protein function prediction.

    PubMed

    Lee, Hyunju; Tu, Zhidong; Deng, Minghua; Sun, Fengzhu; Chen, Ting

    2006-01-01

    Assigning functions to unknown proteins is one of the most important problems in proteomics. Several approaches have used protein-protein interaction data to predict protein functions. We previously developed a Markov random field (MRF) based method to infer a protein's functions using protein-protein interaction data and the functional annotations of its protein interaction partners. In the original model, only direct interactions were considered and each function was considered separately. In this study, we develop a new model which extends direct interactions to all neighboring proteins, and one function to multiple functions. The goal is to understand a protein's function based on information on all the neighboring proteins in the interaction network. We first developed a novel kernel logistic regression (KLR) method based on diffusion kernels for protein interaction networks. The diffusion kernels provide means to incorporate all neighbors of proteins in the network. Second, we identified a set of functions that are highly correlated with the function of interest, referred to as the correlated functions, using the chi-square test. Third, the correlated functions were incorporated into our new KLR model. Fourth, we extended our model by incorporating multiple biological data sources such as protein domains, protein complexes, and gene expressions by converting them into networks. We showed that the KLR approach of incorporating all protein neighbors significantly improved the accuracy of protein function predictions over the MRF model. The incorporation of multiple data sets also improved prediction accuracy. The prediction accuracy is comparable to another protein function classifier based on the support vector machine (SVM), using a diffusion kernel. The advantages of the KLR model include its simplicity as well as its ability to explore the contribution of neighbors to the functions of proteins of interest.

  12. Effects of Grade Level and Subject on Student Test Score Predictions.

    ERIC Educational Resources Information Center

    Barnett, Jerrold E.; Hixon, Jon E.

    1997-01-01

    Interviews with elementary students before and after tests in three subjects investigated how grade level and subject affected students' ability to predict test scores. Results found a significant grade-subject area interaction for predictions prior to testing. Posttest predictions differed only slightly from pretest. Prediction accuracy was…

  13. 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.

  14. 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…

  15. Ecological validity of the Multiple Errands Test using predictive models of dysexecutive problems in everyday life.

    PubMed

    Cuberos-Urbano, Gustavo; Caracuel, Alfonso; Vilar-López, Raquel; Valls-Serrano, Carlos; Bateman, Andrew; Verdejo-García, Antonio

    2013-01-01

    The"dysexecutive syndrome" is composed of a range of cognitive, emotional, and behavioral deficits that are difficult to evaluate using traditional neuropsychological tests. The Multiple Errands Test (MET) was originally developed to systematize the assessment of the more elusive manifestations of the dysexecutive syndrome. The aims of this study were to examining the reliability of the MET and to investigate the predictive ability of its indices to explain a range of "dysexecutive"-related symptoms in everyday life. Thirty patients with acquired brain injury participated in this study. The MET showed an adequate inter-rater reliability and ecological validity. The main performance indices from the MET were able to significantly predict severity of everyday life executive problems, with different indices predicting particular manifestations of different components of executive functions.

  16. Predictable convergence in hemoglobin function has unpredictable molecular underpinnings.

    PubMed

    Natarajan, Chandrasekhar; Hoffmann, Federico G; Weber, Roy E; Fago, Angela; Witt, Christopher C; Storz, Jay F

    2016-10-21

    To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues. Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history. Mutations that produce an adaptive change in one species may represent precluded possibilities in other species because of differences in genetic background. Copyright © 2016, American Association for the Advancement of Science.

  17. Screening Test Items for Differential Item Functioning

    ERIC Educational Resources Information Center

    Longford, Nicholas T.

    2014-01-01

    A method for medical screening is adapted to differential item functioning (DIF). Its essential elements are explicit declarations of the level of DIF that is acceptable and of the loss function that quantifies the consequences of the two kinds of inappropriate classification of an item. Instead of a single level and a single function, sets of…

  18. Screening Test Items for Differential Item Functioning

    ERIC Educational Resources Information Center

    Longford, Nicholas T.

    2014-01-01

    A method for medical screening is adapted to differential item functioning (DIF). Its essential elements are explicit declarations of the level of DIF that is acceptable and of the loss function that quantifies the consequences of the two kinds of inappropriate classification of an item. Instead of a single level and a single function, sets of…

  19. 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

    2016-01-04

    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.

  20. Predicting the Development of Tuberculosis with the Tuberculin Skin Test and QuantiFERON Testing.

    PubMed

    Altet, Neus; Dominguez, José; Souza-Galvão, Maria-Luiza de; Jiménez-Fuentes, M Ángeles; Milà, Célia; Solsona, Jordi; Soriano-Arandés, Antonio; Latorre, Irene; Lara, Elisa; Cantos, Adela; Ferrer, María Dolores; Orcau, Àngels; Ruiz-Manzano, Juan; Caylà, Joan

    2015-05-01

    The identification of patients with latent tuberculosis infection, who are at higher risk to develop active disease, is an important component of disease control. We aim to compare the usefulness of the QuantiFERON-TB Gold in-tube assay and the tuberculin skin test to predict the development of active tuberculosis during follow-up, using positive and negative predictive values, positive likelihood ratios, and stratified level of risk. The study included contacts of tuberculosis cases diagnosed between 2007 and 2009. All contacts included were from the first circle of exposure. Tuberculin skin test and QuantiFERON test were performed and a chest radiograph was obtained during the contact's study. A total of 1,335 contacts were followed up for 4 years: a smear-positive index case was identified for 937 contacts, of whom 15 developed active tuberculosis and had initially presented with positive tuberculin skin test/QuantiFERON results, a normal chest radiograph, and no symptoms. The positive predictive value was 4% for QuantiFERON and 2% for the tuberculin skin test (when ≥5 mm). The probability of developing active disease was 2.36 times higher with a positive QuantiFERON, and 1.3 times higher with a positive tuberculin skin test. The positive predictive value was 17%, and the positive likelihood ratio was 7.53 for untreated contacts with a positive QuantiFERON. Stratifying according to initial QuantiFERON results showed a 6.36 times higher risk of developing active tuberculosis for patients with a QuantiFERON result greater than or equal to 10 IU/ml. Among bacillus Calmette-Guérin-vaccinated patients, a tuberculin skin test induration greater than or equal to 15 mm correlated better with a positive QuantiFERON. QuantiFERON results were more accurate than tuberculin skin test results in predicting tuberculosis. Although all contacts with QuantiFERON-positive results are at risk of developing tuberculosis, those with a tuberculin skin test induration greater than

  1. 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.

  2. Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins.

    PubMed

    Warden, Charles D; Kim, Seong-Ho; Yi, Soojin V

    2008-02-13

    Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.

  3. [Pulmonary function testing in Japan: present status and new developments].

    PubMed

    Tojo, Naoko

    2012-09-01

    In 2004, the Japanese Respiratory Society issued an initial set of recommendations on the standardized measurement of the most frequently used tests for pulmonary function, i.e., tests to assess slow vital capacity, forced vital capacity, and single-breath carbon monoxide diffusing capacity. This statement has not been updated, and the prediction equations for pulmonary function testing are not fully established. Thus, the guidelines will need to be periodically updated in accordance with new developments in this rapidly evolving field. Nitric oxide (NO) is now recognized as a biological mediator in animals and humans. The human lung produces NO and exhales it in breath. The fractional nitric oxide (NO) concentration in exhaled breath (FE(NO)) can be quantitatively measured by a simple, safe, and noninvasive procedure as a complementary tool for assessing airway inflammation in airway diseases such as asthma. While the measurement of exhaled NO is standardized for clinical use, FE(NO) measurement is not approved or covered under the public health insurance system in Japan.

  4. 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

  5. Ferromagnetic elements by epitaxial growth: A density functional prediction

    NASA Astrophysics Data System (ADS)

    Schönecker, Stephan; Richter, Manuel; Koepernik, Klaus; Eschrig, Helmut

    2012-01-01

    The periodic table contains only six natural elements with a ferromagnetic ground state. For example, the metal uranium, which is magnetically ordered in many compounds, is paramagnetic in all its known elemental bulk phases. Also, the iron-group elements ruthenium and osmium are known to be bulk paramagnets. We predict by means of density functional calculations that epitaxial growth of uranium, ruthenium, or osmium on suitable substrates may allow stabilization of bulklike films with tetragonal structures showing ferromagnetic order.

  6. Bedside tests to predict laryngoscopic difficulty in pediatric patients.

    PubMed

    Mansano, André Marques; Módolo, Norma Sueli Pinheiro; Silva, Leopoldo Muniz da; Ganem, Eliana Maria; Braz, Leandro Gobbo; Knabe, Andrea de Carvalho; Freitas, Fernanda Moreira de

    2016-04-01

    Pediatric airway management is a priority during anesthesia, critical care and emergency medicine. The purpose of this study is to validate bedside tests that predict airway management difficulty in anesthetized children. Children under 12 years of age were recruited in a cross-sectional study to assess the value of some anthropometric measures as predictors of laryngoscopic difficulty. The patients were divided into three groups by age. Weight, height, neck circumference, BMI (body mass index), inter incisors distance thyromental distance, sternomental distance, frontal plane to chin distance (FPCD) and the Mallampati index were determined and were correlated with the CML (Cormack & Lehane classification). The incidence of difficult laryngoscopy (CML 3 or 4) was 3.58%. Factors that were significantly associated with laryngoscopic difficulty included short inter incisors distance, high FPCD, thyromental distance, sternomental distance and the Mallampati index. The FPCD/weight index exhibited a higher area under the ROC curve than any other variable considered. This study confirms that the FPCD and the FPCD/weight ratio are the most consistent predictors of laryngoscopic difficulty in pediatric patients. For patients over 6 months of age, the IID also correlated with laryngoscopic difficulty. For children who were capable of obeying simple orders, the Mallampati test correlated better with laryngoscopic difficulty than did the Mallampati test with phonation. Our results strongly suggest that skilled professionals should perform airway management in children, especially in patients with a high FPCD or a high FPCD/weight ratio. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. 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

  8. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

    PubMed

    Nabieva, Elena; Jim, Kam; Agarwal, Amit; Chazelle, Bernard; Singh, Mona

    2005-06-01

    Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships between proteins, including genetic interactions, knowledge about co-expression and shared evolutionary history. Taken together, these pairwise linkages can be used to build whole-proteome protein interaction maps. We develop a network-flow based algorithm, FunctionalFlow, that exploits the underlying structure of protein interaction maps in order to predict protein function. In cross-validation testing on the yeast proteome, we show that FunctionalFlow has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors. By comparing several methods that use protein interaction maps to predict protein function, we demonstrate that FunctionalFlow performs well because it takes advantage of both network topology and some measure of locality. Finally, we show that performance can be improved substantially as we consider multiple data sources and use them to create weighted interaction networks. http://compbio.cs.princeton.edu/function

  9. Functional testing methods for the antiplatelet effects of aspirin.

    PubMed

    Schrör, Karsten; Huber, Kurt; Hohlfeld, Thomas

    2011-02-01

    At antiplatelet doses of 75-325 mg/day, aspirin irreversibly inhibits the platelet cyclooxygenase (COX)-1-dependent thromboxane A(2) (TXA(2)) formation. This is the pharmacological mode of action of aspirin, and it can be predicted that if aspirin does not inhibit COX-1 sufficiently, patients will not benefit from its antiplatelet effects. A pharmacodynamic failure of aspirin occurs in 1-2% of patients. The vast majority of atherothrombotic events in patients treated with aspirin result from mechanisms that are dependent on residual (non-COX-1-dependent) platelet reactivity. Global tests of platelet activation in vitro may identify patients with high residual platelet reactivity but are not sufficiently specific to test the pharmacological effect of aspirin. A further problem is the absence of standardized normal ranges for many assays and the fact that different equipment measures different signals, which are also influenced by the agonist and the anticoagulant used. Similar considerations apply for the determination of platelet-derived biomarkers such as circulating P-selectin, soluble CD40 ligand and others. The direct measurement of inhibition of thromboxane-forming capacity is the most specific pharmacological assay for aspirin. However, there is no linear correlation between inhibition of TXA(2) formation and inhibition of platelet function. Measurement of urinary levels of the TXB(2) metabolite, 11-dehydro-thromboxane B(2), represents an index of TXA(2) biosynthesis in vivo, but is also sensitive to other cellular sources of TXA(2). One general problem of all assays is the relationship with clinical outcome, which is still unclear. Monitoring aspirin treatment by testing platelet function or measuring biomarkers in clinical practice should not be recommended until a clear relationship for the predictive value of these assays for clinical outcome has been established.

  10. Using compound similarity and functional domain composition for prediction of drug-target interaction networks.

    PubMed

    Chen, Lei; He, Zhi-Song; Huang, Tao; Cai, Yu-Dong

    2010-11-01

    Study of interactions between drugs and target proteins is an essential step in genomic drug discovery. It is very hard to determine the compound-protein interactions or drug-target interactions by experiment alone. As supplementary, effective prediction model using machine learning or data mining methods can provide much help. In this study, a prediction method based on Nearest Neighbor Algorithm and a novel metric, which was obtained by combining compound similarity and functional domain composition, was proposed. The target proteins were divided into the following groups: enzymes, ion channels, G protein-coupled receptors, and nuclear receptors. As a result, four predictors with the optimal parameters were established. The overall prediction accuracies, evaluated by jackknife cross-validation test, for four groups of target proteins are 90.23%, 94.74%, 97.80%, and 97.51%, respectively, indicating that compound similarity and functional domain composition are very effective to predict drug-target interaction networks.

  11. Positive symptoms and duration of illness predict functional laterality and attention modulation in schizophrenia.

    PubMed

    Løberg, E-M; Jørgensen, H A; Green, M F; Rund, B R; Lund, A; Diseth, A; Oie, M; Hugdahl, K

    2006-04-01

    Dichotic listening (DL) performance in schizophrenia, reflecting hemispheric asymmetry and the functional integrity of the left temporal lobe, can vary with clinical characteristics. Previous studies have not taken the co-linearity of clinical variables into account. The aim of the present study was to evaluate the roles of positive symptoms and duration of illness in DL through Structural Equation Modeling (SEM), thus allowing for complex relationships between the variables. We pooled patients from four previous DL studies to create a heterogeneous group of 129 schizophrenic patients, all tested with a consonant-vowel syllables DL procedure that included attentional instructions. A model where positive symptoms predicted a laterality component and duration of illness predicted an attention component in DL was confirmed. Positive symptoms predicted reduced functional laterality, suggesting involvement of left temporal lobe language processing. Duration of illness predicted impaired attention modulation, possibly reflecting the involvement of frontotemporal networks.

  12. 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.

  13. 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.

  14. Functional brain imaging predicts public health campaign success

    PubMed Central

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

    2016-01-01

    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 R2 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. Testing a predictive model of what makes a critical thinker.

    PubMed

    Rapps, J; Riegel, B; Glaser, D

    2001-10-01

    The goal of nursing education is to help individuals become self-determining, independent thinkers. Cognitive development may be the outcome that best characterizes such a thinker. The purpose of this study was to test a model of cognitive development in which four independent variables--knowledge base, critical thinking skills, critical thinking dispositions, and experience--were used to predict cognitive development. Data were analyzed from 232 practicing registered nurses. Three hierarchical levels of cognitive development were examined: dualism, relativism, and commitment. Critical thinking skill was a significant contributor only to the dualistic level of cognitive development. Critical thinking dispositions contributed to all three levels of cognitive development. Experience contributed only to the commitment level. The results of this study suggest that the development of a critical thinker may require time and experience. These findings can be used to examine current policy regarding the criteria used to evaluate nursing education.

  16. 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.

  17. 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.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

    Cole, B L; Maddocks, J D

    1998-11-01

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

  20. Prediction of Lateral Ankle Sprains in Football Players Based on Clinical Tests and Body Mass Index.

    PubMed

    Gribble, Phillip A; Terada, Masafumi; Beard, Megan Q; Kosik, Kyle B; Lepley, Adam S; McCann, Ryan S; Pietrosimone, Brian G; Thomas, Abbey C

    2016-02-01

    The lateral ankle sprain (LAS) is the most common injury suffered in sports, especially in football. While suggested in some studies, a predictive role of clinical tests for LAS has not been established. To determine which clinical tests, focused on potentially modifiable factors of movement patterns and body mass index (BMI), could best demonstrate risk of LAS among high school and collegiate football players. Case-control study; Level of evidence, 3. A total of 539 high school and collegiate football players were evaluated during the preseason with the Star Excursion Balance Test (SEBT) and Functional Movement Screen as well as BMI. Results were compared between players who did and did not suffer an LAS during the season. Logistic regression analyses and calculated odds ratios were used to determine which measures predicted risk of LAS. The LAS group performed worse on the SEBT-anterior reaching direction (SEBT-ANT) and had higher BMI as compared with the noninjured group (P < .001). The strongest prediction models corresponded with the SEBT-ANT. Low performance on the SEBT-ANT predicted a risk of LAS in football players. BMI was also significantly higher in football players who sustained an LAS. Identifying clinical tools for successful LAS injury risk prediction will be a critical step toward the creation of effective prevention programs to reduce risk of sustaining an LAS during participation in football. © 2015 The Author(s).

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

    PubMed

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

    2016-09-01

    Pollen allergies have long been a major pandemic health problem for human. However, the evolutionary events and biological function of pollen allergens in plants remain largely unknown. Here, we report the genome-wide prediction of pollen allergens and their biological function in the dicotyledonous model plant Arabidopsis (Arabidopsis thaliana) and the monocotyledonous model plant rice (Oryza sativa). In total, 145 and 107 pollen allergens were predicted from rice and Arabidopsis, respectively. These pollen allergens are putatively involved in stress responses and metabolic processes such as cell wall metabolism during pollen development. Interestingly, these putative pollen allergen genes were derived from large gene families and became diversified during evolution. Sequence analysis across 25 plant species from green alga to angiosperms suggest that about 40% of putative pollen allergenic proteins existed in both lower and higher plants, while other allergens emerged during evolution. Although a high proportion of gene duplication has been observed among allergen-coding genes, our data show that these genes might have undergone purifying selection during evolution. We also observed that epitopes of an allergen might have a biological function, as revealed by comprehensive analysis of two known allergens, expansin and profilin. This implies a crucial role of conserved amino acid residues in both in planta biological function and allergenicity. Finally, a model explaining how pollen allergens were generated and maintained in plants is proposed. Prediction and systematic analysis of pollen allergens in model plants suggest that pollen allergens were evolved by gene duplication and then functional specification. This study provides insight into the phylogenetic and evolutionary scenario of pollen allergens that will be helpful to future characterization and epitope screening of pollen allergens. © 2016 American Society of Plant Biologists. All rights reserved.

  2. 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

  3. Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.

    PubMed

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

    2011-12-01

    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.

  4. Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach

    PubMed Central

    Ezkurdia, Iakes; Andrés-León, Eduardo; Valencia, Alfonso

    2010-01-01

    Background Molecular biology is currently facing the challenging task of functionally characterizing the proteome. The large number of possible protein-protein interactions and complexes, the variety of environmental conditions and cellular states in which these interactions can be reorganized, and the multiple ways in which a protein can influence the function of others, requires the development of experimental and computational approaches to analyze and predict functional associations between proteins as part of their activity in the interactome. Methodology/Principal Findings We have studied the possibility of constructing a classifier in order to combine the output of the several protein interaction prediction methods. The AODE (Averaged One-Dependence Estimators) machine learning algorithm is a suitable choice in this case and it provides better results than the individual prediction methods, and it has better performances than other tested alternative methods in this experimental set up. To illustrate the potential use of this new AODE-based Predictor of Protein InterActions (APPIA), when analyzing high-throughput experimental data, we show how it helps to filter the results of published High-Throughput proteomic studies, ranking in a significant way functionally related pairs. Availability: All the predictions of the individual methods and of the combined APPIA predictor, together with the used datasets of functional associations are available at http://ecid.bioinfo.cnio.es/. Conclusions We propose a strategy that integrates the main current computational techniques used to predict functional associations into a unified classifier system, specifically focusing on the evaluation of poorly characterized protein pairs. We selected the AODE classifier as the appropriate tool to perform this task. AODE is particularly useful to extract valuable information from large unbalanced and heterogeneous data sets. The combination of the information provided by five

  5. Esophageal function testing: beyond manometry and impedance.

    PubMed

    Mittal, Ravinder K

    2014-10-01

    Manometry and impedance provide only surrogate information regarding longitudinal wall function and are focused on contractile amplitude and lumen content. Ultrasound imaging provides a unique perspective of esophageal function by providing important information regarding longitudinal muscle contraction. Laser Doppler assessment of perfusion may be an important complementary tool to assess abnormal wall blood perfusion as a possible mechanism of pain. Published by Elsevier Inc.

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

    PubMed

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

    2012-07-01

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

  7. Predicting functional outcomes among college drinkers: reliability and predictive validity of the Young Adult Alcohol Consequences Questionnaire.

    PubMed

    Read, Jennifer P; Merrill, Jennifer E; Kahler, Christopher W; Strong, David R

    2007-11-01

    Heavy drinking and associated consequences are widespread among U.S. college students. Recently, Read et al. (Read, J. P., Kahler, C. W., Strong, D., & Colder, C. R. (2006). Development and preliminary validation of the Young Adult Alcohol Consequences Questionnaire. Journal of Studies on Alcohol, 67, 169-178) developed the Young Adult Alcohol Consequences Questionnaire (YAACQ) to assess the broad range of consequences that may result from heavy drinking in the college milieu. In the present study, we sought to add to the psychometric validation of this measure by employing a prospective design to examine the test-retest reliability, concurrent validity, and predictive validity of the YAACQ. We also sought to examine the utility of the YAACQ administered early in the semester in the prediction of functional outcomes later in the semester, including the persistence of heavy drinking, and academic functioning. Ninety-two college students (48 females) completed a self-report assessment battery during the first weeks of the Fall semester, and approximately one week later. Additionally, 64 subjects (37 females) participated at an optional third time point at the end of the semester. Overall, the YAACQ demonstrated strong internal consistency, test-retest reliability, and concurrent and predictive validity. YAACQ scores also were predictive of both drinking frequency, and "binge" drinking frequency. YAACQ total scores at baseline were an early indicator of academic performance later in the semester, with greater number of total consequences experienced being negatively associated with end-of-semester grade point average. Specific YAACQ subscale scores (Impaired Control, Dependence Symptoms, Blackout Drinking) showed unique prediction of persistent drinking and academic outcomes.

  8. 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.

  9. Modified 30-second Sit to Stand test predicts falls in a cohort of institutionalized older veterans

    PubMed Central

    Chassé, Kathleen

    2017-01-01

    Physical function performance tests, including sit to stand tests and Timed Up and Go, assess the functional capacity of older adults. Their ability to predict falls warrants further investigation. The objective was to determine if a modified 30-second Sit to Stand test that allowed upper extremity use and Timed Up and Go test predicted falls in institutionalized Veterans. Fifty-three older adult Veterans (mean age = 91 years, 49 men) residing in a long-term care hospital completed modified 30-second Sit to Stand and Timed Up and Go tests. The number of falls over one year was collected. The ability of modified 30-second Sit to Stand or Timed Up and Go to predict if participants had fallen was examined using logistic regression. The ability of these tests to predict the number of falls was examined using negative binomial regression. Both analyses controlled for age, history of falls, cognition, and comorbidities. The modified 30-second Sit to Stand was significantly (p < 0.05) related to if participants fell (odds ratio = 0.75, 95% confidence interval = 0.58, 0.97) and the number of falls (incidence rate ratio = 0.82, 95% confidence interval = 0.68, 0.98); decreased repetitions were associated with increased number of falls. Timed Up and Go was not significantly (p > 0.05) related to if participants fell (odds ratio = 1.03, 95% confidence interval = 0.96, 1.10) or the number of falls (incidence rate ratio = 1.01, 95% confidence interval = 0.98, 1.05). The modified 30-second Sit to Stand that allowed upper extremity use offers an alternative method to screen for fall risk in older adults in long-term care. PMID:28464024

  10. Modified 30-second Sit to Stand test predicts falls in a cohort of institutionalized older veterans.

    PubMed

    Applebaum, Eva V; Breton, Dominic; Feng, Zhuo Wei; Ta, An-Tchi; Walsh, Kayley; Chassé, Kathleen; Robbins, Shawn M

    2017-01-01

    Physical function performance tests, including sit to stand tests and Timed Up and Go, assess the functional capacity of older adults. Their ability to predict falls warrants further investigation. The objective was to determine if a modified 30-second Sit to Stand test that allowed upper extremity use and Timed Up and Go test predicted falls in institutionalized Veterans. Fifty-three older adult Veterans (mean age = 91 years, 49 men) residing in a long-term care hospital completed modified 30-second Sit to Stand and Timed Up and Go tests. The number of falls over one year was collected. The ability of modified 30-second Sit to Stand or Timed Up and Go to predict if participants had fallen was examined using logistic regression. The ability of these tests to predict the number of falls was examined using negative binomial regression. Both analyses controlled for age, history of falls, cognition, and comorbidities. The modified 30-second Sit to Stand was significantly (p < 0.05) related to if participants fell (odds ratio = 0.75, 95% confidence interval = 0.58, 0.97) and the number of falls (incidence rate ratio = 0.82, 95% confidence interval = 0.68, 0.98); decreased repetitions were associated with increased number of falls. Timed Up and Go was not significantly (p > 0.05) related to if participants fell (odds ratio = 1.03, 95% confidence interval = 0.96, 1.10) or the number of falls (incidence rate ratio = 1.01, 95% confidence interval = 0.98, 1.05). The modified 30-second Sit to Stand that allowed upper extremity use offers an alternative method to screen for fall risk in older adults in long-term care.

  11. The use of the theory of planned behavior to predict engagement in functional behaviors in schizophrenia.

    PubMed

    Mausbach, Brent T; Moore, Raeanne C; Davine, Taylor; Cardenas, Veronica; Bowie, Christopher R; Ho, Jennifer; Jeste, Dilip V; Patterson, Thomas L

    2013-01-30

    In schizophrenia, low motivation may play a role in the initiation and frequency of functional behaviors. Several reviews support the efficacy of the Theory of Planned Behavior (TPB) to predict engagement in various behaviors, but little research has utilized the TPB to explain functional behavior in schizophrenia. This study tested the TPB for predicting prospective engagement in functional behaviors in a sample of 64 individuals with schizophrenia. Participants completed questionnaires assessing their attitudes toward, social norms regarding, perceived behavioral control over, and intention to engage in various functional behaviors during the upcoming week. Follow-up questionnaires assessed engagement in functional behaviors. Zero-order correlations indicated that positive attitudes, social norms, and perceived behavioral control were positively correlated with intentions to engage in functional behaviors. In turn, intentions were positively correlated with engagement in functional behaviors. Using path analysis, social norms and control were significantly related to intentions, which in turn predicted greater engagement in functional behaviors. Results suggest that patients with schizophrenia make reasoned decisions for or against engaging in functional behaviors. Skills training interventions that also target components of the TPB may be effective for increasing motivation to engage in learned behaviors.

  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.

  13. [Pulmonary function testing before ablative methods].

    PubMed

    Ewert, R; Opitz, C

    2004-07-01

    Laser-induced thermotherapy (LITT) and radiofrequency thermoablation (RFTA) are increasingly used for pulmonary interventions. Primarily patients with severe functional limitations precluding a surgical approach are selected for these procedures. In this patient group a valid preinterventional risk assessment is of paramount importance. The occurrence of a pneumothorax is one of the most important complications associated with these procedures. Therefore, the functional capacity and pulmonary reserve of these patients should allow for at least short periods of lung collapse. The periinterventional risk of these patients can be estimated from basic lung function studies when certain comorbidities are excluded.

  14. 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.

  15. 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

  16. 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.

  17. Community-Wide Evaluation of Computational Function Prediction.

    PubMed

    Friedberg, Iddo; Radivojac, Predrag

    2017-01-01

    A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product. Therefore, to gain insights into the activity of these molecules and guide experiments, we must rely on computational means to functionally annotate the majority of sequence data. To understand how well these algorithms perform, we have established a challenge involving a broad scientific community in which we evaluate different annotation methods according to their ability to predict the associations between previously unannotated protein sequences and Gene Ontology terms. Here we discuss the rationale, benefits, and issues associated with evaluating computational methods in an ongoing community-wide challenge.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  20. Variability in Cumulative Habitual Sleep Duration Predicts Waking Functional Connectivity.

    PubMed

    Khalsa, Sakh; Mayhew, Stephen D; Przezdzik, Izabela; Wilson, Rebecca; Hale, Joanne; Goldstone, Aimee; Bagary, Manny; Bagshaw, Andrew P

    2016-01-01

    We examined whether interindividual differences in habitual sleep patterns, quantified as the cumulative habitual total sleep time (cTST) over a 2-w period, were reflected in waking measurements of intranetwork and internetwork functional connectivity (FC) between major nodes of three intrinsically connected networks (ICNs): default mode network (DMN), salience network (SN), and central executive network (CEN). Resting state functional magnetic resonance imaging (fMRI) study using seed-based FC analysis combined with 14-d wrist actigraphy, sleep diaries, and subjective questionnaires (N = 33 healthy adults, mean age 34.3, standard deviation ± 11.6 y). Data were statistically analyzed using multiple linear regression. Fourteen consecutive days of wrist actigraphy in participant's home environment and fMRI scanning on day 14 at the Birmingham University Imaging Centre. Seed-based FC analysis on ICNs from resting-state fMRI data and multiple linear regression analysis performed for each ICN seed and target. cTST was used to predict FC (controlling for age). cTST was specific predictor of intranetwork FC when the mesial prefrontal cortex (MPFC) region of the DMN was used as a seed for FC, with a positive correlation between FC and cTST observed. No significant relationship between FC and cTST was seen for any pair of nodes not including the MPFC. Internetwork FC between the DMN (MPFC) and SN (right anterior insula) was also predicted by cTST, with a negative correlation observed between FC and cTST. This study improves understanding of the relationship between intranetwork and internetwork functional connectivity of intrinsically connected networks (ICNs) in relation to habitual sleep quality and duration. The cumulative amount of sleep that participants achieved over a 14-d period was significantly predictive of intranetwork and inter-network functional connectivity of ICNs, an observation that may underlie the link between sleep status and cognitive performance.

  1. Brain natriuretic peptide predicts functional outcome in ischemic stroke

    PubMed Central

    Rost, Natalia S; Biffi, Alessandro; Cloonan, Lisa; Chorba, John; Kelly, Peter; Greer, David; Ellinor, Patrick; Furie, Karen L

    2011-01-01

    Background Elevated serum levels of brain natriuretic peptide (BNP) have been associated with cardioembolic (CE) stroke and increased post-stroke mortality. We sought to determine whether BNP levels were associated with functional outcome after ischemic stroke. Methods We measured BNP in consecutive patients aged ≥18 years admitted to our Stroke Unit between 2002–2005. BNP quintiles were used for analysis. Stroke subtypes were assigned using TOAST criteria. Outcomes were measured as 6-month modified Rankin Scale score (“good outcome” = 0–2 vs. “poor”) as well as mortality. Multivariate logistic regression was used to assess association between the quintiles of BNP and outcomes. Predictive performance of BNP as compared to clinical model alone was assessed by comparing ROC curves. Results Of 569 ischemic stroke patients, 46% were female; mean age was 67.9 ± 15 years. In age- and gender-adjusted analysis, elevated BNP was associated with lower ejection fraction (p<0.0001) and left atrial dilatation (p<0.001). In multivariate analysis, elevated BNP decreased the odds of good functional outcome (OR 0.64, 95%CI 0.41–0.98) and increased the odds of death (OR 1.75, 95%CI 1.36–2.24) in these patients. Addition of BNP to multivariate models increased their predictive performance for functional outcome (p=0.013) and mortality (p<0.03) after CE stroke. Conclusions Serum BNP levels are strongly associated with CE stroke and functional outcome at 6 months after ischemic stroke. Inclusion of BNP improved prediction of mortality in patients with CE stroke. PMID:22116811

  2. Integrating phenotype and gene expression data for predicting gene function.

    PubMed

    Malone, Brandon M; Perkins, Andy D; Bridges, Susan M

    2009-10-08

    This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing similarities based upon both gene expression and textual phenotype data. This integrated graph is then used to make predictions about whether individual genes should be assigned a particular annotation from the Gene Ontology. A combined graph was generated from publicly-available gene expression data and phenotypic information from Saccharomyces cerevisiae. This graph was used to assign annotations to genes, as were graphs constructed from gene expression data and textual phenotype information alone. While the F-measure appeared similar for all three methods, annotations based upon the integrated similarity graph exhibited a better overall precision than gene expression or phenotype information alone can generate. The integrated approach was also able to assign almost as many annotations as the gene expression method alone, and generated significantly more total and correct assignments than the phenotype information could provide. These results suggest that augmenting standard gene expression data sets with publicly-available textual phenotype data can help generate more precise functional annotation predictions while mitigating the weaknesses of a standard textual phenotype approach.

  3. "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. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    PubMed

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

    2012-07-05

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

  5. Word List Memory Predicts Everyday Function and Problem-Solving in the Elderly: Results from the ACTIVE Cognitive Intervention Trial

    PubMed Central

    Gross, Alden L.; Rebok, George W.; Unverzagt, Frederick W.; Willis, Sherry L.; Brandt, Jason

    2011-01-01

    Data from the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) trial (N=2,802) were analyzed to examine whether word list learning predicts future everyday functioning. Using stepwise random effects modeling, measures from the modified administrations of the Hopkins Verbal Learning Test (HVLT) and the Auditory Verbal Learning Test (AVLT) were independently predictive of everyday IADL functioning, problem-solving, and psychomotor speed. Associations between memory scores and everyday functioning outcomes remained significant across follow-up intervals spanning five years. HVLT total recall score was consistently the strongest predictor of each functional outcome. Results suggest that verbal memory measures are uniquely associated with both current and future functioning and that specific verbal memory tests like the HVLT and AVLT have important clinical utility in predicting future functional ability among older adults. PMID:21069610

  6. 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.

  7. Testing the Relative Performance of Data Adaptive Prediction Algorithms: A Generalized Test of Conditional Risk Differences

    PubMed Central

    Polley, Eric C.; Briggs, Farren B. S.; van der Laan, Mark J.; Hubbard, Alan

    2016-01-01

    Comparing the relative fit of competing models can be used to address many different scientific questions. In classical statistics one can, if appropriate, use likelihood ratio tests and information based criterion, whereas clinical medicine has tended to rely on comparisons of fit metrics like C-statistics. However, for many data adaptive modelling procedures such approaches are not suitable. In these cases, statisticians have used cross-validation, which can make inference challenging. In this paper we propose a general approach that focuses on the “conditional” risk difference (conditional on the model fits being fixed) for the improvement in prediction risk. Specifically, we derive a Wald-type test statistic and associated confidence intervals for cross-validated test sets utilizing the independent validation within cross-validation in conjunction with a test for multiple comparisons. We show that this test maintains proper Type I Error under the null fit, and can be used as a general test of relative fit for any semi-parametric model alternative. We apply the test to a candidate gene study to test for the association of a set of genes in a genetic pathway. PMID:26529567

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

    ERIC Educational Resources Information Center

    La Rue, Asenath; Jarvik, Lissy F.

    1987-01-01

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

  9. 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.

  10. Premotor functional connectivity predicts impulsivity in juvenile offenders.

    PubMed

    Shannon, Benjamin J; Raichle, Marcus E; Snyder, Abraham Z; Fair, Damien A; Mills, Kathryn L; Zhang, Dongyang; Bache, Kevin; Calhoun, Vince D; Nigg, Joel T; Nagel, Bonnie J; Stevens, Alexander A; Kiehl, Kent A

    2011-07-05

    Teenagers are often impulsive. In some cases this is a phase of normal development; in other cases impulsivity contributes to criminal behavior. Using functional magnetic resonance imaging, we examined resting-state functional connectivity among brain systems and behavioral measures of impulsivity in 107 juveniles incarcerated in a high-security facility. In less-impulsive juveniles and normal controls, motor planning regions were correlated with brain networks associated with spatial attention and executive control. In more-impulsive juveniles, these same regions correlated with the default-mode network, a constellation of brain areas associated with spontaneous, unconstrained, self-referential cognition. The strength of these brain-behavior relationships was sufficient to predict impulsivity scores at the individual level. Our data suggest that increased functional connectivity of motor-planning regions with networks subserving unconstrained, self-referential cognition, rather than those subserving executive control, heightens the predisposition to impulsive behavior in juvenile offenders. To further explore the relationship between impulsivity and neural development, we studied functional connectivity in the same motor-planning regions in 95 typically developing individuals across a wide age span. The change in functional connectivity with age mirrored that of impulsivity: younger subjects tended to exhibit functional connectivity similar to the more-impulsive incarcerated juveniles, whereas older subjects exhibited a less-impulsive pattern. This observation suggests that impulsivity in the offender population is a consequence of a delay in typical development, rather than a distinct abnormality.

  11. Premotor functional connectivity predicts impulsivity in juvenile offenders

    PubMed Central

    Shannon, Benjamin J.; Raichle, Marcus E.; Snyder, Abraham Z.; Fair, Damien A.; Mills, Kathryn L.; Zhang, Dongyang; Bache, Kevin; Calhoun, Vince D.; Nigg, Joel T.; Nagel, Bonnie J.; Stevens, Alexander A.; Kiehl, Kent A.

    2011-01-01

    Teenagers are often impulsive. In some cases this is a phase of normal development; in other cases impulsivity contributes to criminal behavior. Using functional magnetic resonance imaging, we examined resting-state functional connectivity among brain systems and behavioral measures of impulsivity in 107 juveniles incarcerated in a high-security facility. In less-impulsive juveniles and normal controls, motor planning regions were correlated with brain networks associated with spatial attention and executive control. In more-impulsive juveniles, these same regions correlated with the default-mode network, a constellation of brain areas associated with spontaneous, unconstrained, self-referential cognition. The strength of these brain–behavior relationships was sufficient to predict impulsivity scores at the individual level. Our data suggest that increased functional connectivity of motor-planning regions with networks subserving unconstrained, self-referential cognition, rather than those subserving executive control, heightens the predisposition to impulsive behavior in juvenile offenders. To further explore the relationship between impulsivity and neural development, we studied functional connectivity in the same motor-planning regions in 95 typically developing individuals across a wide age span. The change in functional connectivity with age mirrored that of impulsivity: younger subjects tended to exhibit functional connectivity similar to the more-impulsive incarcerated juveniles, whereas older subjects exhibited a less-impulsive pattern. This observation suggests that impulsivity in the offender population is a consequence of a delay in typical development, rather than a distinct abnormality. PMID:21709236

  12. The predictability of molecular evolution during functional innovation.

    PubMed

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

    2014-02-25

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

  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. Variability in Cumulative Habitual Sleep Duration Predicts Waking Functional Connectivity

    PubMed Central

    Khalsa, Sakh; Mayhew, Stephen D.; Przezdzik, Izabela; Wilson, Rebecca; Hale, Joanne; Goldstone, Aimee; Bagary, Manny; Bagshaw, Andrew P.

    2016-01-01

    Study Objectives: We examined whether interindividual differences in habitual sleep patterns, quantified as the cumulative habitual total sleep time (cTST) over a 2-w period, were reflected in waking measurements of intranetwork and internetwork functional connectivity (FC) between major nodes of three intrinsically connected networks (ICNs): default mode network (DMN), salience network (SN), and central executive network (CEN). Methods: Resting state functional magnetic resonance imaging (fMRI) study using seed-based FC analysis combined with 14-d wrist actigraphy, sleep diaries, and subjective questionnaires (N = 33 healthy adults, mean age 34.3, standard deviation ± 11.6 y). Data were statistically analyzed using multiple linear regression. Fourteen consecutive days of wrist actigraphy in participant's home environment and fMRI scanning on day 14 at the Birmingham University Imaging Centre. Seed-based FC analysis on ICNs from resting-state fMRI data and multiple linear regression analysis performed for each ICN seed and target. cTST was used to predict FC (controlling for age). Results: cTST was specific predictor of intranetwork FC when the mesial prefrontal cortex (MPFC) region of the DMN was used as a seed for FC, with a positive correlation between FC and cTST observed. No significant relationship between FC and cTST was seen for any pair of nodes not including the MPFC. Internetwork FC between the DMN (MPFC) and SN (right anterior insula) was also predicted by cTST, with a negative correlation observed between FC and cTST. Conclusions: This study improves understanding of the relationship between intranetwork and internetwork functional connectivity of intrinsically connected networks (ICNs) in relation to habitual sleep quality and duration. The cumulative amount of sleep that participants achieved over a 14-d period was significantly predictive of intranetwork and inter-network functional connectivity of ICNs, an observation that may underlie the link

  15. 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.

  16. 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.

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

    PubMed

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

    2014-12-01

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

  18. Predicting acute recovery of physical function following total knee joint arthroplasty.

    PubMed

    Robbins, Shawn M; Rastogi, Ravi; McLaughlin, Terry-Lyne

    2014-02-01

    The objective was to explore predictors of physical function during acute in-patient rehabilitation within a few days after TKA. Physical function status of participants (n = 72) three days after total knee arthroplasty (TKA) was measured using the Timed Up and Go Test (TUG) and the function subscale of the Western Ontario McMaster Universities Index of Osteoarthritis (WOMAC-function). Potential predictors of physical function were measured day one post-TKA. Their relationship with physical function was examined using backward elimination, multiple regression analyses. Older age and increased comorbidity were associated (R(2) = 0.20) with worse TUG times. Increased pain severity was associated (R(2) = 0.08) with worse WOMAC-function scores. Age, comorbidity, and pain severity should be considered when predicting which patients will struggle with acute recovery post-TKA.

  19. 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

  20. Visual function tests on the Internet--sense or nonsense?

    PubMed

    Kuchenbecker, J; Lindner, H

    2004-06-01

    The quantitative capability of the visual system can be tested using graphic presentations with defined size, form and color. For presentations, a chart projector or monitor can be used. Today, the number of visual function tests on the Internet is increasing constantly. Options and limitations of visual function tests using the Internet and the authors' own test results are described. Several visual function tests, such as visual acuity tests, the Amsler-Grid, stereo and color vision tests, can already be given via Internet. The variability of the tests ranges from the simple presentation of graphic elements to the laboriously programmed interactive input by the user to specify the test result. Under standardized examination conditions, there was a very high correspondence between the results of the authors' own web-based color vision test and those of luminescence color test plates and conventional pigment color plates. However, the interpretation of the test results is difficult due to the absence of controls during the test as well as the heterogeneity of the hardware. In order to obtain comparable test results, differences in size and resolution as well as in brightness, contrast and color of computer monitors must be taken into consideration. Due to the deficits described in the tests, the value of visual function tests on the Internet is rather limited. Currently, the data of test distributers with respect to the test conditions are all still insufficient. Standards need to be defined for Internet-based visual function tests. However, visual function tests on the Internet can achieve test results comparable to those of conventional visual function tests under standardized examination conditions in clinical practice. Further studies are needed to check the accuracy of web-based screening examinations in ophthalmology.

  1. Simple Test Functions in Meshless Local Petrov-Galerkin Methods

    NASA Technical Reports Server (NTRS)

    Raju, Ivatury S.

    2016-01-01

    Two meshless local Petrov-Galerkin (MLPG) methods based on two different trial functions but that use a simple linear test function were developed for beam and column problems. These methods used generalized moving least squares (GMLS) and radial basis (RB) interpolation functions as trial functions. These two methods were tested on various patch test problems. Both methods passed the patch tests successfully. Then the methods were applied to various beam vibration problems and problems involving Euler and Beck's columns. Both methods yielded accurate solutions for all problems studied. The simple linear test function offers considerable savings in computing efforts as the domain integrals involved in the weak form are avoided. The two methods based on this simple linear test function method produced accurate results for frequencies and buckling loads. Of the two methods studied, the method with radial basis trial functions is very attractive as the method is simple, accurate, and robust.

  2. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Application of radial basis function neural network to predict soil sorption partition coefficient using topological descriptors.

    PubMed

    Sabour, Mohammad Reza; Moftakhari Anasori Movahed, Saman

    2017-02-01

    The soil sorption partition coefficient logKoc is an indispensable parameter that can be used in assessing the environmental risk of organic chemicals. In order to predict soil sorption partition coefficient for different and even unknown compounds in a fast and accurate manner, a radial basis function neural network (RBFNN) model was developed. Eight topological descriptors of 800 organic compounds were used as inputs of the model. These 800 organic compounds were chosen from a large and very diverse data set. Generalized Regression Neural Network (GRNN) was utilized as the function in this neural network model due to its capability to adapt very quickly. Hence, it can be used to predict logKoc for new chemicals, as well. Out of total data set, 560 organic compounds were used for training and 240 to test efficiency of the model. The obtained results indicate that the model performance is very well. The correlation coefficients (R2) for training and test sets were 0.995 and 0.933, respectively. The root-mean square errors (RMSE) were 0.2321 for training set and 0.413 for test set. As the results for both training and test set are extremely satisfactory, the proposed neural network model can be employed not only to predict logKoc of known compounds, but also to be adaptive for prediction of this value precisely for new products that enter the market each year.

  4. The predictive role of daily cognitive stimulation on executive functions in bipolar disorder.

    PubMed

    Cotrena, Charles; Damiani Branco, Laura; Ponsoni, André; Milman Shansis, Flávio; Kochhann, Renata; Paz Fonseca, Rochele

    2017-03-07

    This study aimed to estimate the predictive role of clinical and demographic variables on the three core executive functions (EF) - working memory (WM), inhibitory control (IC) and cognitive flexibility (CF) - in bipolar disorder (BD). The sample consisted of 38 patients with BD type I, 39 with BD type II, and 106 control participants with no mood disorders. Subjects completed the Hayling Test, Trail Making Test, Digit Span Backwards, Sentence Word Span Test, and Stroop Color-Word Test. Composite scores for WM, IC and CF were calculated, and their correlations with clinical and demographic variables were analyzed. Stepwise hierarchical regression models including all significant correlates, gender, and diagnosis, revealed that the frequency of reading and writing habits (FRWH), IQ and diagnosis predicted 38.1% of the variance in IC. Diagnosis and IQ predicted 24.9% of the variance in WM scores. CF was predicted by the FRWH only, which accounted for 7.6% of the variance in this construct. These results suggest that daily cognitive stimulation through reading and writing make a significant positive contribution to executive functioning in BD, even in the absence of continued education. These and other forms of routine cognitive stimulation should be further emphasized in intervention programs for BD.

  5. [Tests of hand functionality in upper limb amputation with prosthesis].

    PubMed

    Bazzini, G; Orlandini, D; Moscato, T A; Nicita, D; Panigazzi, M

    2007-01-01

    The need for standardized instruments for clinical measurements has become pressing in the fields of occupational rehabilitation and ergonomics. This is particularly the case for instruments that allow a quantitative evaluation of upper limb function, and especially hand function in patients who have undergone an amputation and then application of an upper limb prosthesis. This study presents a review of the main tests used to evaluate hand function, with a critical analysis of their use in subjects with an upper limb prosthesis. The tests are divided into: tests to evaluate strength, tests to evaluate co-ordination and dexterity, tests of global or overall function, and tests proposed specifically for subjects with an upper limb prosthesis. Of the various tests presented, the authors give their preference to the Bimanual Functional Assessment, Abilhand and/or the ADL Questionnaire, because of the practical usefulness, clinimetric features, simplicity and ease of administration of these tests.

  6. Prediction of Dislocation Cores in Aluminum from Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Woodward, C.; Trinkle, D. R.; Hector, L. G., Jr.; Olmsted, D. L.

    2008-02-01

    The strain field of isolated screw and edge dislocation cores in aluminum are calculated using density-functional theory and a flexible boundary condition method. Nye tensor density contours and differential displacement fields are used to accurately bound Shockley partial separation distances. Our results of 5 7.5 Å (screw) and 7.0 9.5 Å (edge) eliminate uncertainties resulting from the wide range of previous results based on Peierls-Nabarro and atomistic methods. Favorable agreement of the predicted cores with limited experimental measurements demonstrates the need for quantum mechanical treatment of dislocation cores.

  7. Pediatric brain injury: Can DTI scalars predict functional outcome?

    PubMed Central

    Xu, Duan; Mukherjee, Pratik; Barkovich, A James

    2013-01-01

    Diffusion imaging has made significant inroads into the clinical diagnosis of a variety of diseases by inferring changes in microstructure, namely cell membranes, myelin sheath and other structures that inhibit water diffusion. This review discusses recent progress in the use of diffusion parameters in predicting functional outcome. Studies in the literature using only scalar parameters from diffusion measurements, such as apparent diffusion coefficient (ADC) and fractional anisotropy (FA), are summarized. Other more complex mathematical models and post-processing uses are also discussed briefly. PMID:23288477

  8. 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.

  9. 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…

  10. Prediction of functional rehabilitation outcomes in clients with stroke.

    PubMed

    Man, David Wai-Kwong; Tam, Sing Fai; Hui-Chan, Christina

    2006-02-01

    To evaluate the validity of the Neurobehavioral Cognitive Status Examination (NCSE or Cognistat) and to determine its effects in order to estimate the functional outcomes of survivors with stroke. The present study first studied the factor structure NCSE in 148 Chinese survivors with stroke (aged 45-91 years). They were admitted to hospital consecutively and recruited prospectively. The relationship of NCSE with Functional Independence Measures (FIM), a set of measures commonly adopted as an indicator of the outcome of rehabilitation, was studied. One hundred and forty-eight patients with stroke (49.3% male, 50.7% female), with a mean age of 70.38 and an average number of years of education of 3.50 years joined the study. A two-factor NCSE structure was obtained, namely verbal-spatial and integrated cognition, accounting for 62.77% of the variance. A significant relationship between NCSE factors and the functional status of clients with stroke on admission and upon discharge, as well as age, years of education and length of hospital stay were indicated. This study supports a systematic relationship between cognitive factors and functional outcome in Chinese patients with stroke. Similarities and differences in the NCSE factor structure between the population with stroke and general neurological populations were discussed and the utility of NCSE in stroke rehabilitation, such as its predictive validity in functional independence is suggested.

  11. Assessing Differential Item Functioning in Performance Tests.

    ERIC Educational Resources Information Center

    Zwick, Rebecca; And Others

    Although the belief has been expressed that performance assessments are intrinsically more fair than multiple-choice measures, some forms of performance assessment may in fact be more likely than conventional tests to tap construct-irrelevant factors. As performance assessment