Sample records for accurately predict concordant

  1. Prediction future asset price which is non-concordant with the historical distribution

    NASA Astrophysics Data System (ADS)

    Seong, Ng Yew; Hin, Pooi Ah

    2015-12-01

    This paper attempts to predict the major characteristics of the future asset price which is non-concordant with the distribution estimated from the price today and the prices on a large number of previous days. The three major characteristics of the i-th non-concordant asset price are the length of the interval between the occurrence time of the previous non-concordant asset price and that of the present non-concordant asset price, the indicator which denotes that the non-concordant price is extremely small or large by its values -1 and 1 respectively, and the degree of non-concordance given by the negative logarithm of the probability of the left tail or right tail of which one of the end points is given by the observed future price. The vector of three major characteristics of the next non-concordant price is modelled to be dependent on the vectors corresponding to the present and l - 1 previous non-concordant prices via a 3-dimensional conditional distribution which is derived from a 3(l + 1)-dimensional power-normal mixture distribution. The marginal distribution for each of the three major characteristics can then be derived from the conditional distribution. The mean of the j-th marginal distribution is an estimate of the value of the j-th characteristics of the next non-concordant price. Meanwhile, the 100(α/2) % and 100(1 - α/2) % points of the j-th marginal distribution can be used to form a prediction interval for the j-th characteristic of the next non-concordant price. The performance measures of the above estimates and prediction intervals indicate that the fitted conditional distribution is satisfactory. Thus the incorporation of the distribution of the characteristics of the next non-concordant price in the model for asset price has a good potential of yielding a more realistic model.

  2. Concordance and predictive value of two adverse drug event data sets.

    PubMed

    Cami, Aurel; Reis, Ben Y

    2014-08-22

    Accurate prediction of adverse drug events (ADEs) is an important means of controlling and reducing drug-related morbidity and mortality. Since no single "gold standard" ADE data set exists, a range of different drug safety data sets are currently used for developing ADE prediction models. There is a critical need to assess the degree of concordance between these various ADE data sets and to validate ADE prediction models against multiple reference standards. We systematically evaluated the concordance of two widely used ADE data sets - Lexi-comp from 2010 and SIDER from 2012. The strength of the association between ADE (drug) counts in Lexi-comp and SIDER was assessed using Spearman rank correlation, while the differences between the two data sets were characterized in terms of drug categories, ADE categories and ADE frequencies. We also performed a comparative validation of the Predictive Pharmacosafety Networks (PPN) model using both ADE data sets. The predictive power of PPN using each of the two validation sets was assessed using the area under Receiver Operating Characteristic curve (AUROC). The correlations between the counts of ADEs and drugs in the two data sets were 0.84 (95% CI: 0.82-0.86) and 0.92 (95% CI: 0.91-0.93), respectively. Relative to an earlier snapshot of Lexi-comp from 2005, Lexi-comp 2010 and SIDER 2012 introduced a mean of 1,973 and 4,810 new drug-ADE associations per year, respectively. The difference between these two data sets was most pronounced for Nervous System and Anti-infective drugs, Gastrointestinal and Nervous System ADEs, and postmarketing ADEs. A minor difference of 1.1% was found in the AUROC of PPN when SIDER 2012 was used for validation instead of Lexi-comp 2010. In conclusion, the ADE and drug counts in Lexi-comp and SIDER data sets were highly correlated and the choice of validation set did not greatly affect the overall prediction performance of PPN. Our results also suggest that it is important to be aware of the

  3. Recovery and concordance in a secure forensic psychiatry hospital - the self rated DUNDRUM-3 programme completion and DUNDRUM-4 recovery scales.

    PubMed

    Davoren, Mary; Hennessy, Sarah; Conway, Catherine; Marrinan, Seamus; Gill, Pauline; Kennedy, Harry G

    2015-03-28

    Detention in a secure forensic psychiatric hospital may inhibit engagement and recovery. Having validated the clinician rated DUNDRUM-3 (programme completion) and DUNDRUM-4 (recovery) in a forensic hospital, we set out to draft and validate scales measuring the same programme completion and recovery items that patients could use to self-rate. Based on previous work, we hypothesised that self-rating scores might be predictors of objective progress including conditional discharge. We hypothesised also that the difference between patients' and clinicians' ratings of progress in treatment and other factors relevant to readiness for discharge (concordance) would diminish as patients neared discharge. We hypothesised also that this difference in matched scores would predict objective progress including conditional discharge. In a prospective naturalistic observational cohort study in a forensic hospital, we examined whether scores on the self-rated DUNDRUM-3 programme completion and DUNDRUM-4 recovery scales or differences between clinician and patient ratings on the same scales (concordance) would predict moves between levels of therapeutic security and conditional discharge over the next twelve months. Both scales stratified along the recovery pathway of the hospital, but clinician ratings matched the level of therapeutic security more accurately than self ratings. The clinician rated scales predicted moves to less secure units and to more secure units and predicted conditional discharge but the self-rated scores did not. The difference between clinician and self-rated scores (concordance) predicted positive and negative moves and conditional discharge, but this was not always an independent predictor as shown by regression analysis. In regression analysis the DUNDRUM-3 predicted moves to less secure places though the HCR-20 C & R score dominated the model. Moves back to more secure places were predicted by lack of concordance on the DUNDRUM-4. Conditional discharge

  4. Concorde noise-induced building vibrations John F. Kennedy International Airport

    NASA Technical Reports Server (NTRS)

    Mayes, W. H.; Deloach, R.; Stephens, D. G.; Cawthorn, J. M.; Holmes, H. K.; Lewis, R. B.; Holliday, B. G.; Ward, D. W.

    1978-01-01

    The outdoor and indoor noise levels resulting from aircraft flyovers and certain nonaircraft events were recorded at six home sites along with the associated vibration levels in the walls, windows, and floors of these test homes. Limited subjective tests conducted to examine the human detection and annoyance thresholds for building vibration and rattle caused by aircraft noise showed that both vibration and rattle were detected subjectively in several houses for some operations of both the Concorde and subsonic aircraft. Preliminary results indicate that the relationship between window vibration and aircraft noise is: (1) linear, with vibration levels being accurately predicted from OASPL levels measured near the window; (2) consistent from flyover to flyover for a given aircraft type under approach conditions; (3) no different for Concorde than for other conventional jet transports (in the case of window vibrations induced under approach power conditions); and (4) relatively high levels of window vibration measured during Concorde operations are due more to higher OASPL levels than to unique Concorde source characteristics.

  5. Concorde noise-induced building vibrations: John F. Kennedy International Airport

    NASA Technical Reports Server (NTRS)

    Mayes, W. H.; Stephens, D. G.; Deloach, R.; Cawthorn, J. M.; Holmes, H. K.; Lewis, R. B.; Holliday, B. G.; Ward, D. W.; Miller, W. T.

    1978-01-01

    Outdoor and indoor noise levels resulting from aircraft flyovers and certain nonaircraft events were recorded at eight homesites and a school along with the associated vibration levels in the walls, windows, and floors at these test sites. Limited subjective tests were conducted to examine the human detection and annoyance thresholds for building vibration and rattle caused by aircraft noise. Both vibration and rattle were detected subjectively in several houses for some operations of both the Concorde and subsonic aircraft. Seated subjects more readily detected floor vibrations than wall or window vibrations. Aircraft noise generally caused more window vibrations than common nonaircraft events such as walking and closing doors. Nonaircraft events and aircraft flyovers resulted in comparable wall vibration levels, while floor vibrations were generally greater for nonaircraft events than for aircraft flyovers. The relationship between structural vibration and aircraft noise is linear, with vibration levels being accurately predicted from overall sound pressure levels (OASPL) measured near the structure. Relatively high levels of structural vibration measured during Concorde operations are due more to higher OASPL levels than to unique Concorde-source characteristics.

  6. Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease.

    PubMed

    Azuaje, Francisco; Zheng, Huiru; Camargo, Anyela; Wang, Haiying

    2011-08-01

    The discovery of novel disease biomarkers is a crucial challenge for translational bioinformatics. Demonstration of both their classification power and reproducibility across independent datasets are essential requirements to assess their potential clinical relevance. Small datasets and multiplicity of putative biomarker sets may explain lack of predictive reproducibility. Studies based on pathway-driven discovery approaches have suggested that, despite such discrepancies, the resulting putative biomarkers tend to be implicated in common biological processes. Investigations of this problem have been mainly focused on datasets derived from cancer research. We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain. A diversity of biosignatures was identified by the different methods. However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis. With a few exceptions, we observed lack of classification reproducibility using independent datasets. Partial overlaps between our putative sets of biomarkers and the primary studies exist. Despite the observed limitations, pathway-driven or gene set analysis can predict potentially novel biomarkers and can jointly point to biomedically-relevant underlying molecular mechanisms. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Mental models accurately predict emotion transitions.

    PubMed

    Thornton, Mark A; Tamir, Diana I

    2017-06-06

    Successful social interactions depend on people's ability to predict others' future actions and emotions. People possess many mechanisms for perceiving others' current emotional states, but how might they use this information to predict others' future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop accurate mental models of others' emotional dynamics. People could then use these mental models of emotion transitions to predict others' future emotions from currently observable emotions. To test this hypothesis, studies 1-3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants' ratings of emotion transitions predicted others' experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation-valence, social impact, rationality, and human mind-inform participants' mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported accurate models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants' accuracy, suggesting that their mental models contain accurate information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone.

  8. Mental models accurately predict emotion transitions

    PubMed Central

    Thornton, Mark A.; Tamir, Diana I.

    2017-01-01

    Successful social interactions depend on people’s ability to predict others’ future actions and emotions. People possess many mechanisms for perceiving others’ current emotional states, but how might they use this information to predict others’ future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop accurate mental models of others’ emotional dynamics. People could then use these mental models of emotion transitions to predict others’ future emotions from currently observable emotions. To test this hypothesis, studies 1–3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants’ ratings of emotion transitions predicted others’ experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation—valence, social impact, rationality, and human mind—inform participants’ mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported accurate models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants’ accuracy, suggesting that their mental models contain accurate information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone. PMID:28533373

  9. Do concordances of social support and relationship quality predict psychological distress and well-being of cancer patients and caregivers?

    PubMed

    Hou, W K; Lau, K M; Shum, T C Y; Cheng, A C K; Lee, T M C

    2018-05-16

    This study examined concordances of cancer patients' received and caregivers' provided support and dyadic relationship quality, and their predictive utility in prospective psychological distress and well-being. A total of 83 Chinese cancer patient-caregiver dyads were recruited in two government-funded hospitals in Hong Kong. Participants reported received (patient)/provided (caregiver) emotional and instrumental support and dyadic relationship quality within 6 months after diagnosis (T1), and anxiety and depressive symptoms, positive affect and life satisfaction at both T1 and 6-month follow-up (T2). We hypothesised that concordances at T1 would predict lower psychological distress and higher psychological well-being among both patients and caregivers at T2. Concordances were indicated by Gwet's AC 2 scores (possible range = -1.00 to 1.00) and as follows: emotional support: M = 0.92, SD = 0.12, range = 0.25-1.00; instrumental support: M = 0.92, SD = 0.16, range = 0.08-1.00; and relationship quality: M = 0.63, SD = 0.27, range = -0.31 to 1.00. Hierarchical multiple regressions revealed that T1 concordances of perceived emotional and instrumental support and dyadic relationship quality positively predicted T2 anxiety symptoms [F(9, 74) = 6.725, ∆R 2  = .031, p < .001)] and state positive affect [F(9, 74) = 3.436, ∆R 2  = .042, p = .001)], whereas inversely predicted T2 depressive symptoms [F(9, 74) = 4.189, ∆R 2  = .042, p < .01)]. Significant associations were found only among caregivers, but not patients. © 2018 John Wiley & Sons Ltd.

  10. Models and methods of emotional concordance.

    PubMed

    Hollenstein, Tom; Lanteigne, Dianna

    2014-04-01

    Theories of emotion generally posit the synchronized, coordinated, and/or emergent combination of psychophysiological, cognitive, and behavioral components of the emotion system--emotional concordance--as a functional definition of emotion. However, the empirical support for this claim has been weak or inconsistent. As an introduction to this special issue on emotional concordance, we consider three domains of explanations as to why this theory-data gap might exist. First, theory may need to be revised to more accurately reflect past research. Second, there may be moderating factors such as emotion regulation, context, or individual differences that have obscured concordance. Finally, the methods typically used to test theory may be inadequate. In particular, we review a variety of potential issues: intensity of emotions elicited in the laboratory, nonlinearity, between- versus within-subject associations, the relative timing of components, bivariate versus multivariate approaches, and diversity of physiological processes. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Race, gender, and language concordance in the primary care setting.

    PubMed

    Martin, Brian C; Shi, Leiyu; Ward, Ryan D

    2009-01-01

    The purpose of this paper is to examine race, gender and language concordance in terms of importance to primary care. The 2003 Medical Expenditure Panel Survey Household Component (MEPS) was used. Four distinguishing primary care attributes and selected measures were operationalized primarily from a sample subset that identified a usual source of care (USC): accessibility to USC; interface between primary care and specialist services; treatment decisions; and preventive services received from the USC. Bivariate and multivariate results are reported. Adjusting for covariates, the following items remained statistically significant: race--choosing primary care physician as USC, USC having office hours, and going to USC for new health problems; gender--choosing primary care physician as USC and USC having office hours; and language--lack of difficulty contacting the USC after hours. However, these items appear to be isolated cases rather than indicators that concordance plays a key role in determining primary care quality. Language barriers/communication issues are the only areas where improvement appears warranted. While the study has strong accessibility and interpersonal relationship measures, service coordination and comprehensiveness indicators are limited. The analyses' cross-sectional nature also poses a problem in drawing causal relationships and conclusive findings. Finally, sample size limitations preclude stratified analyses across racial/ethnic groups, an important consideration as the relationships between concordance and quality may vary across groups. This study indicates that more research is needed in this area to determine future resource allocation and policy direction. The unique contribution of the study is to suggest that race and gender concordance may not accurately predict primary health care quality.

  12. Concordance between clinical and histopathologic diagnoses of oral mucosal lesions.

    PubMed

    Patel, Kush J; De Silva, Harsha L; Tong, Darryl C; Love, Robert M

    2011-01-01

    To study the epidemiology of oral soft tissue lesions in New Zealand from 2002 to 2006 and to determine the concordance between the clinical diagnosis and the definitive histopathologic diagnosis achieved by general dental practitioners and by specialists. The details from biopsy referrals and the corresponding histopathologic reports of oral soft tissue lesions were recorded into a statistical software package, and the concordance between the clinical diagnosis and histopathologic diagnosis was determined for all the lesions. Most biopsies were benign lesions, and both clinician groups achieved a high diagnostic concordance for these lesions. However, when considering all lesion types, the overall concordance for both groups was a moderate 50.6%, with little difference between specialists and general dental practitioners, although specialists were more accurate in diagnosing a malignant or premalignant lesion. The clinical and histopathologic concordance achieved by oral health practitioners in New Zealand appears to be moderate. Copyright © 2011 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

  13. Internet stream synchronization using Concord

    NASA Astrophysics Data System (ADS)

    Sreenan, Cormac J.; Narendran, B.; Agrawal, Prathima; Shivakumar, Narayanan

    1996-03-01

    Using packet networks to transport multimedia introduces delay variations within and across streams, necessitating synchronization at the receiver. This requires stream data to be buffered prior to presentation, which also increases its total end to end delay. Concord recognizes that applications may wish to influence the underlying synchronization policy in terms of its effect on quality of service. It provides a single framework for synchronization within and across streams and employs an application specific tradeoff between packet losses, delay and inter- stream skew. We present a new predictive approach for synchronization and a selection of results from an extensive evaluation of Concord for use in the Internet. A trace driven simulator is used, allowing a direct comparison with alternative approaches. We demonstrate that Concord can operate with lower maximum delay and less variation in total end to end delay, which in turn can allow receiver buffer requirements to be reduced.

  14. Real external predictivity of QSAR models: how to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient.

    PubMed

    Chirico, Nicola; Gramatica, Paola

    2011-09-26

    The main utility of QSAR models is their ability to predict activities/properties for new chemicals, and this external prediction ability is evaluated by means of various validation criteria. As a measure for such evaluation the OECD guidelines have proposed the predictive squared correlation coefficient Q(2)(F1) (Shi et al.). However, other validation criteria have been proposed by other authors: the Golbraikh-Tropsha method, r(2)(m) (Roy), Q(2)(F2) (Schüürmann et al.), Q(2)(F3) (Consonni et al.). In QSAR studies these measures are usually in accordance, though this is not always the case, thus doubts can arise when contradictory results are obtained. It is likely that none of the aforementioned criteria is the best in every situation, so a comparative study using simulated data sets is proposed here, using threshold values suggested by the proponents or those widely used in QSAR modeling. In addition, a different and simple external validation measure, the concordance correlation coefficient (CCC), is proposed and compared with other criteria. Huge data sets were used to study the general behavior of validation measures, and the concordance correlation coefficient was shown to be the most restrictive. On using simulated data sets of a more realistic size, it was found that CCC was broadly in agreement, about 96% of the time, with other validation measures in accepting models as predictive, and in almost all the examples it was the most precautionary. The proposed concordance correlation coefficient also works well on real data sets, where it seems to be more stable, and helps in making decisions when the validation measures are in conflict. Since it is conceptually simple, and given its stability and restrictiveness, we propose the concordance correlation coefficient as a complementary, or alternative, more prudent measure of a QSAR model to be externally predictive.

  15. Concordance between actual and pharmacogenetic predicted desvenlafaxine dose needed to achieve remission in major depressive disorder: a 10-week open-label study.

    PubMed

    Bousman, Chad A; Müller, Daniel J; Ng, Chee H; Byron, Keith; Berk, Michael; Singh, Ajeet B

    2017-01-01

    Pharmacogenetic-based dosing support tools have been developed to personalize antidepressant-prescribing practice. However, the clinical validity of these tools has not been adequately tested, particularly for specific antidepressants. To examine the concordance between the actual dose and a polygene pharmacogenetic predicted dose of desvenlafaxine needed to achieve symptom remission. A 10-week, open-label, prospective trial of desvenlafaxine among Caucasian adults with major depressive disorder (n=119) was conducted. Dose was clinically adjusted and at the completion of the trial, the clinical dose needed to achieve remission was compared with the predicted dose needed to achieve remission. Among remitters (n=95), there was a strong concordance (Kendall's τ-b=0.84, P=0.0001; Cohen's κ=0.82, P=0.0001) between the actual and the predicted dose need to achieve symptom remission, showing high sensitivity (≥85%), specificity (≥86%), and accuracy (≥89%) of the tool. Findings provide initial evidence for the clinical validity of a polygene pharmacogenetic-based tool for desvenlafaxine dosing.

  16. Addressing issues associated with evaluating prediction models for survival endpoints based on the concordance statistic.

    PubMed

    Wang, Ming; Long, Qi

    2016-09-01

    Prediction models for disease risk and prognosis play an important role in biomedical research, and evaluating their predictive accuracy in the presence of censored data is of substantial interest. The standard concordance (c) statistic has been extended to provide a summary measure of predictive accuracy for survival models. Motivated by a prostate cancer study, we address several issues associated with evaluating survival prediction models based on c-statistic with a focus on estimators using the technique of inverse probability of censoring weighting (IPCW). Compared to the existing work, we provide complete results on the asymptotic properties of the IPCW estimators under the assumption of coarsening at random (CAR), and propose a sensitivity analysis under the mechanism of noncoarsening at random (NCAR). In addition, we extend the IPCW approach as well as the sensitivity analysis to high-dimensional settings. The predictive accuracy of prediction models for cancer recurrence after prostatectomy is assessed by applying the proposed approaches. We find that the estimated predictive accuracy for the models in consideration is sensitive to NCAR assumption, and thus identify the best predictive model. Finally, we further evaluate the performance of the proposed methods in both settings of low-dimensional and high-dimensional data under CAR and NCAR through simulations. © 2016, The International Biometric Society.

  17. Biomarker Surrogates Do Not Accurately Predict Sputum Eosinophils and Neutrophils in Asthma

    PubMed Central

    Hastie, Annette T.; Moore, Wendy C.; Li, Huashi; Rector, Brian M.; Ortega, Victor E.; Pascual, Rodolfo M.; Peters, Stephen P.; Meyers, Deborah A.; Bleecker, Eugene R.

    2013-01-01

    Background Sputum eosinophils (Eos) are a strong predictor of airway inflammation, exacerbations, and aid asthma management, whereas sputum neutrophils (Neu) indicate a different severe asthma phenotype, potentially less responsive to TH2-targeted therapy. Variables such as blood Eos, total IgE, fractional exhaled nitric oxide (FeNO) or FEV1% predicted, may predict airway Eos, while age, FEV1%predicted, or blood Neu may predict sputum Neu. Availability and ease of measurement are useful characteristics, but accuracy in predicting airway Eos and Neu, individually or combined, is not established. Objectives To determine whether blood Eos, FeNO, and IgE accurately predict sputum eosinophils, and age, FEV1% predicted, and blood Neu accurately predict sputum neutrophils (Neu). Methods Subjects in the Wake Forest Severe Asthma Research Program (N=328) were characterized by blood and sputum cells, healthcare utilization, lung function, FeNO, and IgE. Multiple analytical techniques were utilized. Results Despite significant association with sputum Eos, blood Eos, FeNO and total IgE did not accurately predict sputum Eos, and combinations of these variables failed to improve prediction. Age, FEV1%predicted and blood Neu were similarly unsatisfactory for prediction of sputum Neu. Factor analysis and stepwise selection found FeNO, IgE and FEV1% predicted, but not blood Eos, correctly predicted 69% of sputum Eospredicted 64% of sputum Neupredict both sputum Eos and Neu accurately assigned only 41% of samples. Conclusion Despite statistically significant associations FeNO, IgE, blood Eos and Neu, FEV1%predicted, and age are poor surrogates, separately and combined, for accurately predicting sputum eosinophils and neutrophils. PMID:23706399

  18. A comparison of predictions obtained from wind tunnel tests and the results from cruising flight: Airbus and Concorde. [conferences

    NASA Technical Reports Server (NTRS)

    Berger, J.

    1979-01-01

    Following a summary of the methods used to establish aerodynamic data and propulsion data, a comparison was made in the form of the drag (or thrust) difference between flight results and predictions made on the basis of these data. Certain hypothesis and improvements on aerodynamic data were presented in order to explain the slight deficit found on Airbus and Concorde.

  19. Concordance between actual and pharmacogenetic predicted desvenlafaxine dose needed to achieve remission in major depressive disorder: a 10-week open-label study

    PubMed Central

    Müller, Daniel J.; Ng, Chee H.; Byron, Keith; Berk, Michael; Singh, Ajeet B.

    2017-01-01

    Background Pharmacogenetic-based dosing support tools have been developed to personalize antidepressant-prescribing practice. However, the clinical validity of these tools has not been adequately tested, particularly for specific antidepressants. Objective To examine the concordance between the actual dose and a polygene pharmacogenetic predicted dose of desvenlafaxine needed to achieve symptom remission. Materials and methods A 10-week, open-label, prospective trial of desvenlafaxine among Caucasian adults with major depressive disorder (n=119) was conducted. Dose was clinically adjusted and at the completion of the trial, the clinical dose needed to achieve remission was compared with the predicted dose needed to achieve remission. Results Among remitters (n=95), there was a strong concordance (Kendall’s τ-b=0.84, P=0.0001; Cohen’s κ=0.82, P=0.0001) between the actual and the predicted dose need to achieve symptom remission, showing high sensitivity (≥85%), specificity (≥86%), and accuracy (≥89%) of the tool. Conclusion Findings provide initial evidence for the clinical validity of a polygene pharmacogenetic-based tool for desvenlafaxine dosing. PMID:27779571

  20. [Inter-rater concordance of the "Nursing Activities Score" in intensive care].

    PubMed

    Valls-Matarín, Josefa; Salamero-Amorós, Maria; Roldán-Gil, Carmen; Quintana-Riera, Salvador

    2015-01-01

    To evaluate inter-rater concordance in the valuation of the "Nursing Activities Score". Cross-sectional descriptive study conducted from December 2012 until June 2013 in a general intensive care unit with twelve beds. Three evaluator nurses, simultaneously and independently, through the patient daily charts, scored the nursing workload using Nursing Activities Score scale in all patients admitted over 18 years old. Three hundreds and thirty-nine records were collected. The intra-class correlation coefficient (ICC) between evaluators was 0.92 (0.89-0.94). A perfect concordance was obtained in 39.1% of the items, with 52.2% having a high, and 8.7% having lower concordance, corresponding to two of the items with multiple scoring options. Significant differences between two of the evaluators (P=.049) were found. Although the inter-rater concordance was high, more accurate records are needed to reduce the variability of the items with multiple options and to allow more accuracy in the interpretation and measurement of the data regarding nursing workload. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  1. Risk prediction for chronic kidney disease progression using heterogeneous electronic health record data and time series analysis.

    PubMed

    Perotte, Adler; Ranganath, Rajesh; Hirsch, Jamie S; Blei, David; Elhadad, Noémie

    2015-07-01

    As adoption of electronic health records continues to increase, there is an opportunity to incorporate clinical documentation as well as laboratory values and demographics into risk prediction modeling. The authors develop a risk prediction model for chronic kidney disease (CKD) progression from stage III to stage IV that includes longitudinal data and features drawn from clinical documentation. The study cohort consisted of 2908 primary-care clinic patients who had at least three visits prior to January 1, 2013 and developed CKD stage III during their documented history. Development and validation cohorts were randomly selected from this cohort and the study datasets included longitudinal inpatient and outpatient data from these populations. Time series analysis (Kalman filter) and survival analysis (Cox proportional hazards) were combined to produce a range of risk models. These models were evaluated using concordance, a discriminatory statistic. A risk model incorporating longitudinal data on clinical documentation and laboratory test results (concordance 0.849) predicts progression from state III CKD to stage IV CKD more accurately when compared to a similar model without laboratory test results (concordance 0.733, P<.001), a model that only considers the most recent laboratory test results (concordance 0.819, P < .031) and a model based on estimated glomerular filtration rate (concordance 0.779, P < .001). A risk prediction model that takes longitudinal laboratory test results and clinical documentation into consideration can predict CKD progression from stage III to stage IV more accurately than three models that do not take all of these variables into consideration. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

  2. 33 CFR 165.1199 - Security Zones; Military Ocean Terminal Concord (MOTCO), Concord, California.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Security Zones; Military Ocean... Coast Guard District § 165.1199 Security Zones; Military Ocean Terminal Concord (MOTCO), Concord..., extending from the surface to the sea floor, within 500 yards of the three Military Ocean Terminal Concord...

  3. 33 CFR 165.1199 - Security Zones; Military Ocean Terminal Concord (MOTCO), Concord, California.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Security Zones; Military Ocean... Coast Guard District § 165.1199 Security Zones; Military Ocean Terminal Concord (MOTCO), Concord..., extending from the surface to the sea floor, within 500 yards of the three Military Ocean Terminal Concord...

  4. 33 CFR 165.1199 - Security Zones; Military Ocean Terminal Concord (MOTCO), Concord, California.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Security Zones; Military Ocean... Coast Guard District § 165.1199 Security Zones; Military Ocean Terminal Concord (MOTCO), Concord..., extending from the surface to the sea floor, within 500 yards of the three Military Ocean Terminal Concord...

  5. 33 CFR 165.1199 - Security Zones; Military Ocean Terminal Concord (MOTCO), Concord, California.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Security Zones; Military Ocean... Coast Guard District § 165.1199 Security Zones; Military Ocean Terminal Concord (MOTCO), Concord..., extending from the surface to the sea floor, within 500 yards of the three Military Ocean Terminal Concord...

  6. 33 CFR 165.1199 - Security Zones; Military Ocean Terminal Concord (MOTCO), Concord, California.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Security Zones; Military Ocean... Coast Guard District § 165.1199 Security Zones; Military Ocean Terminal Concord (MOTCO), Concord..., extending from the surface to the sea floor, within 500 yards of the three Military Ocean Terminal Concord...

  7. Accurate Identification of Fear Facial Expressions Predicts Prosocial Behavior

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2007-05-01

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

  9. Accurate Binding Free Energy Predictions in Fragment Optimization.

    PubMed

    Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

    2015-11-23

    Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

  10. Can phenological models predict tree phenology accurately under climate change conditions?

    NASA Astrophysics Data System (ADS)

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean Michel; García de Cortázar-Atauri, Inaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2014-05-01

    The onset of the growing season of trees has been globally earlier by 2.3 days/decade during the last 50 years because of global warming and this trend is predicted to continue according to climate forecast. The effect of temperature on plant phenology is however not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud dormancy, and on the other hand higher temperatures are necessary to promote bud cells growth afterwards. Increasing phenological changes in temperate woody species have strong impacts on forest trees distribution and productivity, as well as crops cultivation areas. Accurate predictions of trees phenology are therefore a prerequisite to understand and foresee the impacts of climate change on forests and agrosystems. Different process-based models have been developed in the last two decades to predict the date of budburst or flowering of woody species. They are two main families: (1) one-phase models which consider only the ecodormancy phase and make the assumption that endodormancy is always broken before adequate climatic conditions for cell growth occur; and (2) two-phase models which consider both the endodormancy and ecodormancy phases and predict a date of dormancy break which varies from year to year. So far, one-phase models have been able to predict accurately tree bud break and flowering under historical climate. However, because they do not consider what happens prior to ecodormancy, and especially the possible negative effect of winter temperature warming on dormancy break, it seems unlikely that they can provide accurate predictions in future climate conditions. It is indeed well known that a lack of low temperature results in abnormal pattern of bud break and development in temperate fruit trees. An accurate modelling of the dormancy break date has thus become a major issue in phenology modelling. Two-phases phenological models predict that global warming should delay

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

    PubMed

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

    2016-11-01

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

  12. Concordant Chemical Reaction Networks

    PubMed Central

    Shinar, Guy; Feinberg, Martin

    2015-01-01

    We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with any weakly monotonic kinetics, invariably give rise to kinetic systems that are injective — a quality that, among other things, precludes the possibility of switch-like transitions between distinct positive steady states. We also provide persistence characteristics of concordant networks, instability implications of discordance, and consequences of stronger variants of concordance. Some of our results are in the spirit of recent ones by Banaji and Craciun, but here we do not require that every species suffer a degradation reaction. This is especially important in studying biochemical networks, for which it is rare to have all species degrade. PMID:22659063

  13. Work happiness among teachers: a day reconstruction study on the role of self-concordance.

    PubMed

    Tadić, Maja; Bakker, Arnold B; Oerlemans, Wido G M

    2013-12-01

    Self-concordant work motivation arises from one's authentic choices, personal values, and interests. In the present study, we investigated whether self-concordant motivation may fluctuate from one work-related task to the next. On the basis of self-determination theory, we hypothesized that momentary self-concordance buffers the negative impact of momentary work demands on momentary happiness. We developed a modified version of the day reconstruction method to investigate self-concordance, work demands, and happiness during specific work-related tasks on a within-person and within-day level. In total, 132 teachers completed a daily diary on three consecutive work days as well as a background questionnaire. The daily diary resulted in 792 reported work activities and activity-related work demands, self-concordance, and happiness scores. Multilevel analysis showed that-for most work activities-state self-concordant motivation buffered the negative association of work demands with happiness. These findings add to the literature on motivation and well-being by showing that the levels of self-concordance and happiness experienced by employees vary significantly on a within-day level and show a predictable pattern. We discuss theoretical and practical implications of the findings to increase employees' well-being. © 2013.

  14. Testing the effects of suppression and reappraisal on emotional concordance using a multivariate multilevel model.

    PubMed

    Butler, Emily A; Gross, James J; Barnard, Kobus

    2014-04-01

    In theory, the essence of emotion is coordination across experiential, behavioral, and physiological systems in the service of functional responding to environmental demands. However, people often regulate emotions, which could either reduce or enhance cross-system concordance. The present study tested the effects of two forms of emotion regulation (expressive suppression, positive reappraisal) on concordance of subjective experience (positive-negative valence), expressive behavior (positive and negative), and physiology (inter-beat interval, skin conductance, blood pressure) during conversations between unacquainted young women. As predicted, participants asked to suppress showed reduced concordance for both positive and negative emotions. Reappraisal instructions also reduced concordance for negative emotions, but increased concordance for positive ones. Both regulation strategies had contagious interpersonal effects on average levels of responding. Suppression reduced overall expression for both regulating and uninstructed partners, while reappraisal reduced negative experience. Neither strategy influenced the uninstructed partners' concordance. These results suggest that emotion regulation impacts concordance by altering the temporal coupling of phasic subsystem responses, rather than by having divergent effects on subsystem tonic levels. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. The relationship between sexual concordance and interoception in anxious and nonanxious women.

    PubMed

    Suschinsky, Kelly D; Lalumière, Martin L

    2014-04-01

    Sexual concordance refers to the association between physiological and self-reported sexual arousal. Women typically exhibit lower sexual concordance scores than men. There is also a sex difference in interoception--awareness of (nonsexual) physiological states or responses--such that women, compared with men, tend to be less aware of and less accurate at detecting changes in their physiological responses. Women with anxiety problems tend to have better interoceptive abilities than nonanxious women. To investigate whether women's lower sexual concordance is associated with interoception using a sample likely to show high variation in interoceptive abilities. Sixteen anxious and 15 nonanxious women were presented with twelve 90 seconds sexual and nonsexual film clips while their genital response, heart rate, and respiration rate were measured. A heartbeat mental tracking task was also employed. Genital response was measured with a vaginal photoplethysmograph. Heart rate was measured with an electrocardiogram and respiration rate with a thermistor. Participants estimated their physiological responses after each film. A mental tracking task was also used to assess participants' awareness of heart rate. Within-subject correlations were computed for each physiological/self-reported response combination. Overall, sexual concordance (i.e., the correlation between genital responses and perceptions of genital response) was not significantly associated with heart rate awareness or respiration rate awareness. Anxious women did not exhibit significantly higher sexual concordance or heart rate awareness than nonanxious women; the nonanxious women actually exhibited higher respiration rate awareness. The results suggest that sexual concordance may be a distinct phenomenon from interoception and in need of its own explanation. © 2013 International Society for Sexual Medicine.

  16. Spousal concordance in attitudes toward violence and reported physical abuse in African couples.

    PubMed

    Alio, Amina P; Clayton, Heather B; Garba, Madeleine; Mbah, Alfred K; Daley, Ellen; Salihu, Hamisu M

    2011-09-01

    We examined the potential association between African couples' concordance on attitudes toward violence (ATV) and risk for intimate partner violence (IPV). Analyses included 13,837 couples from Demographic and Health Surveys conducted between 2003 and 2007, from six African countries. Concordance on ATV was defined as both spouses justifying physical abuse, and IPV was defined as incidence of a physically violent act against the wife. We constructed a concordance measure from the surveys to assess overall and country-level differences in couple's ATV concordance rates and assessed the association between concordance in ATV and IPV using hierarchical regression modeling that adjusted for multilevel influences on risk estimates. Negative concordance (perfect agreement in negative ATV) was used as referent category in all analyses. Overall, spousal ATV concordance was associated with higher likelihood for IPV (adjusted odds ratio [AOR] = 2.27, 95% confidence interval [CI] = [2.01, 2.56]). The level of wealth, educational attainment, rural/urban residence, presence of a cowife, religion, maternal age, and parity were characteristics that predicted the occurrence of IPV within couples. Spousal ATV concordance was significantly associated with violence in every African nation included in the analysis except Rwanda. African couples with high rates of ATV concor- dance experience higher risks for IPV, with some variation in magnitude of risk across countries. In African settings, ATV positive concordance could serve as a supplemental screening tool to detect spousal violence. Understanding ATV could potentially enhance our ability to formulate public health intervention to detect and prevent spousal abuse.

  17. Fulminant clostridium difficile colitis: comparing computed tomography with histopathology: are they concordant?

    PubMed

    Felder, Seth I; Larson, Brent; Balzer, Bonnie; Wachsman, Ashley; Haker, Katherine; Fleshner, Phillip; Annamalai, Alagappan; Margulies, Daniel R

    2014-10-01

    A Total abdominal colectomy (TAC) is recommended for fulminant Clostridium difficile colitis (FCDC) because intraoperative assessment of diseased segments is inaccurate. To determine whether computerized tomography (CT) provides an accurate assessment of disease, we examined the concordance between CT and histopathologic colitis distribution in patients undergoing TAC for FCDC. The ileocolon was divided into seven distinct segments. Of 20 patients meeting criteria, the median interval between preoperative CT and TAC was 1.5 days (range, 0 to 23 days), and mortality was 65 per cent. The CT distribution of colitis was pancolitis in 12 patients and segmental in eight. Nine of the 12 patients with CT pancolitis had histologic pancolitis (75% concordance). Four of the eight patients with CT-diagnosed segmental disease had histologic segmental disease (50% concordance). For patients with FCDC, the distribution of colitis on CT agrees with the histopathologic extent of disease in the majority of patients. However, discordance between CT and histologic extent of disease was present in 25 to 50 per cent of patients. Therefore, the recommendation for TAC rather than segmental resection for FCDC remains justified.

  18. Mohs Micrographic Surgery Dermatopathology Concordance in Canada: A Single-Institution Experience.

    PubMed

    Chia, Justin C; Abi Daoud, Marie S; Williamson, Tyler S; Kurwa, Habib A

    2018-06-01

    Mohs micrographic surgery (MMS) is a surgical modality that achieves high cure rates of nonmelanoma skin cancers but is dependent on accurate histologic examination of surgical margins. Therefore, quality assurance is essential to ongoing assessment of histological margins. To prospectively determine the concordance rate between a Mohs surgeon (MS) and dermatopathologist (DP) with respect to tumour status (ie, present or absent) and tumour type. Secondary end points were to determine the relationship between discordant interpretations and slide quality and to assess the feasibility of using an electronic webform for data collection. Ten percent (10%) of the planned MMS cases between January 2015 and March 2016 were randomly selected by a histotechnologist at the start of each month. The MS and DP were blinded to the chosen cases, and slides were reviewed independently at the beginning of the following month. Data were collected using an online webform. A blinded third party determined if there were discrepancies in interpretation, and any discordant slides were reviewed together and a consensus was reached. A total of 270 slides from 54 total cases were reviewed. The overall tumour status concordance rate was 93.6%. Cohen's κ was 0.86. Tumour type concordance was 98.9%. No discrepancy required a change in patient care. All discrepant slides were from cases that required multiple stages. This is the first study looking at MS-DP concordance in Canada, and our findings support the MS acting as his or her own pathologist.

  19. Diagnostic concordance between mobile interfaces and conventional workstations for emergency imaging assessment.

    PubMed

    Venson, José Eduardo; Bevilacqua, Fernando; Berni, Jean; Onuki, Fabio; Maciel, Anderson

    2018-05-01

    Mobile devices and software are now available with sufficient computing power, speed and complexity to allow for real-time interpretation of radiology exams. In this paper, we perform a multivariable user study that investigates concordance of image-based diagnoses provided using mobile devices on the one hand and conventional workstations on the other hand. We performed a between-subjects task-analysis using CT, MRI and radiography datasets. Moreover, we investigated the adequacy of the screen size, image quality, usability and the availability of the tools necessary for the analysis. Radiologists, members of several teams, participated in the experiment under real work conditions. A total of 64 studies with 93 main diagnoses were analyzed. Our results showed that 56 cases were classified with complete concordance (87.69%), 5 cases with almost complete concordance (7.69%) and 1 case (1.56%) with partial concordance. Only 2 studies presented discordance between the reports (3.07%). The main reason to explain the cause of those disagreements was the lack of multiplanar reconstruction tool in the mobile viewer. Screen size and image quality had no direct impact on the mobile diagnosis process. We concluded that for images from emergency modalities, a mobile interface provides accurate interpretation and swift response, which could benefit patients' healthcare. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Accurate Prediction of Motor Failures by Application of Multi CBM Tools: A Case Study

    NASA Astrophysics Data System (ADS)

    Dutta, Rana; Singh, Veerendra Pratap; Dwivedi, Jai Prakash

    2018-02-01

    Motor failures are very difficult to predict accurately with a single condition-monitoring tool as both electrical and the mechanical systems are closely related. Electrical problem, like phase unbalance, stator winding insulation failures can, at times, lead to vibration problem and at the same time mechanical failures like bearing failure, leads to rotor eccentricity. In this case study of a 550 kW blower motor it has been shown that a rotor bar crack was detected by current signature analysis and vibration monitoring confirmed the same. In later months in a similar motor vibration monitoring predicted bearing failure and current signature analysis confirmed the same. In both the cases, after dismantling the motor, the predictions were found to be accurate. In this paper we will be discussing the accurate predictions of motor failures through use of multi condition monitoring tools with two case studies.

  1. Radiomics biomarkers for accurate tumor progression prediction of oropharyngeal cancer

    NASA Astrophysics Data System (ADS)

    Hadjiiski, Lubomir; Chan, Heang-Ping; Cha, Kenny H.; Srinivasan, Ashok; Wei, Jun; Zhou, Chuan; Prince, Mark; Papagerakis, Silvana

    2017-03-01

    Accurate tumor progression prediction for oropharyngeal cancers is crucial for identifying patients who would best be treated with optimized treatment and therefore minimize the risk of under- or over-treatment. An objective decision support system that can merge the available radiomics, histopathologic and molecular biomarkers in a predictive model based on statistical outcomes of previous cases and machine learning may assist clinicians in making more accurate assessment of oropharyngeal tumor progression. In this study, we evaluated the feasibility of developing individual and combined predictive models based on quantitative image analysis from radiomics, histopathology and molecular biomarkers for oropharyngeal tumor progression prediction. With IRB approval, 31, 84, and 127 patients with head and neck CT (CT-HN), tumor tissue microarrays (TMAs) and molecular biomarker expressions, respectively, were collected. For 8 of the patients all 3 types of biomarkers were available and they were sequestered in a test set. The CT-HN lesions were automatically segmented using our level sets based method. Morphological, texture and molecular based features were extracted from CT-HN and TMA images, and selected features were merged by a neural network. The classification accuracy was quantified using the area under the ROC curve (AUC). Test AUCs of 0.87, 0.74, and 0.71 were obtained with the individual predictive models based on radiomics, histopathologic, and molecular features, respectively. Combining the radiomics and molecular models increased the test AUC to 0.90. Combining all 3 models increased the test AUC further to 0.94. This preliminary study demonstrates that the individual domains of biomarkers are useful and the integrated multi-domain approach is most promising for tumor progression prediction.

  2. Embodied simulation as part of affective evaluation processes: task dependence of valence concordant EMG activity.

    PubMed

    Weinreich, André; Funcke, Jakob Maria

    2014-01-01

    Drawing on recent findings, this study examines whether valence concordant electromyography (EMG) responses can be explained as an unconditional effect of mere stimulus processing or as somatosensory simulation driven by task-dependent processing strategies. While facial EMG over the Corrugator supercilii and the Zygomaticus major was measured, each participant performed two tasks with pictures of album covers. One task was an affective evaluation task and the other was to attribute the album covers to one of five decades. The Embodied Emotion Account predicts that valence concordant EMG is more likely to occur if the task necessitates a somatosensory simulation of the evaluative meaning of stimuli. Results support this prediction with regard to Corrugator supercilii in that valence concordant EMG activity was only present in the affective evaluation task but not in the non-evaluative task. Results for the Zygomaticus major were ambiguous. Our findings are in line with the view that EMG activity is an embodied part of the evaluation process and not a mere physical outcome.

  3. SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

    PubMed

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-05-01

    Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are

  4. SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

    PubMed Central

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-01-01

    Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of

  5. Where Do Self-Concordant Goals Come From? The Role of Domain-Specific Psychological Need Satisfaction.

    PubMed

    Milyavskaya, Marina; Nadolny, Daniel; Koestner, Richard

    2014-06-01

    Previous research has shown that self-concordant goals are more likely to be attained. But what leads someone to adopt a self-concordant goal in the first place? The present research addresses this question by looking at the domains in which goals are set, focusing on the amount of psychological need satisfaction experienced in these domains. Across three experimental studies, we demonstrate that domain-related need satisfaction predicts the extent to which people adopt self-concordant goals in a given domain, laying the foundation for successful goal pursuit. In addition, we show that need satisfaction influences goal self-concordance because in need-satisfying domains people are both more likely to choose the most self-concordant goal (among a set of comparable choices), and are more likely to internalize the possible goals. The implications of this research for goal setting and pursuit as well as for the importance of examining goals within their broader motivational framework are discussed. © 2014 by the Society for Personality and Social Psychology, Inc.

  6. Phenotypic concordance in familial inflammatory bowel disease (IBD). Results of a nationwide IBD Spanish database.

    PubMed

    Cabré, Eduard; Mañosa, Míriam; García-Sánchez, Valle; Gutiérrez, Ana; Ricart, Elena; Esteve, Maria; Guardiola, Jordi; Aguas, Mariam; Merino, Olga; Ponferrada, Angel; Gisbert, Javier P; Garcia-Planella, Esther; Ceña, Gloria; Cabriada, José L; Montoro, Miguel; Domènech, Eugeni

    2014-07-01

    Disease outcome has been found to be poorer in familial inflammatory bowel disease (IBD) than in sporadic forms, but assessment of phenotypic concordance in familial IBD provided controversial results. We assessed the concordance for disease type and phenotypic features in IBD families. Patients with familial IBD were identified from the IBD Spanish database ENEIDA. Families in whom at least two members were in the database were selected for concordance analysis (κ index). Concordance for type of IBD [Crohn's disease (CD) vs. ulcerative colitis (UC)], as well as for disease extent, localization and behaviour, perianal disease, extraintestinal manifestations, and indicators of severe disease (i.e., need for immunosuppressors, biological agents, and surgery) for those pairs concordant for IBD type, were analyzed. 798 out of 11,905 IBD patients (7%) in ENEIDA had familial history of IBD. Complete data of 107 families (231 patients and 144 consanguineous pairs) were available for concordance analyses. The youngest members of the pairs were diagnosed with IBD at a significantly younger age (p<0.001) than the oldest ones. Seventy-six percent of pairs matched up for the IBD type (κ=0.58; 95%CI: 0.42-0.73, moderate concordance). There was no relevant concordance for any of the phenotypic items assessed in both diseases. Familial IBD is associated with diagnostic anticipation in younger individuals. Familial history does not allow predicting any phenotypic feature other than IBD type. Copyright © 2013 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

  7. Molecular classification of endometrial carcinoma on diagnostic specimens is highly concordant with final hysterectomy: Earlier prognostic information to guide treatment.

    PubMed

    Talhouk, Aline; Hoang, Lien N; McConechy, Melissa K; Nakonechny, Quentin; Leo, Joyce; Cheng, Angela; Leung, Samuel; Yang, Winnie; Lum, Amy; Köbel, Martin; Lee, Cheng-Han; Soslow, Robert A; Huntsman, David G; Gilks, C Blake; McAlpine, Jessica N

    2016-10-01

    Categorization and risk stratification of endometrial carcinomas is inadequate; histomorphologic assessment shows considerable interobserver variability, and risk of metastases and recurrence can only be derived after surgical staging. We have developed a Proactive Molecular Risk classification tool for Endometrial cancers (ProMisE) that identifies four distinct prognostic subgroups. Our objective was to assess whether molecular classification could be performed on diagnostic endometrial specimens obtained prior to surgical staging and its concordance with molecular classification performed on the subsequent hysterectomy specimen. Sequencing of tumors for exonuclease domain mutations (EDMs) in POLE and immunohistochemistry for mismatch repair (MMR) proteins and p53 were applied to both pre- and post-staging archival specimens from 60 individuals to identify four molecular subgroups: MMR-D, POLE EDM, p53 wild type, p53 abn (abnormal). Three gynecologic subspecialty pathologists assigned histotype and grade to a subset of samples. Concordance of molecular and clinicopathologic subgroup assignments were determined, comparing biopsy/curetting to hysterectomy specimens. Complete molecular and pathologic categorization was achieved in 57 cases. Concordance metrics for pre- vs. post-staging endometrial samples categorized by ProMisE were highly favorable; average per ProMisE class sensitivity(0.9), specificity(0.96), PPV(0.9), NPV(0.96) and kappa statistic 0.86(95%CI, 0.72-0.93), indicating excellent agreement. We observed the highest level of concordance for 'p53 abn' tumors, the group associated with the worst prognosis. In contrast, grade and histotype assignment from original pathology reports pre- vs. post-staging showed only moderate levels of agreement (kappa=0.55 and 0.44 respectively); even with subspecialty pathology review only moderate levels of agreement were observed. Molecular classification can be achieved on diagnostic endometrial samples and accurately

  8. PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

    PubMed Central

    Bendl, Jaroslav; Stourac, Jan; Salanda, Ondrej; Pavelka, Antonin; Wieben, Eric D.; Zendulka, Jaroslav; Brezovsky, Jan; Damborsky, Jiri

    2014-01-01

    Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp. PMID:24453961

  9. Goal striving, goal attainment, and well-being: adapting and testing the self-concordance model in sport.

    PubMed

    Smith, Alison; Ntoumanis, Nikos; Duda, Joan

    2007-12-01

    Grounded in self-determination theory (Deci & Ryan, 1985) and the self-concordance model (Sheldon & Elliot, 1999), this study examined the motivational processes underlying goal striving in sport as well as the role of perceived coach autonomy support in the goal process. Structural equation modeling with a sample of 210 British athletes showed that autonomous goal motives positively predicted effort, which, in turn, predicted goal attainment. Goal attainment was positively linked to need satisfaction, which, in turn, predicted psychological well-being. Effort and need satisfaction were found to mediate the associations between autonomous motives and goal attainment and between attainment and well-being, respectively. Controlled motives negatively predicted well-being, and coach autonomy support positively predicted both autonomous motives and need satisfaction. Associations of autonomous motives with effort were not reducible to goal difficulty, goal specificity, or goal efficacy. These findings support the self-concordance model as a framework for further research on goal setting in sport.

  10. Heart rate during basketball game play and volleyball drills accurately predicts oxygen uptake and energy expenditure.

    PubMed

    Scribbans, T D; Berg, K; Narazaki, K; Janssen, I; Gurd, B J

    2015-09-01

    There is currently little information regarding the ability of metabolic prediction equations to accurately predict oxygen uptake and exercise intensity from heart rate (HR) during intermittent sport. The purpose of the present study was to develop and, cross-validate equations appropriate for accurately predicting oxygen cost (VO2) and energy expenditure from HR during intermittent sport participation. Eleven healthy adult males (19.9±1.1yrs) were recruited to establish the relationship between %VO2peak and %HRmax during low-intensity steady state endurance (END), moderate-intensity interval (MOD) and high intensity-interval exercise (HI), as performed on a cycle ergometer. Three equations (END, MOD, and HI) for predicting %VO2peak based on %HRmax were developed. HR and VO2 were directly measured during basketball games (6 male, 20.8±1.0 yrs; 6 female, 20.0±1.3yrs) and volleyball drills (12 female; 20.8±1.0yrs). Comparisons were made between measured and predicted VO2 and energy expenditure using the 3 equations developed and 2 previously published equations. The END and MOD equations accurately predicted VO2 and energy expenditure, while the HI equation underestimated, and the previously published equations systematically overestimated VO2 and energy expenditure. Intermittent sport VO2 and energy expenditure can be accurately predicted from heart rate data using either the END (%VO2peak=%HRmax x 1.008-17.17) or MOD (%VO2peak=%HRmax x 1.2-32) equations. These 2 simple equations provide an accessible and cost-effective method for accurate estimation of exercise intensity and energy expenditure during intermittent sport.

  11. Correlates of and Couples’ Concordance in Reports of Recent Sexual Behavior and Contraceptive Use

    PubMed Central

    Koffi, Alain K.; Adjiwanou, Visseho D.; Becker, Stan; Olaolorun, Funmilola; Tsui, Amy O.

    2014-01-01

    This study uses couple-level data to measure couples’ concordance of self-reported time since last coitus and of condom and other contraceptive use at last sexual intercourse among monogamous couples in Liberia (N = 1,673), Madagascar (N = 4,138), and Namibia (N = 588). The study also examines the characteristics associated with sexual behavior and contraceptive use occurring in the 28 days prior to the interviews among couples whose reports are concordant. Overall, our study finds less than 75 percent concordance in reporting of time since last coitus. Use of condoms and other contraceptives yielded fair (0.27) to substantial (0.67) agreement on the kappa index. Factors predicting a shorter time since last coitus among concordant couples in at least two of the countries included wealth, spousal age difference, education, and both partners wanting another child. The discordant reports of recent sexual behavior and contraceptive use suggest that caution should be exercised when inferring couples’ behavior from the report of one spouse, that concordant reports should be examined when possible, that methodological changes to improve the validity of spousal reports should be pursued, and that family planning and HIV-prevention programs should target those groups found to be using condoms and other contraceptives less frequently, particularly poorer couples. PMID:23185870

  12. Correlates of and couples' concordance in reports of recent sexual behavior and contraceptive use.

    PubMed

    Koffi, Alain K; Adjiwanou, Visseho D; Becker, Stan; Olaolorun, Funmilola; Tsui, Amy O

    2012-03-01

    This study uses couple-level data to measure couples' concordance of self-reported time since last coitus and of condom and other contraceptive use at last sexual intercourse among monogamous couples in Liberia (N = 1,673), Madagascar (N = 4,138), and Namibia (N = 588). The study also examines the characteristics associated with sexual behavior and contraceptive use occurring in the 28 days prior to the interviews among couples whose reports are concordant. Overall, our study finds less than 75 percent concordance in reporting of time since last coitus. Use of condoms and other contraceptives yielded fair (0.27) to substantial (0.67) agreement on the kappa index. Factors predicting a shorter time since last coitus among concordant couples in at least two of the countries included wealth, spousal age difference, education, and both partners wanting another child. The discordant reports of recent sexual behavior and contraceptive use suggest that caution should be exercised when inferring couples' behavior from the report of one spouse, that concordant reports should be examined when possible, that methodological changes to improve the validity of spousal reports should be pursued, and that family planning and HIV-prevention programs should target those groups found to be using condoms and other contraceptives less frequently, particularly poorer couples.

  13. Super Memory Bros.: going from mirror patterns to concordant patterns via similarity enhancements.

    PubMed

    Ozubko, Jason D; Joordens, Steve

    2008-12-01

    When memory is contrasted for stimuli belonging to distinct stimulus classes, one of two patterns is observed: a mirror pattern, in which one stimulus gives rise to higher hits but lower false alarms (e.g., the frequency-based mirror effect) or a concordant pattern, in which one stimulus class gives rise both to higher hits and to higher false alarms (e.g., the pseudoword effect). On the basis of the dual-process account proposed by Joordens and Hockley (2000), we predict that mirror patterns occur when one stimulus class is more familiar and less distinctive than another, whereas concordant patterns occur when one stimulus class is more familiar than another. We tested these assumptions within a video game paradigm using novel stimuli that allow manipulations in terms of distinctiveness and familiarity (via similarity). When more distinctive, less familiar items are contrasted with less distinctive, more familiar items, a mirror pattern is observed. Systematically enhancing the familiarity of stimuli transforms the mirror pattern to a concordant pattern as predicted. Although our stimuli differ considerably from those used in examinations of the frequency-based mirror effect and the pseudoword effect, the implications of our findings with respect to those phenomena are also discussed.

  14. No decision about me without me: concordance operationalised.

    PubMed

    Snowden, Austyn; Marland, Glenn

    2013-05-01

    To demonstrate that concordance can be operationalised to the benefit of patients. Concordance can be understood as a composite of knowledge, health beliefs and collaboration. In discussing any clinical decision, it would be ideal if different views could be incorporated to reach the most coherent decision. This is a definition of concordance, a widely agreed ideal in nursing. There are limits, however, that make the practice of concordance problematic. Sometimes there is little time or willingness to discuss issues in depth. Some views of the world are considered more worthy than others. As a consequence, clinical guidelines currently prioritise easier to measure outcomes of negotiation, such as adherence. This discursive article argues that prioritising adherence is a fundamental error, incoherent with current strategic rhetoric such as the Department of Health's 'no decision about me without me'. The impact of prioritising concordance is contrasted with adherence-based interventions. Where adherence is a goal of treatment, non-adherence is considered problematic. This value judgment is not useful and does not occur in a consultation that prioritises concordance. However, concordance is difficult to translate into clinical practice. This article shows that concordance can be operationalised by considering it a composite of health beliefs, knowledge and collaboration. The main thesis is that different behaviours can always be incorporated into a concordance framework. This negates the necessity for adherence as an endpoint in itself. Fifty per cent of people do not take medicines as prescribed. Interventions focused towards improving adherence are only ever partially successful. This is because it presupposes the clinician is right. Concordance by contrast is more coherent with person centred care and thus more likely to generate clinically meaningful outcomes for patients. © 2012 Blackwell Publishing Ltd.

  15. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  16. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

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

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, andmore » its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.« less

  17. Consanguinity and spousal concordance in Kuwait.

    PubMed

    al-Kandari, Y; Crews, D E; Poirier, F E

    2002-12-01

    Consanguineous marriage is favored in Kuwait. This research focuses on the relationship of physical and cultural traits to marriage types in Kuwait and examines concordance as a function of consanguinity and marriage duration. In a nonrandom opportunistic sample of 242 couples anthropometric and blood pressure data have been collected as well as data on acculturation, religiosity, Farsi proficiency, level of education, occupation, and attitudes regarding fertility. Significant concordances occur in cultural characteristics among couples in all three types of marriages with respect to the degree of religiosity, acculturation, language similarity, education, and occupation. Non-consanguineous spouses have the highest concordance in educational level, occupation, and degree of acculturation, but the lowest for religiosity and Farsi proficiency. Nonkin marriages seem to be based on personal preferences. In the wider potential nonkin marriage pool spouses show more concordance in stature and education indicating the positive assortative mating for those traits. Non-consanguineous spouses show a significant association for triceps and subscapular skinfold thicknesses hip and waist circumferences, and body fat distribution. Unrelated spouses exhibit more concordance for physical traits than do related spouses. There is a significant correlation between spouses in first and double cousin marriages as well as in spouses in second and less than second cousin unions for systolic and diastolic blood pressure, while non-consanguineous spouses show a significant association in diastolic blood pressure only.

  18. Daily Concordance between Parent and Adolescent Sleep Habits

    PubMed Central

    Fuligni, Andrew J.; Tsai, Kim M.; Krull, Jennifer L.; Gonzales, Nancy A.

    2014-01-01

    Purpose To assess the daily concordance between parent and adolescent daily sleep habits, how that concordance compares to other predictors of sleep, and whether the degree of concordance varies across families. Methods A total of 421 adolescents (Mage = 15.03 years) and their primary caregivers (Mage = 41.93 years) reported their sleep, bed, and wake times on a daily basis for a two-week period. Approximately 80% of the sample repeated the same protocol one year later. Results Multi-level modeling indicated a significant concordance between parent and adolescent sleep, bed, and wake times on a daily basis. Concordance existed independent of other predictors of sleep such as day of the week and adolescent study time. Larger families and those with higher levels of parent-adolescent support exhibited greater concordance. Conclusions Adolescent sleep is connected to the sleep habits of their parents, above and beyond commonly-known structural and experiential factors that can shape teenage sleep. Efforts to improve teenage sleep should pay greater attention to the sleep patterns of parents and potentially other family members. PMID:25620309

  19. Disease-Concordant Twins Empower Genetic Association Studies.

    PubMed

    Tan, Qihua; Li, Weilong; Vandin, Fabio

    2017-01-01

    Genome-wide association studies with moderate sample sizes are underpowered, especially when testing SNP alleles with low allele counts, a situation that may lead to high frequency of false-positive results and lack of replication in independent studies. Related individuals, such as twin pairs concordant for a disease, should confer increased power in genetic association analysis because of their genetic relatedness. We conducted a computer simulation study to explore the power advantage of the disease-concordant twin design, which uses singletons from disease-concordant twin pairs as cases and ordinary healthy samples as controls. We examined the power gain of the twin-based design for various scenarios (i.e., cases from monozygotic and dizygotic twin pairs concordant for a disease) and compared the power with the ordinary case-control design with cases collected from the unrelated patient population. Simulation was done by assigning various allele frequencies and allelic relative risks for different mode of genetic inheritance. In general, for achieving a power estimate of 80%, the sample sizes needed for dizygotic and monozygotic twin cases were one half and one fourth of the sample size of an ordinary case-control design, with variations depending on genetic mode. Importantly, the enriched power for dizygotic twins also applies to disease-concordant sibling pairs, which largely extends the application of the concordant twin design. Overall, our simulation revealed a high value of disease-concordant twins in genetic association studies and encourages the use of genetically related individuals for highly efficiently identifying both common and rare genetic variants underlying human complex diseases without increasing laboratory cost. © 2016 John Wiley & Sons Ltd/University College London.

  20. Accurate prediction of energy expenditure using a shoe-based activity monitor.

    PubMed

    Sazonova, Nadezhda; Browning, Raymond C; Sazonov, Edward

    2011-07-01

    The aim of this study was to develop and validate a method for predicting energy expenditure (EE) using a footwear-based system with integrated accelerometer and pressure sensors. We developed a footwear-based device with an embedded accelerometer and insole pressure sensors for the prediction of EE. The data from the device can be used to perform accurate recognition of major postures and activities and to estimate EE using the acceleration, pressure, and posture/activity classification information in a branched algorithm without the need for individual calibration. We measured EE via indirect calorimetry as 16 adults (body mass index=19-39 kg·m) performed various low- to moderate-intensity activities and compared measured versus predicted EE using several models based on the acceleration and pressure signals. Inclusion of pressure data resulted in better accuracy of EE prediction during static postures such as sitting and standing. The activity-based branched model that included predictors from accelerometer and pressure sensors (BACC-PS) achieved the lowest error (e.g., root mean squared error (RMSE)=0.69 METs) compared with the accelerometer-only-based branched model BACC (RMSE=0.77 METs) and nonbranched model (RMSE=0.94-0.99 METs). Comparison of EE prediction models using data from both legs versus models using data from a single leg indicates that only one shoe needs to be equipped with sensors. These results suggest that foot acceleration combined with insole pressure measurement, when used in an activity-specific branched model, can accurately estimate the EE associated with common daily postures and activities. The accuracy and unobtrusiveness of a footwear-based device may make it an effective physical activity monitoring tool.

  1. Are EMS call volume predictions based on demand pattern analysis accurate?

    PubMed

    Brown, Lawrence H; Lerner, E Brooke; Larmon, Baxter; LeGassick, Todd; Taigman, Michael

    2007-01-01

    Most EMS systems determine the number of crews they will deploy in their communities and when those crews will be scheduled based on anticipated call volumes. Many systems use historical data to calculate their anticipated call volumes, a method of prediction known as demand pattern analysis. To evaluate the accuracy of call volume predictions calculated using demand pattern analysis. Seven EMS systems provided 73 consecutive weeks of hourly call volume data. The first 20 weeks of data were used to calculate three common demand pattern analysis constructs for call volume prediction: average peak demand (AP), smoothed average peak demand (SAP), and 90th percentile rank (90%R). The 21st week served as a buffer. Actual call volumes in the last 52 weeks were then compared to the predicted call volumes by using descriptive statistics. There were 61,152 hourly observations in the test period. All three constructs accurately predicted peaks and troughs in call volume but not exact call volume. Predictions were accurate (+/-1 call) 13% of the time using AP, 10% using SAP, and 19% using 90%R. Call volumes were overestimated 83% of the time using AP, 86% using SAP, and 74% using 90%R. When call volumes were overestimated, predictions exceeded actual call volume by a median (Interquartile range) of 4 (2-6) calls for AP, 4 (2-6) for SAP, and 3 (2-5) for 90%R. Call volumes were underestimated 4% of time using AP, 4% using SAP, and 7% using 90%R predictions. When call volumes were underestimated, call volumes exceeded predictions by a median (Interquartile range; maximum under estimation) of 1 (1-2; 18) call for AP, 1 (1-2; 18) for SAP, and 2 (1-3; 20) for 90%R. Results did not vary between systems. Generally, demand pattern analysis estimated or overestimated call volume, making it a reasonable predictor for ambulance staffing patterns. However, it did underestimate call volume between 4% and 7% of the time. Communities need to determine if these rates of over

  2. Concorde Re-visited

    NASA Astrophysics Data System (ADS)

    Horton, Peter; Moore, Peter

    This year marks the twentieth anniversary of the introduction of Concorde into commercial airline service. The first commercial flights were on 21 January 1976 - British Airways from Heathrow to Bahrain and Air France from Paris to Rio via Dakar. Later in that year commercial flights to Washington/Dulles began on 24 May. Services to New York were delayed until 22 November 1977. The first flight of Concorde was some seven years earlier. The prototype took off out of Toulouse on 2 March 1969 and this was followed by 002 from Filton to Fairford on 9 April. At the time it was anticipated that this was the beginning of an era when supersonic flight would be the normal way to travel long distances. Now, in 1996, Concorde is still the world's only supersonic commercial passenger airliner in airline service. This is an extraordinary achievement. The Boeing SST proved to be too ambitious and the programme was halted in 1971 after the United States Government withdrew support, while the Russian TU 144 was beset with problems. One TU 144 crashed at the Paris Air Show in 1973. The aircraft entered internal airline service in December 1975, flying supersonically between Moscow and Alma-Ata, capital of Kazakhstan, carrying mail and freight, but it did not have the range to operate viable intercontinental passenger serives. Certainly by 1985, if not many years before, the TU 144 was out of service.

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

    PubMed

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

    2012-01-01

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

  4. Patient-provider language concordance and colorectal cancer screening.

    PubMed

    Linsky, Amy; McIntosh, Nathalie; Cabral, Howard; Kazis, Lewis E

    2011-02-01

    Patient-provider language barriers may play a role in health-care disparities, including obtaining colorectal cancer (CRC) screening. Professional interpreters and language-concordant providers may mitigate these disparities. DESIGN, SUBJECTS, AND MAIN MEASURES: We performed a retrospective cohort study of individuals age 50 years and older who were categorized as English-Concordant (spoke English at home, n = 21,594); Other Language-Concordant (did not speak English at home but someone at their provider's office spoke their language, n = 1,463); or Other Language-Discordant (did not speak English at home and no one at their provider's spoke their language, n = 240). Multivariate logistic regression assessed the association of language concordance with colorectal cancer screening. Compared to English speakers, non-English speakers had lower use of colorectal cancer screening (30.7% vs 50.8%; OR, 0.63; 95% CI, 0.51-0.76). Compared to the English-Concordant group, the Language-Discordant group had similar screening (adjusted OR, 0.84; 95% CI, 0.58-1.21), while the Language-Concordant group had lower screening (adjusted OR, 0.57; 95% CI, 0.46-0.71). Rates of CRC screening are lower in individuals who do not speak English at home compared to those who do. However, the Language-Discordant cohort had similar rates to those with English concordance, while the Language-Concordant cohort had lower rates of CRC screening. This may be due to unmeasured differences among the cohorts in patient, provider, and health care system characteristics. These results suggest that providers should especially promote the importance of CRC screening to non-English speaking patients, but that language barriers do not fully account for CRC screening rate disparities in these populations.

  5. Exact and efficient simulation of concordant computation

    NASA Astrophysics Data System (ADS)

    Cable, Hugo; Browne, Daniel E.

    2015-11-01

    Concordant computation is a circuit-based model of quantum computation for mixed states, that assumes that all correlations within the register are discord-free (i.e. the correlations are essentially classical) at every step of the computation. The question of whether concordant computation always admits efficient simulation by a classical computer was first considered by Eastin in arXiv:quant-ph/1006.4402v1, where an answer in the affirmative was given for circuits consisting only of one- and two-qubit gates. Building on this work, we develop the theory of classical simulation of concordant computation. We present a new framework for understanding such computations, argue that a larger class of concordant computations admit efficient simulation, and provide alternative proofs for the main results of arXiv:quant-ph/1006.4402v1 with an emphasis on the exactness of simulation which is crucial for this model. We include detailed analysis of the arithmetic complexity for solving equations in the simulation, as well as extensions to larger gates and qudits. We explore the limitations of our approach, and discuss the challenges faced in developing efficient classical simulation algorithms for all concordant computations.

  6. Daily concordance between parent and adolescent sleep habits.

    PubMed

    Fuligni, Andrew J; Tsai, Kim M; Krull, Jennifer L; Gonzales, Nancy A

    2015-02-01

    To assess the daily concordance between parent and adolescent daily sleep habits, how that concordance compares to other predictors of sleep, and whether the degree of concordance varies across families. A total of 421 adolescents (Mage = 15.03 years) and their primary caregivers (Mage = 41.93 years) reported their sleep, bed, and wake times on a daily basis for a 2-week period. Approximately 80% of the sample repeated the same protocol 1 year later. Multilevel modeling indicated a significant concordance between parent and adolescent sleep, bed, and wake times on a daily basis. Concordance existed independent of other predictors of sleep such as day of the week and adolescent study time. Larger families and those with higher levels of parent-adolescent support exhibited greater concordance. Adolescent sleep is connected to the sleep habits of their parents, above and beyond commonly known structural and experiential factors that can shape teenage sleep. Efforts to improve teenage sleep should pay greater attention to the sleep patterns of parents and potentially other family members. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

  7. Concordant and discordant alcohol, tobacco, and marijuana use as predictors of marital dissolution

    PubMed Central

    Leonard, Kenneth E.; Smith, Philip H.; Homish, Gregory G.

    2014-01-01

    Objective This study examined concordant and discrepant alcohol, tobacco, and marijuana use among couples to determine whether they predicted marital separation/divorce over nine years. Method The study recruited 634 couples as they applied for their marriage license and assessed them at that time, and re-assessed them with mailed questionnaires at their 1st, 2nd, 4th, 7th, and 9th anniversaries. Approximately 60% of the men and women were European-American, and approximately 1/3 were African-American. The frequency of drinking to intoxication and binge drinking (more than 5 drinks in an occasion) were assessed, as were the use of cigarettes and marijuana. At each assessment, each member of the couple was asked about the occurrence of marital separations and divorce. Results Bivariate analyses indicated that tobacco and marijuana use, whether discrepant or concordant, were associated with marital disruptions. However, discrepant heavy drinking was associated with disruptions but concordant heavy drinking was not. Concordant and discordant marijuana use were not associated with divorce when analyses controlled for alcohol and tobacco use. Concordant and discordant tobacco use was not associated with divorce when analyses controlled for sociodemographic and personality factors. However, discrepant alcohol use was related to divorce after controlling for the other substances in one analysis and after controlling for the sociodemographic factors in a separate analysis. Conclusions Tobacco and marijuana use were related to divorce through their associations with other variables. However, results suggested that discrepant alcohol use may lead to marital disruptions and should be addressed with couples seeking marital treatment. PMID:24128287

  8. Are Physicians and Patients in Agreement? Exploring Dyadic Concordance

    ERIC Educational Resources Information Center

    Coran, Justin J.; Koropeckyj-Cox, Tanya; Arnold, Christa L.

    2013-01-01

    Dyadic concordance in physician-patient interactions can be defined as the extent of agreement between physicians and patients in their perceptions of the clinical encounter. The current research specifically examined two types of concordance: informational concordance--the extent of agreement in physician and patient responses regarding patient…

  9. Moderators of Implicit-Explicit Exercise Cognition Concordance.

    PubMed

    Berry, Tanya R; Rodgers, Wendy M; Markland, David; Hall, Craig R

    2016-12-01

    Investigating implicit-explicit concordance can aid in understanding underlying mechanisms and possible intervention effects. This research examined the concordance between implicit associations of exercise with health or appearance and related explicit motives. Variables considered as possible moderators were behavioral regulations, explicit attitudes, and social desirability. Participants (N = 454) completed measures of implicit associations of exercise with health and appearance and questionnaire measures of health and appearance motives, attitudes, social desirability, and behavioral regulations. Attitudes significantly moderated the relationship between implicit associations of exercise with health and health motives. Identified regulations significantly moderated implicit-explicit concordance with respect to associations with appearance. These results suggest that implicit and explicit exercise-related cognitions are not necessarily independent and their relationship to each other may be moderated by attitudes or some forms of behavioral regulation. Future research that takes a dual-processing approach to exercise behavior should consider potential theoretical moderators of concordance.

  10. Structure-Activity Relationship Models for Rat Carcinogenesis and Assessing the Role Mutagens Play in Model Predictivity

    PubMed Central

    Carrasquer, C. Alex; Batey, Kaylind; Qamar, Shahid; Cunningham, Albert R.; Cunningham, Suzanne L.

    2016-01-01

    We previously demonstrated that fragment based cat-SAR carcinogenesis models consisting solely of mutagenic or non-mutagenic carcinogens varied greatly in terms of their predictive accuracy. This led us to investigate how well the rat cancer cat-SAR model predicted mutagens and non-mutagens in their learning set. Four rat cancer cat-SAR models were developed: Complete Rat, Transgender Rat, Male Rat, and Female Rat, with leave-one-out (LOO) validation concordance values of 69%, 74%, 67%, and 73%, respectively. The mutagenic carcinogens produced concordance values in the range of 69–76% as compared to only 47–53% for non-mutagenic carcinogens. As a surrogate for mutagenicity comparisons between single site and multiple site carcinogen SAR models was analyzed. The LOO concordance values for models consisting of 1-site, 2-site, and 4+-site carcinogens were 66%, 71%, and 79%, respectively. As expected, the proportion of mutagens to non-mutagens also increased, rising from 54% for 1-site to 80% for 4+-site carcinogens. This study demonstrates that mutagenic chemicals, in both SAR learning sets and test sets, are influential in assessing model accuracy. This suggests that SAR models for carcinogens may require a two-step process in which mutagenicity is first determined before carcinogenicity can be accurately predicted. PMID:24697549

  11. Multi-fidelity machine learning models for accurate bandgap predictions of solids

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

    Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

    Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

  12. Multi-fidelity machine learning models for accurate bandgap predictions of solids

    DOE PAGES

    Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

    2016-12-28

    Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

  13. Measuring the value of accurate link prediction for network seeding.

    PubMed

    Wei, Yijin; Spencer, Gwen

    2017-01-01

    The influence-maximization literature seeks small sets of individuals whose structural placement in the social network can drive large cascades of behavior. Optimization efforts to find the best seed set often assume perfect knowledge of the network topology. Unfortunately, social network links are rarely known in an exact way. When do seeding strategies based on less-than-accurate link prediction provide valuable insight? We introduce optimized-against-a-sample ([Formula: see text]) performance to measure the value of optimizing seeding based on a noisy observation of a network. Our computational study investigates [Formula: see text] under several threshold-spread models in synthetic and real-world networks. Our focus is on measuring the value of imprecise link information. The level of investment in link prediction that is strategic appears to depend closely on spread model: in some parameter ranges investments in improving link prediction can pay substantial premiums in cascade size. For other ranges, such investments would be wasted. Several trends were remarkably consistent across topologies.

  14. Validity and concordance between self-reported and clinical diagnosis of hypertension among elderly residents in northeastern Brazil.

    PubMed

    de Menezes, Tarciana Nobre; Oliveira, Elaine Cristina Tôrres; de Sousa Fischer, Milena Abreu Tavares

    2014-02-01

    Self-reported information has been used as an easy and quick method to estimate the prevalence of systemic hypertension in populations. However, verification of whether self-reports of the disease are consistent with clinical diagnosis is essential for proper use of this information. This study aimed to verify the validity and concordance between self-reported and clinical diagnosis of hypertension in the elderly population of a city in northeastern Brazil. This was a cross-sectional and population-based study. The prevalence of diagnosed and self-reported hypertension and the validity and concordance between self-reported and clinical diagnosis and their distribution according to demographic and socioeconomic variables were assessed. The validity of self-reported hypertension was determined by sensitivity, specificity, and positive and negative predictive value. Overall, 795 elderly patients were evaluated (69.1% women). There was a high prevalence of hypertension among the elderly (diagnosed: 75.1%, 95% confidence interval (CI) = 71.1%-77.9%; self-reported: 59.7%, 95% CI = 56.3%-63.1%). For self-reported hypertension, sensitivity was substantial (77.1%), specificity was excellent (93.4%), positive predictive value was excellent (97.3%), and negative predictive value was moderate (57.2%). There was a moderate concordance between self-reported and clinical diagnosis of hypertension (kappa = 0.59; P < 0.001). Reasonable validity and moderate concordance of self-reported information on hypertension was observed, which reinforces the idea that this information can be used as strategy for detecting the disease prevalence in this population. However, because of nonachievement of excellence in the validity and reliability of the measured blood pressure, this information should be carefully considered for the strategic planning of health services.

  15. Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

    PubMed

    Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

    2013-01-02

    Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

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

    PubMed

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

    2017-05-01

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

  17. Concordance of self-report and measured height and weight of college students.

    PubMed

    Quick, Virginia; Byrd-Bredbenner, Carol; Shoff, Suzanne; White, Adrienne A; Lohse, Barbara; Horacek, Tanya; Kattelmann, Kendra; Phillips, Beatrice; Hoerr, Sharon L; Greene, Geoffrey

    2015-01-01

    This study examined associations between college students' self-report and measured height and weight. Participants (N = 1,686) were 77% white, 62% female, aged 18-24 years (mean ± SD, 19.1 ± 1.1 years), and enrolled at 8 US universities. Body mass index (BMI) was calculated for self-report (via online survey); trained researchers measured height and weight and categorized them as normal (18.5 to < 25), overweight (25 to < 30), obese (30 to < 35), and morbidly obese (≥ 35). Concordance of self-report vs objectively measured BMI groups using chi-square revealed that 93% were accurate, 4% were underestimated, and 2.7% were overestimated. Pearson correlations and adjusted linear regression revealed significant associations between self-report and measured BMI (r = .97; P < .001) and BMI adjusted for age, gender, and race/ethnicity (R² = .94). Concordance was also high between BMI categories (kappa = 0.77; P < .001). Findings provide support for the utility of self-report height and weight for survey research in college students. Copyright © 2015 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  18. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins

    PubMed Central

    Li, Bian; Mendenhall, Jeffrey; Nguyen, Elizabeth Dong; Weiner, Brian E.; Fischer, Axel W.; Meiler, Jens

    2017-01-01

    Prediction of the three-dimensional (3D) structures of proteins by computational methods is acknowledged as an unsolved problem. Accurate prediction of important structural characteristics such as contact number is expected to accelerate the otherwise slow progress being made in the prediction of 3D structure of proteins. Here, we present a dropout neural network-based method, TMH-Expo, for predicting the contact number of transmembrane helix (TMH) residues from sequence. Neuronal dropout is a strategy where certain neurons of the network are excluded from back-propagation to prevent co-adaptation of hidden-layer neurons. By using neuronal dropout, overfitting was significantly reduced and performance was noticeably improved. For multi-spanning helical membrane proteins, TMH-Expo achieved a remarkable Pearson correlation coefficient of 0.69 between predicted and experimental values and a mean absolute error of only 1.68. In addition, among those membrane protein–membrane protein interface residues, 76.8% were correctly predicted. Mapping of predicted contact numbers onto structures indicates that contact numbers predicted by TMH-Expo reflect the exposure patterns of TMHs and reveal membrane protein–membrane protein interfaces, reinforcing the potential of predicted contact numbers to be used as restraints for 3D structure prediction and protein–protein docking. TMH-Expo can be accessed via a Web server at www.meilerlab.org. PMID:26804342

  19. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  20. Accuracy of algorithms to predict accessory pathway location in children with Wolff-Parkinson-White syndrome.

    PubMed

    Wren, Christopher; Vogel, Melanie; Lord, Stephen; Abrams, Dominic; Bourke, John; Rees, Philip; Rosenthal, Eric

    2012-02-01

    The aim of this study was to examine the accuracy in predicting pathway location in children with Wolff-Parkinson-White syndrome for each of seven published algorithms. ECGs from 100 consecutive children with Wolff-Parkinson-White syndrome undergoing electrophysiological study were analysed by six investigators using seven published algorithms, six of which had been developed in adult patients. Accuracy and concordance of predictions were adjusted for the number of pathway locations. Accessory pathways were left-sided in 49, septal in 20 and right-sided in 31 children. Overall accuracy of prediction was 30-49% for the exact location and 61-68% including adjacent locations. Concordance between investigators varied between 41% and 86%. No algorithm was better at predicting septal pathways (accuracy 5-35%, improving to 40-78% including adjacent locations), but one was significantly worse. Predictive accuracy was 24-53% for the exact location of right-sided pathways (50-71% including adjacent locations) and 32-55% for the exact location of left-sided pathways (58-73% including adjacent locations). All algorithms were less accurate in our hands than in other authors' own assessment. None performed well in identifying midseptal or right anteroseptal accessory pathway locations.

  1. An accurate model for predicting high frequency noise of nanoscale NMOS SOI transistors

    NASA Astrophysics Data System (ADS)

    Shen, Yanfei; Cui, Jie; Mohammadi, Saeed

    2017-05-01

    A nonlinear and scalable model suitable for predicting high frequency noise of N-type Metal Oxide Semiconductor (NMOS) transistors is presented. The model is developed for a commercial 45 nm CMOS SOI technology and its accuracy is validated through comparison with measured performance of a microwave low noise amplifier. The model employs the virtual source nonlinear core and adds parasitic elements to accurately simulate the RF behavior of multi-finger NMOS transistors up to 40 GHz. For the first time, the traditional long-channel thermal noise model is supplemented with an injection noise model to accurately represent the noise behavior of these short-channel transistors up to 26 GHz. The developed model is simple and easy to extract, yet very accurate.

  2. Fast and Accurate Prediction of Stratified Steel Temperature During Holding Period of Ladle

    NASA Astrophysics Data System (ADS)

    Deodhar, Anirudh; Singh, Umesh; Shukla, Rishabh; Gautham, B. P.; Singh, Amarendra K.

    2017-04-01

    Thermal stratification of liquid steel in a ladle during the holding period and the teeming operation has a direct bearing on the superheat available at the caster and hence on the caster set points such as casting speed and cooling rates. The changes in the caster set points are typically carried out based on temperature measurements at the end of tundish outlet. Thermal prediction models provide advance knowledge of the influence of process and design parameters on the steel temperature at various stages. Therefore, they can be used in making accurate decisions about the caster set points in real time. However, this requires both fast and accurate thermal prediction models. In this work, we develop a surrogate model for the prediction of thermal stratification using data extracted from a set of computational fluid dynamics (CFD) simulations, pre-determined using design of experiments technique. Regression method is used for training the predictor. The model predicts the stratified temperature profile instantaneously, for a given set of process parameters such as initial steel temperature, refractory heat content, slag thickness, and holding time. More than 96 pct of the predicted values are within an error range of ±5 K (±5 °C), when compared against corresponding CFD results. Considering its accuracy and computational efficiency, the model can be extended for thermal control of casting operations. This work also sets a benchmark for developing similar thermal models for downstream processes such as tundish and caster.

  3. Competitive Abilities in Experimental Microcosms Are Accurately Predicted by a Demographic Index for R*

    PubMed Central

    Murrell, Ebony G.; Juliano, Steven A.

    2012-01-01

    Resource competition theory predicts that R*, the equilibrium resource amount yielding zero growth of a consumer population, should predict species' competitive abilities for that resource. This concept has been supported for unicellular organisms, but has not been well-tested for metazoans, probably due to the difficulty of raising experimental populations to equilibrium and measuring population growth rates for species with long or complex life cycles. We developed an index (Rindex) of R* based on demography of one insect cohort, growing from egg to adult in a non-equilibrium setting, and tested whether Rindex yielded accurate predictions of competitive abilities using mosquitoes as a model system. We estimated finite rate of increase (λ′) from demographic data for cohorts of three mosquito species raised with different detritus amounts, and estimated each species' Rindex using nonlinear regressions of λ′ vs. initial detritus amount. All three species' Rindex differed significantly, and accurately predicted competitive hierarchy of the species determined in simultaneous pairwise competition experiments. Our Rindex could provide estimates and rigorous statistical comparisons of competitive ability for organisms for which typical chemostat methods and equilibrium population conditions are impractical. PMID:22970128

  4. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    PubMed Central

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

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

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

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

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

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

    DOE PAGES

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

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

  7. XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.

    PubMed

    Zaretzki, Jed; Matlock, Matthew; Swamidass, S Joshua

    2013-12-23

    Understanding how xenobiotic molecules are metabolized is important because it influences the safety, efficacy, and dose of medicines and how they can be modified to improve these properties. The cytochrome P450s (CYPs) are proteins responsible for metabolizing 90% of drugs on the market, and many computational methods can predict which atomic sites of a molecule--sites of metabolism (SOMs)--are modified during CYP-mediated metabolism. This study improves on prior methods of predicting CYP-mediated SOMs by using new descriptors and machine learning based on neural networks. The new method, XenoSite, is faster to train and more accurate by as much as 4% or 5% for some isozymes. Furthermore, some "incorrect" predictions made by XenoSite were subsequently validated as correct predictions by revaluation of the source literature. Moreover, XenoSite output is interpretable as a probability, which reflects both the confidence of the model that a particular atom is metabolized and the statistical likelihood that its prediction for that atom is correct.

  8. Behavioral and neural concordance in parent-child dyadic sleep patterns.

    PubMed

    Lee, Tae-Ho; Miernicki, Michelle E; Telzer, Eva H

    2017-08-01

    Sleep habits developed in adolescence shape long-term trajectories of psychological, educational, and physiological well-being. Adolescents' sleep behaviors are shaped by their parents' sleep at both the behavioral and biological levels. In the current study, we sought to examine how neural concordance in resting-state functional connectivity between parent-child dyads is associated with dyadic concordance in sleep duration and adolescents' sleep quality. To this end, we scanned both parents and their child (N=28 parent-child dyads; parent M age =42.8years; adolescent M age =14.9years; 14.3% father; 46.4% female adolescent) as they each underwent a resting-state scan. Using daily diaries, we also assessed dyadic concordance in sleep duration across two weeks. Our results show that greater daily concordance in sleep behavior is associated with greater neural concordance in default-mode network connectivity between parents and children. Moreover, greater neural and behavioral concordances in sleep is associated with more optimal sleep quality in adolescents. The current findings expand our understanding of dyadic concordance by providing a neurobiological mechanism by which parents and children share daily sleep behaviors. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Concordant Chemical Reaction Networks and the Species-Reaction Graph

    PubMed Central

    Shinar, Guy; Feinberg, Martin

    2015-01-01

    In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class. In particular, multiple equilibria are precluded, as are degenerate positive equilibria. Moreover, under certain circumstances, also related to concordance, all real eigenvalues associated with a positive equilibrium are negative. Although concordance of a reaction network can be decided by readily available computational means, we show here that, when a nondegenerate network’s Species-Reaction Graph satisfies certain mild conditions, concordance and its dynamical consequences are ensured. These conditions are weaker than earlier ones invoked to establish kinetic system injectivity, which, in turn, is just one ramification of network concordance. Because the Species-Reaction Graph resembles pathway depictions often drawn by biochemists, results here expand the possibility of inferring significant dynamical information directly from standard biochemical reaction diagrams. PMID:22940368

  10. Accurate prediction of personalized olfactory perception from large-scale chemoinformatic features.

    PubMed

    Li, Hongyang; Panwar, Bharat; Omenn, Gilbert S; Guan, Yuanfang

    2018-02-01

    The olfactory stimulus-percept problem has been studied for more than a century, yet it is still hard to precisely predict the odor given the large-scale chemoinformatic features of an odorant molecule. A major challenge is that the perceived qualities vary greatly among individuals due to different genetic and cultural backgrounds. Moreover, the combinatorial interactions between multiple odorant receptors and diverse molecules significantly complicate the olfaction prediction. Many attempts have been made to establish structure-odor relationships for intensity and pleasantness, but no models are available to predict the personalized multi-odor attributes of molecules. In this study, we describe our winning algorithm for predicting individual and population perceptual responses to various odorants in the DREAM Olfaction Prediction Challenge. We find that random forest model consisting of multiple decision trees is well suited to this prediction problem, given the large feature spaces and high variability of perceptual ratings among individuals. Integrating both population and individual perceptions into our model effectively reduces the influence of noise and outliers. By analyzing the importance of each chemical feature, we find that a small set of low- and nondegenerative features is sufficient for accurate prediction. Our random forest model successfully predicts personalized odor attributes of structurally diverse molecules. This model together with the top discriminative features has the potential to extend our understanding of olfactory perception mechanisms and provide an alternative for rational odorant design.

  11. A Critical Review for Developing Accurate and Dynamic Predictive Models Using Machine Learning Methods in Medicine and Health Care.

    PubMed

    Alanazi, Hamdan O; Abdullah, Abdul Hanan; Qureshi, Kashif Naseer

    2017-04-01

    Recently, Artificial Intelligence (AI) has been used widely in medicine and health care sector. In machine learning, the classification or prediction is a major field of AI. Today, the study of existing predictive models based on machine learning methods is extremely active. Doctors need accurate predictions for the outcomes of their patients' diseases. In addition, for accurate predictions, timing is another significant factor that influences treatment decisions. In this paper, existing predictive models in medicine and health care have critically reviewed. Furthermore, the most famous machine learning methods have explained, and the confusion between a statistical approach and machine learning has clarified. A review of related literature reveals that the predictions of existing predictive models differ even when the same dataset is used. Therefore, existing predictive models are essential, and current methods must be improved.

  12. Investigating Female Sexual Concordance: Do Sexual Excitation and Sexual Inhibition Moderate the Agreement of Genital and Subjective Sexual Arousal in Women?

    PubMed

    Velten, Julia; Scholten, Saskia; Graham, Cynthia A; Adolph, Dirk; Margraf, Jürgen

    2016-11-01

    The agreement of subjective and genital sexual response, also referred to as sexual concordance, shows substantial variability between women. Identifying predictors of sexual arousal and sexual concordance is important to improve our understanding of female sexual response and its relationship to sexual function or dysfunction. The aim of this study was to assess the relevance of sexual excitation and sexual inhibition as predictors of subjective sexual arousal, genital arousal, and sexual concordance. In a laboratory setting, sexual arousal was induced by erotic video stimuli. Subjective sexual arousal was assessed continuously during stimulus presentation and genital arousal was measured with vaginal photoplethysmography. Data of 58 women (M age = 24.95, SD = 4.65) were analyzed using multilevel analyses (HLM). This data analytic technique estimates the within-subject associations of subjective and genital arousal, by controlling for between-subject differences. An interaction term of sexual excitation and sexual inhibition significantly predicted genital sexual arousal. In exploratory analyses, two lower order factors of sexual inhibition (Concerns about Sexual Function and Arousal Contingency) were predictive of sexual concordance. Further examination of these associations might increase our knowledge of female sexual function and deepen our understanding of how sexual excitation and sexual inhibition affect sexual arousal and consequently, impact sexual behaviors, in women.

  13. Assessing the Relationship Between Sexual Concordance, Sexual Attractions, and Sexual Identity in Women.

    PubMed

    Suschinsky, Kelly D; Dawson, Samantha J; Chivers, Meredith L

    2017-01-01

    On average, there is a gender difference in sexual concordance, with men exhibiting greater agreement between genital and self-reported sexual arousal, relative to women. Much less is known about the substantial variation in women's sexual concordance; women's genital and self-reported sexual responses may correlate strongly and positively, not at all, or even strongly negatively. The within-gender variation in sexual concordance suggests that individual differences may be related to sexual concordance. We examined whether sexual concordance varies as a function of sexual orientation (based on self-reported sexual attractions and sexual identity labels) in a sample (N = 76) that included exclusively androphilic, predominantly androphilic, ambiphilic, and predominantly/exclusively gynephilic women. Participants viewed sexual and nonsexual stimuli that varied by actor gender while their vaginal vasocongestion and subjective sexual responses were measured. Women's sexual concordance varied as a function of their sexual attractions; women with any degree of gynephilia exhibited higher sexual concordance than exclusively androphilic women across a variety of sexual concordance measures, and these effects were demonstrated using correlation and multi-level modeling analyses. Only sexual concordance based on overall feelings of arousal varied by sexual identity, with heterosexual women exhibiting the lowest sexual concordance. Stimulus gender significantly influenced sexual concordance for most groups of women: Ambiphilic and predominantly/exclusively gynephilic women exhibited greater sexual concordance to female stimuli and exclusively androphilic women exhibited greater sexual concordance to male stimuli. These findings suggest that sexual orientation (particularly one's degree of gynephilia) may explain some of the within-gender variation seen in women's sexual concordance.

  14. Is sexual concordance related to awareness of physiological states?

    PubMed

    Suschinsky, Kelly D; Lalumière, Martin L

    2012-02-01

    Sexual concordance refers to the degree to which two aspects of human sexual arousal (genital response and self-reported sexual arousal) correspond with each other. Researchers have consistently reported a sex difference in sexual concordance: The relationship between genital responses and reported feelings of sexual arousal in men is positive and large, whereas the relationship in women is positive but much smaller than that seen in men. The study of interoception--people's awareness of their physiological states--reveals a similar sex difference: Men are more aware of a variety of (non-genital) responses (e.g., heart rate) than women in the laboratory. The purpose of the current study was to investigate whether the sex difference in sexual concordance was related to a broader sex difference in interoception. Twenty men and 20 women were presented with twelve 90 s sexual and non-sexual film clips while their genital responses, heart rate, and respiration rate were measured. Participants also estimated their physiological responses. As expected, men were significantly more sexually concordant than women. Men were also significantly more aware of their heart rate, but there was no significant sex difference in respiration rate awareness. Sexual concordance was not significantly correlated with either heart rate or respiration rate awareness. The results suggest that the sex difference in sexual concordance may be a unique phenomenon, separate from general awareness of physiological states.

  15. Diagnostic concordance among pathologists interpreting breast biopsy specimens.

    PubMed

    Elmore, Joann G; Longton, Gary M; Carney, Patricia A; Geller, Berta M; Onega, Tracy; Tosteson, Anna N A; Nelson, Heidi D; Pepe, Margaret S; Allison, Kimberly H; Schnitt, Stuart J; O'Malley, Frances P; Weaver, Donald L

    2015-03-17

    A breast pathology diagnosis provides the basis for clinical treatment and management decisions; however, its accuracy is inadequately understood. To quantify the magnitude of diagnostic disagreement among pathologists compared with a consensus panel reference diagnosis and to evaluate associated patient and pathologist characteristics. Study of pathologists who interpret breast biopsies in clinical practices in 8 US states. Participants independently interpreted slides between November 2011 and May 2014 from test sets of 60 breast biopsies (240 total cases, 1 slide per case), including 23 cases of invasive breast cancer, 73 ductal carcinoma in situ (DCIS), 72 with atypical hyperplasia (atypia), and 72 benign cases without atypia. Participants were blinded to the interpretations of other study pathologists and consensus panel members. Among the 3 consensus panel members, unanimous agreement of their independent diagnoses was 75%, and concordance with the consensus-derived reference diagnoses was 90.3%. The proportions of diagnoses overinterpreted and underinterpreted relative to the consensus-derived reference diagnoses were assessed. Sixty-five percent of invited, responding pathologists were eligible and consented to participate. Of these, 91% (N = 115) completed the study, providing 6900 individual case diagnoses. Compared with the consensus-derived reference diagnosis, the overall concordance rate of diagnostic interpretations of participating pathologists was 75.3% (95% CI, 73.4%-77.0%; 5194 of 6900 interpretations). Among invasive carcinoma cases (663 interpretations), 96% (95% CI, 94%-97%) were concordant, and 4% (95% CI, 3%-6%) were underinterpreted; among DCIS cases (2097 interpretations), 84% (95% CI, 82%-86%) were concordant, 3% (95% CI, 2%-4%) were overinterpreted, and 13% (95% CI, 12%-15%) were underinterpreted; among atypia cases (2070 interpretations), 48% (95% CI, 44%-52%) were concordant, 17% (95% CI, 15%-21%) were overinterpreted, and 35% (95

  16. Ensemble predictive model for more accurate soil organic carbon spectroscopic estimation

    NASA Astrophysics Data System (ADS)

    Vašát, Radim; Kodešová, Radka; Borůvka, Luboš

    2017-07-01

    A myriad of signal pre-processing strategies and multivariate calibration techniques has been explored in attempt to improve the spectroscopic prediction of soil organic carbon (SOC) over the last few decades. Therefore, to come up with a novel, more powerful, and accurate predictive approach to beat the rank becomes a challenging task. However, there may be a way, so that combine several individual predictions into a single final one (according to ensemble learning theory). As this approach performs best when combining in nature different predictive algorithms that are calibrated with structurally different predictor variables, we tested predictors of two different kinds: 1) reflectance values (or transforms) at each wavelength and 2) absorption feature parameters. Consequently we applied four different calibration techniques, two per each type of predictors: a) partial least squares regression and support vector machines for type 1, and b) multiple linear regression and random forest for type 2. The weights to be assigned to individual predictions within the ensemble model (constructed as a weighted average) were determined by an automated procedure that ensured the best solution among all possible was selected. The approach was tested at soil samples taken from surface horizon of four sites differing in the prevailing soil units. By employing the ensemble predictive model the prediction accuracy of SOC improved at all four sites. The coefficient of determination in cross-validation (R2cv) increased from 0.849, 0.611, 0.811 and 0.644 (the best individual predictions) to 0.864, 0.650, 0.824 and 0.698 for Site 1, 2, 3 and 4, respectively. Generally, the ensemble model affected the final prediction so that the maximal deviations of predicted vs. observed values of the individual predictions were reduced, and thus the correlation cloud became thinner as desired.

  17. Genotype-Specific Concordance of Chlamydia trachomatis Genital Infection Within Heterosexual Partnerships.

    PubMed

    Schillinger, Julia A; Katz, Barry P; Markowitz, Lauri E; Braslins, Phillip G; Shrier, Lydia A; Madico, Guillermo; Van Der Pol, Barbara; Orr, Donald P; Rice, Peter A; Batteiger, Byron E

    2016-12-01

    Sexual transmission rates of Chlamydia trachomatis (Ct) cannot be measured directly; however, the study of concordance of Ct infection in sexual partnerships (dyads) can help to illuminate factors influencing Ct transmission. Heterosexual men and women with Ct infection and their sex partners were enrolled and partner-specific coital and behavioral data collected for the prior 30 days. Microbiological data included Ct culture, and nucleic acid amplification testing (NAAT), quantitative Ct polymerase chain reaction, and ompA genotyping. We measured Ct concordance in dyads and factors (correlates) associated with concordance. One hundred twenty-one women and 125 men formed 128 dyads. Overall, 72.9% of male partners of NAAT-positive women and 68.6% of female partners of NAAT-positive men were Ct-infected. Concordance was more common in dyads with culture-positive members (78.6% of male partners, 77% of female partners). Partners of women and men who were NAAT-positive only had lower concordance (33.3%, 46.4%, respectively). Women in concordant dyads had significantly higher median endocervical quantitative Ct polymerase chain reaction values (3,032) compared with CT-infected women in discordant dyads (1013 inclusion forming units DNA equivalents per mL; P < 0.01). Among 54 Ct-concordant dyads with ompA genotype data for both members, 96.2% had identical genotypes. Higher organism load appears associated with concordance among women. Same-genotype chlamydial concordance was high in sexual partnerships. No behavioral factors were sufficiently discriminating to guide partner services activities. Findings may help model coitus-specific transmission probabilities.

  18. Towards First Principles-Based Prediction of Highly Accurate Electrochemical Pourbaix Diagrams

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

    Zeng, Zhenhua; Chan, Maria K. Y.; Zhao, Zhi-Jian

    2015-08-13

    Electrochemical potential/pH (Pourbaix) diagrams underpin many aqueous electrochemical processes and are central to the identification of stable phases of metals for processes ranging from electrocatalysis to corrosion. Even though standard DFT calculations are potentially powerful tools for the prediction of such diagrams, inherent errors in the description of transition metal (hydroxy)oxides, together with neglect of van der Waals interactions, have limited the reliability of such predictions for even the simplest pure metal bulk compounds, and corresponding predictions for more complex alloy or surface structures are even more challenging. In the present work, through synergistic use of a Hubbard U correction,more » a state-of-the-art dispersion correction, and a water-based bulk reference state for the calculations, these errors are systematically corrected. The approach describes the weak binding that occurs between hydroxyl-containing functional groups in certain compounds in Pourbaix diagrams, corrects for self-interaction errors in transition metal compounds, and reduces residual errors on oxygen atoms by preserving a consistent oxidation state between the reference state, water, and the relevant bulk phases. The strong performance is illustrated on a series of bulk transition metal (Mn, Fe, Co and Ni) hydroxides, oxyhydroxides, binary, and ternary oxides, where the corresponding thermodynamics of redox and (de)hydration are described with standard errors of 0.04 eV per (reaction) formula unit. The approach further preserves accurate descriptions of the overall thermodynamics of electrochemically-relevant bulk reactions, such as water formation, which is an essential condition for facilitating accurate analysis of reaction energies for electrochemical processes on surfaces. The overall generality and transferability of the scheme suggests that it may find useful application in the construction of a broad array of electrochemical phase diagrams, including

  19. Assessing clinical reasoning in optometry using the script concordance test.

    PubMed

    Faucher, Caroline; Dufour-Guindon, Marie-Pier; Lapointe, Gabrielle; Gagnon, Robert; Charlin, Bernard

    2016-05-01

    Clinical reasoning is central to any health profession but its development among learners is difficult to assess. Over the last few decades, the script concordance test (SCT) has been developed to solve this dilemma and has been used in many health professions; however, no study has been published on the use of the script concordance test in optometry. The purpose of this study was to develop and validate a script concordance test for the field of optometry. A 101-question script concordance test (27 short clinical scenarios) was developed and administered online to a convenience sample of 23 second-year and 19 fourth-year students of optometry. It was also administered to a reference panel of 12 experienced optometrists to develop the scoring key. An item-total correlation was calculated for each question. Cronbach's alpha coefficient was used to evaluate the script concordance test reliability and a t-test compared the two groups. A final 77-question script concordance test was created by eliminating questions with low item-total correlation. Cronbach's alpha for this optimised 77-question script concordance test was 0.80. A group comparison revealed that the second-year students' scores (n = 23; mean score = 66.4 ± 7.87 per cent) were statistically lower (t = -4.141; p < 0.001) than those of the fourth-year students (n = 19; mean score = 75.5 ± 5.97 per cent). The online script concordance test developed for this study was found to be both reliable and capable of discriminating between second- and fourth-year optometric students. These results demonstrate that the script concordance test may be considered as a new tool in the optometric educators' assessment arsenal. Further studies will be needed to cover additional levels of professional development. © 2016 The Authors. Clinical and Experimental Optometry © 2016 Optometry Australia.

  20. Are physicians and patients in agreement? Exploring dyadic concordance.

    PubMed

    Coran, Justin J; Koropeckyj-Cox, Tanya; Arnold, Christa L

    2013-10-01

    Dyadic concordance in physician-patient interactions can be defined as the extent of agreement between physicians and patients in their perceptions of the clinical encounter. The current research specifically examined two types of concordance: informational concordance-the extent of agreement in physician and patient responses regarding patient information (education, self-rated health, pain); and interactional concordance-the extent of physician-patient agreement regarding the patient's level of confidence and trust in the physician and the perceived quality of explanations concerning diagnosis and treatment. Using a convenience sample of physicians and patients (N = 50 dyads), a paired survey method was tested, which measured and compared physician and patient reports to identify informational and interactional concordances. Factors potentially related to dyadic concordance were also measured, including demographic characteristics (patient race, gender, age, and education) and clinical factors (whether this was a first visit and physician specialty in family medicine or oncology). The paired survey showed informational discordances, as physicians tended to underestimate patients' pain and overestimate patient education. Interactional discordances included overestimating patients' understanding of diagnosis and treatment explanations and patients' level of confidence and trust. Discordances were linked to patient dissatisfaction with physician listening, having unanswered questions, and feeling the physician had not spent enough time. The paired survey method effectively identified physician-patient discordances that may interfere with effective medical practice; this method may be used in various settings to identify potential areas of improvement in health communication and education.

  1. Highly accurate prediction of emotions surrounding the attacks of September 11, 2001 over 1-, 2-, and 7-year prediction intervals.

    PubMed

    Doré, Bruce P; Meksin, Robert; Mather, Mara; Hirst, William; Ochsner, Kevin N

    2016-06-01

    In the aftermath of a national tragedy, important decisions are predicated on judgments of the emotional significance of the tragedy in the present and future. Research in affective forecasting has largely focused on ways in which people fail to make accurate predictions about the nature and duration of feelings experienced in the aftermath of an event. Here we ask a related but understudied question: can people forecast how they will feel in the future about a tragic event that has already occurred? We found that people were strikingly accurate when predicting how they would feel about the September 11 attacks over 1-, 2-, and 7-year prediction intervals. Although people slightly under- or overestimated their future feelings at times, they nonetheless showed high accuracy in forecasting (a) the overall intensity of their future negative emotion, and (b) the relative degree of different types of negative emotion (i.e., sadness, fear, or anger). Using a path model, we found that the relationship between forecasted and actual future emotion was partially mediated by current emotion and remembered emotion. These results extend theories of affective forecasting by showing that emotional responses to an event of ongoing national significance can be predicted with high accuracy, and by identifying current and remembered feelings as independent sources of this accuracy. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  2. Highly accurate prediction of emotions surrounding the attacks of September 11, 2001 over 1-, 2-, and 7-year prediction intervals

    PubMed Central

    Doré, B.P.; Meksin, R.; Mather, M.; Hirst, W.; Ochsner, K.N

    2016-01-01

    In the aftermath of a national tragedy, important decisions are predicated on judgments of the emotional significance of the tragedy in the present and future. Research in affective forecasting has largely focused on ways in which people fail to make accurate predictions about the nature and duration of feelings experienced in the aftermath of an event. Here we ask a related but understudied question: can people forecast how they will feel in the future about a tragic event that has already occurred? We found that people were strikingly accurate when predicting how they would feel about the September 11 attacks over 1-, 2-, and 7-year prediction intervals. Although people slightly under- or overestimated their future feelings at times, they nonetheless showed high accuracy in forecasting 1) the overall intensity of their future negative emotion, and 2) the relative degree of different types of negative emotion (i.e., sadness, fear, or anger). Using a path model, we found that the relationship between forecasted and actual future emotion was partially mediated by current emotion and remembered emotion. These results extend theories of affective forecasting by showing that emotional responses to an event of ongoing national significance can be predicted with high accuracy, and by identifying current and remembered feelings as independent sources of this accuracy. PMID:27100309

  3. Estimating HPV DNA Deposition Between Sexual Partners Using HPV Concordance, Y Chromosome DNA Detection, and Self-reported Sexual Behaviors.

    PubMed

    Malagón, Talía; Burchell, Ann N; El-Zein, Mariam; Guénoun, Julie; Tellier, Pierre-Paul; Coutlée, François; Franco, Eduardo L

    2017-12-05

    Detection of human papillomavirus (HPV) DNA in genital samples may not always represent true infections but may be depositions from infected sexual partners. We examined whether sexual risk factors and a biomarker (Y chromosome DNA) were associated with genital HPV partner concordance and estimated the fraction of HPV detections potentially attributable to partner deposition. The HITCH study enrolled young women attending a university or college in Montréal, Canada, and their male partners, from 2005 to 2010. We tested baseline genital samples for Y chromosome DNA and HPV DNA using polymerase chain reaction. Type-specific HPV concordance was 42.4% in partnerships where at least one partner was HPV DNA positive. Y chromosome DNA predicted type-specific HPV concordance in univariate analyses, but in multivariable models the independent predictors of concordance were days since last vaginal sex (26.5% higher concordance 0-1 vs 8-14 days after last vaginal sex) and condom use (22.6% higher concordance in never vs always users). We estimated that 14.1% (95% confidence interval [CI], 6.3-21.9%) of HPV DNA detections in genital samples were attributable to vaginal sex in the past week. A substantial proportion of HPV DNA detections may be depositions due to recent unprotected vaginal sex. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  4. The CpG island methylator phenotype is concordant between primary colorectal carcinoma and matched distant metastases.

    PubMed

    Cohen, Stacey A; Yu, Ming; Baker, Kelsey; Redman, Mary; Wu, Chen; Heinzerling, Tai J; Wirtz, Ralph M; Charalambous, Elpida; Pentheroudakis, George; Kotoula, Vassiliki; Kalogeras, Konstantine T; Fountzilas, George; Grady, William M

    2017-01-01

    The CpG island methylator phenotype (CIMP) in stage III colon cancer (CRC) has been associated with improved survival after treatment with adjuvant irinotecan-based chemotherapy. In this analysis, we determine whether CIMP status in the primary CRC is concordant with the CIMP status of matched metastases in order to determine if assessment of CIMP status in the primary tumor can be used to predict CIMP status of metastatic disease, which is relevant for patient management as well as for understanding the biology of CIMP CRCs. We assessed the CIMP status of 70 pairs of primary CRC and matched metastases using a CRC-specific panel of five markers ( CACNA1G , IGF2 , NEUROG1 , RUNX3 , and SOCS1 ) where CIMP positive was defined as 3/5 positive markers at a percent methylated reference threshold of ≥10%. Concordance was compared using the Fisher's exact test and P  < 0.05 was considered significant. Sixty-nine of the pairs (98.6%) showed concordant CIMP status in the primary tumor and matched metastasis; five (7.0%) of the pairs were concordantly CIMP positive. Only one pair (1.4%) had divergent CIMP status, demonstrating CIMP positivity (4/5 markers positive) in the primary tumor, while the matched metastasis was CIMP negative (0 markers positive). CIMP status is generally concordant between primary CRCs and matched metastases. Thus, CIMP status in the primary tumor is maintained in matched metastases and can be used to inform CIMP-based therapy options for the metastases.

  5. High Order Schemes in Bats-R-US for Faster and More Accurate Predictions

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Toth, G.; Gombosi, T. I.

    2014-12-01

    BATS-R-US is a widely used global magnetohydrodynamics model that originally employed second order accurate TVD schemes combined with block based Adaptive Mesh Refinement (AMR) to achieve high resolution in the regions of interest. In the last years we have implemented fifth order accurate finite difference schemes CWENO5 and MP5 for uniform Cartesian grids. Now the high order schemes have been extended to generalized coordinates, including spherical grids and also to the non-uniform AMR grids including dynamic regridding. We present numerical tests that verify the preservation of free-stream solution and high-order accuracy as well as robust oscillation-free behavior near discontinuities. We apply the new high order accurate schemes to both heliospheric and magnetospheric simulations and show that it is robust and can achieve the same accuracy as the second order scheme with much less computational resources. This is especially important for space weather prediction that requires faster than real time code execution.

  6. Acoustic propagation and atmosphere characteristics derived from infrasonic waves generated by the Concorde.

    PubMed

    Le, Pichon Alexis; Garcés, Milton; Blanc, Elisabeth; Barthélémy, Maud; Drob, Doug P

    2002-01-01

    Infrasonic signals generated by daily supersonic Concorde flights between North America and Europe have been consistently recorded by an array of microbarographs in France. These signals are used to investigate the effects of atmospheric variability on long-range sound propagation. Statistical analysis of wave parameters shows seasonal and daily variations associated with changes in the wind structure of the atmosphere. The measurements are compared to the predictions obtained by tracing rays through realistic atmospheric models. Theoretical ray paths allow a consistent interpretation of the observed wave parameters. Variations in the reflection level, travel time, azimuth deviation and propagation range are explained by the source and propagation models. The angular deviation of a ray's azimuth direction, due to the seasonal and diurnal fluctuations of the transverse wind component, is found to be approximately 5 degrees from the initial launch direction. One application of the seasonal and diurnal variations of the observed phase parameters is the use of ground measurements to estimate fluctuations in the wind velocity at the reflection heights. The simulations point out that care must be taken when ascribing a phase velocity to a turning height. Ray path simulations which allow the correct computation of reflection heights are essential for accurate phase identifications.

  7. Accurate high-throughput structure mapping and prediction with transition metal ion FRET

    PubMed Central

    Yu, Xiaozhen; Wu, Xiongwu; Bermejo, Guillermo A.; Brooks, Bernard R.; Taraska, Justin W.

    2013-01-01

    Mapping the landscape of a protein’s conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein Maltose Binding Protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells. PMID:23273426

  8. Investigating spousal concordance of diabetes through statistical analysis and data mining.

    PubMed

    Wang, Jong-Yi; Liu, Chiu-Shong; Lung, Chi-Hsuan; Yang, Ya-Tun; Lin, Ming-Hung

    2017-01-01

    Spousal clustering of diabetes merits attention. Whether old-age vulnerability or a shared family environment determines the concordance of diabetes is also uncertain. This study investigated the spousal concordance of diabetes and compared the risk of diabetes concordance between couples and noncouples by using nationally representative data. A total of 22,572 individuals identified from the 2002-2013 National Health Insurance Research Database of Taiwan constituted 5,643 couples and 5,643 noncouples through 1:1 dual propensity score matching (PSM). Factors associated with concordance in both spouses with diabetes were analyzed at the individual level. The risk of diabetes concordance between couples and noncouples was compared at the couple level. Logistic regression was the main statistical method. Statistical data were analyzed using SAS 9.4. C&RT and Apriori of data mining conducted in IBM SPSS Modeler 13 served as a supplement to statistics. High odds of the spousal concordance of diabetes were associated with old age, middle levels of urbanization, and high comorbidities (all P < 0.05). The dual PSM analysis revealed that the risk of diabetes concordance was significantly higher in couples (5.19%) than in noncouples (0.09%; OR = 61.743, P < 0.0001). A high concordance rate of diabetes in couples may indicate the influences of assortative mating and shared environment. Diabetes in a spouse implicates its risk in the partner. Family-based diabetes care that emphasizes the screening of couples at risk of diabetes by using the identified risk factors is suggested in prospective clinical practice interventions.

  9. Investigating spousal concordance of diabetes through statistical analysis and data mining

    PubMed Central

    Liu, Chiu-Shong; Lung, Chi-Hsuan; Yang, Ya-Tun; Lin, Ming-Hung

    2017-01-01

    Objective Spousal clustering of diabetes merits attention. Whether old-age vulnerability or a shared family environment determines the concordance of diabetes is also uncertain. This study investigated the spousal concordance of diabetes and compared the risk of diabetes concordance between couples and noncouples by using nationally representative data. Methods A total of 22,572 individuals identified from the 2002–2013 National Health Insurance Research Database of Taiwan constituted 5,643 couples and 5,643 noncouples through 1:1 dual propensity score matching (PSM). Factors associated with concordance in both spouses with diabetes were analyzed at the individual level. The risk of diabetes concordance between couples and noncouples was compared at the couple level. Logistic regression was the main statistical method. Statistical data were analyzed using SAS 9.4. C&RT and Apriori of data mining conducted in IBM SPSS Modeler 13 served as a supplement to statistics. Results High odds of the spousal concordance of diabetes were associated with old age, middle levels of urbanization, and high comorbidities (all P < 0.05). The dual PSM analysis revealed that the risk of diabetes concordance was significantly higher in couples (5.19%) than in noncouples (0.09%; OR = 61.743, P < 0.0001). Conclusions A high concordance rate of diabetes in couples may indicate the influences of assortative mating and shared environment. Diabetes in a spouse implicates its risk in the partner. Family-based diabetes care that emphasizes the screening of couples at risk of diabetes by using the identified risk factors is suggested in prospective clinical practice interventions. PMID:28817654

  10. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.

    PubMed

    Lundegaard, Claus; Lund, Ole; Nielsen, Morten

    2008-06-01

    Several accurate prediction systems have been developed for prediction of class I major histocompatibility complex (MHC):peptide binding. Most of these are trained on binding affinity data of primarily 9mer peptides. Here, we show how prediction methods trained on 9mer data can be used for accurate binding affinity prediction of peptides of length 8, 10 and 11. The method gives the opportunity to predict peptides with a different length than nine for MHC alleles where no such peptides have been measured. As validation, the performance of this approach is compared to predictors trained on peptides of the peptide length in question. In this validation, the approximation method has an accuracy that is comparable to or better than methods trained on a peptide length identical to the predicted peptides. The algorithm has been implemented in the web-accessible servers NetMHC-3.0: http://www.cbs.dtu.dk/services/NetMHC-3.0, and NetMHCpan-1.1: http://www.cbs.dtu.dk/services/NetMHCpan-1.1

  11. Mindfulness-Based Sex Therapy Improves Genital-Subjective Arousal Concordance in Women With Sexual Desire/Arousal Difficulties.

    PubMed

    Brotto, Lori A; Chivers, Meredith L; Millman, Roanne D; Albert, Arianne

    2016-11-01

    There is emerging evidence for the efficacy of mindfulness-based interventions for improving women's sexual functioning. To date, this literature has been limited to self-reports of sexual response and distress. Sexual arousal concordance-the degree of agreement between self-reported sexual arousal and psychophysiological sexual response-has been of interest due to the speculation that it may be a key component to healthy sexual functioning in women. We examined the effects of mindfulness-based sex therapy on sexual arousal concordance in a sample of women with sexual desire/arousal difficulties (n = 79, M age 40.8 years) who participated in an in-laboratory assessment of sexual arousal using a vaginal photoplethysmograph before and after four sessions of group mindfulness-based sex therapy. Genital-subjective sexual arousal concordance significantly increased from pre-treatment levels, with changes in subjective sexual arousal predicting contemporaneous genital sexual arousal (but not the reverse). These findings have implications for our understanding of the mechanisms by which mindfulness-based sex therapy improves sexual functioning in women, and suggest that such treatment may lead to an integration of physical and subjective arousal processes. Moreover, our findings suggest that future research might consider the adoption of sexual arousal concordance as a relevant endpoint in treatment outcome research of women with sexual desire/arousal concerns.

  12. Dry Eye Disease: Concordance Between the Diagnostic Tests in African Eyes.

    PubMed

    Onwubiko, Stella N; Eze, Boniface I; Udeh, Nnenma N; Onwasigwe, Ernest N; Umeh, Rich E

    2016-11-01

    To assess the concordance between the diagnostic tests for dry eye disease (DED) in a Nigerian hospital population. The study was a hospital-based cross-sectional survey of adults (≥18 years) presenting at the eye clinic of the University of Nigeria Teaching Hospital (UNTH), Enugu; September-December, 2011. Participants' socio-demographic data were collected. Each subject was assessed for DED using the "Ocular Surface Disease Index" (OSDI) questionnaire, tear-film breakup time (TBUT), and Schirmer test. The intertest concordance was assessed using kappa statistic, correlation, and regression coefficients. The participants (n=402; men: 193) were aged 50.1±19.1 standard deviation years (range: 18-94 years). Dry eye disease was diagnosed in 203 by TBUT, 170 by Schirmer test, and 295 by OSDI; the concordance between the tests were OSDI versus TBUT (Kappa, κ=-0.194); OSDI versus Schirmer (κ=-0.276); and TBUT versus Schirmer (κ=0.082). Ocular Surface Disease Index was inversely correlated with Schirmer test (Spearman ρ=-0.231, P<0.001) and TBUT (ρ=-0.237, P<0.001). In the linear regression model, OSDI was poorly predicted by TBUT (β=-0.09; 95% confidence interval (CI): -0.26 to -0.03, P=0.14) and Schirmer test (β=-0.35, 95% CI: -0.53 to -0.18, P=0.18). At UNTH, there is poor agreement, and almost equal correlation, between the subjective and objective tests for DED. Therefore, the selection of diagnostic test for DED should be informed by cost-effectiveness and diagnostic resource availability, not diagnostic efficiency or utility.

  13. Performance of immunological response in predicting virological failure.

    PubMed

    Ingole, Nayana; Mehta, Preeti; Pazare, Amar; Paranjpe, Supriya; Sarkate, Purva

    2013-03-01

    In HIV-infected individuals on antiretroviral therapy (ART), the decision on when to switch from first-line to second-line therapy is dictated by treatment failure, and this can be measured in three ways: clinically, immunologically, and virologically. While viral load (VL) decreases and CD4 cell increases typically occur together after starting ART, discordant responses may be seen. Hence the current study was designed to determine the immunological and virological response to ART and to evaluate the utility of immunological response to predict virological failure. All treatment-naive HIV-positive individuals aged >18 years who were eligible for ART were enrolled and assessed at baseline, 6 months, and 12 months clinically and by CD4 cell count and viral load estimations. The patients were categorized as showing concordant favorable (CF), immunological only (IO), virological only (VO), and concordant unfavorable responses (CU). The efficiency of immunological failure to predict virological failure was analyzed across various levels of virological failure (VL>50, >500, and >5,000 copies/ml). At 6 months, 87(79.81%), 7(5.5%), 13 (11.92%), and 2 (1.83%) patients and at 12 months 61(69.3%), 9(10.2%), 16 (18.2%), and 2 (2.3%) patients had CF, IO, VO, and CU responses, respectively. Immunological failure criteria had a very low sensitivity (11.1-40%) and positive predictive value (8.3-25%) to predict virological failure. Immunological criteria do not accurately predict virological failure resulting in significant misclassification of therapeutic responses. There is an urgent need for inclusion of viral load testing in the initiation and monitoring of ART.

  14. Receipt of Guideline-Concordant Treatment in Elderly Prostate Cancer Patients

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

    Chen, Ronald C., E-mail: Ronald_chen@med.unc.edu; Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

    2014-02-01

    Purpose: To examine the proportion of elderly prostate cancer patients receiving guideline-concordant treatment, using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database. Methods and Materials: A total of 29,001 men diagnosed in 2004-2007 with localized prostate cancer, aged 66 to 79 years, were included. We characterized the proportion of men who received treatment concordant with the National Comprehensive Cancer Network guidelines, stratified by risk group and age. Logistic regression was used to examine covariates associated with receipt of guideline-concordant management. Results: Guideline concordance was 79%-89% for patients with low- or intermediate-risk disease. Among high-risk patients, 66.6% of those agedmore » 66-69 years received guideline-concordant management, compared with 51.9% of those aged 75-79 years. Discordance was mainly due to conservative management—no treatment or hormone therapy alone. Among the subgroup of patients aged ≤76 years with no measured comorbidity, findings were similar. On multivariable analysis, older age (75-79 vs 66-69 years, odds ratio 0.51, 95% confidence interval 0.50-0.57) was associated with a lower likelihood of guideline concordance for high-risk prostate cancer, but comorbidity was not. Conclusions: There is undertreatment of elderly but healthy patients with high-risk prostate cancer, the most aggressive form of this disease.« less

  15. Concordance of adolescent human papillomavirus vaccination parental report with provider report in the National Immunization Survey-Teen (2008-2013).

    PubMed

    Hirth, Jacqueline; Kuo, Yong-Fang; Laz, Tabassum Haque; Starkey, Jonathan M; Rupp, Richard E; Rahman, Mahbubur; Berenson, Abbey B

    2016-08-17

    To examine the accuracy of parental report of HPV vaccination through examination of concordance, with healthcare provider vaccination report as the comparison. The 2008-2013 National Immunization Survey (NIS)-Teen was used to examine accuracy of parent reports of HPV vaccination for their female daughters aged 13-17years, as compared with provider report of initiation and number of doses. Multivariable logistic regression models were used to examine associations related to concordance of parent and provider report. Of 51,746 adolescents, 84% concordance for HPV vaccine initiation and 70% concordance for number of doses was observed. Accuracy varied by race/ethnicity, region, time, and income. The parent report of number of doses was more likely to be accurate among parents of 13 and 14year old females than 17year olds. Accuracy of initiation and number of doses were lower among Hispanic and black adolescents compared to white parents. The odds of over-report was higher among minorities compared to whites, but the odds of underreport was also markedly higher in these groups compared to parents of white teens. Accuracy of parental vaccine report decreased across time. These findings are important for healthcare providers who need to ascertain the vaccination status of young adults. Strengthening existing immunization registries to improve data sharing capabilities and record completeness could improve vaccination rates, while avoiding costs associated with over-vaccination. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break.

    PubMed

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean-Michel; García de Cortázar-Atauri, Iñaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2016-10-01

    The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. The effect of temperature on plant phenology is, however, not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process-based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future. © 2016 John Wiley & Sons Ltd.

  17. How accurate is our clinical prediction of "minimal prostate cancer"?

    PubMed

    Leibovici, Dan; Shikanov, Sergey; Gofrit, Ofer N; Zagaja, Gregory P; Shilo, Yaniv; Shalhav, Arieh L

    2013-07-01

    Recommendations for active surveillance versus immediate treatment for low risk prostate cancer are based on biopsy and clinical data, assuming that a low volume of well-differentiated carcinoma will be associated with a low progression risk. However, the accuracy of clinical prediction of minimal prostate cancer (MPC) is unclear. To define preoperative predictors for MPC in prostatectomy specimens and to examine the accuracy of such prediction. Data collected on 1526 consecutive radical prostatectomy patients operated in a single center between 2003 and 2008 included: age, body mass index, preoperative prostate-specific antigen level, biopsy Gleason score, clinical stage, percentage of positive biopsy cores, and maximal core length (MCL) involvement. MPC was defined as < 5% of prostate volume involvement with organ-confined Gleason score < or = 6. Univariate and multivariate logistic regression analyses were used to define independent predictors of minimal disease. Classification and Regression Tree (CART) analysis was used to define cutoff values for the predictors and measure the accuracy of prediction. MPC was found in 241 patients (15.8%). Clinical stage, biopsy Gleason's score, percent of positive biopsy cores, and maximal involved core length were associated with minimal disease (OR 0.42, 0.1, 0.92, and 0.9, respectively). Independent predictors of MPC included: biopsy Gleason score, percent of positive cores and MCL (OR 0.21, 095 and 0.95, respectively). CART showed that when the MCL exceeded 11.5%, the likelihood of MPC was 3.8%. Conversely, when applying the most favorable preoperative conditions (Gleason < or = 6, < 20% positive cores, MCL < or = 11.5%) the chance of minimal disease was 41%. Biopsy Gleason score, the percent of positive cores and MCL are independently associated with MPC. While preoperative prediction of significant prostate cancer was accurate, clinical prediction of MPC was incorrect 59% of the time. Caution is necessary when

  18. KWICgrouper--Designing a Tool for Corpus-Driven Concordance Analysis

    ERIC Educational Resources Information Center

    O'Donnell, Matthew Brook

    2008-01-01

    The corpus-driven analysis of concordance data often results in the identification of groups of lines in which repeated patterns around the node item establish membership in a particular function meaning group (Mahlberg, 2005). This paper explains the KWICgrouper, a concept designed to support this kind of concordance analysis. Groups are defined…

  19. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  20. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  1. How accurate are resting energy expenditure prediction equations in obese trauma and burn patients?

    PubMed

    Stucky, Chee-Chee H; Moncure, Michael; Hise, Mary; Gossage, Clint M; Northrop, David

    2008-01-01

    While the prevalence of obesity continues to increase in our society, outdated resting energy expenditure (REE) prediction equations may overpredict energy requirements in obese patients. Accurate feeding is essential since overfeeding has been demonstrated to adversely affect outcomes. The first objective was to compare REE calculated by prediction equations to the measured REE in obese trauma and burn patients. Our hypothesis was that an equation using fat-free mass would give a more accurate prediction. The second objective was to consider the effect of a commonly used injury factor on the predicted REE. A retrospective chart review was performed on 28 patients. REE was measured using indirect calorimetry and compared with the Harris-Benedict and Cunningham equations, and an equation using type II diabetes as a factor. Statistical analyses used were paired t test, +/-95% confidence interval, and the Bland-Altman method. Measured average REE in trauma and burn patients was 21.37 +/- 5.26 and 21.81 +/- 3.35 kcal/kg/d, respectively. Harris-Benedict underpredicted REE in trauma and burn patients to the least extent, while the Cunningham equation underpredicted REE in both populations to the greatest extent. Using an injury factor of 1.2, Cunningham continued to underestimate REE in both populations, while the Harris-Benedict and Diabetic equations overpredicted REE in both populations. The measured average REE is significantly less than current guidelines. This finding suggests that a hypocaloric regimen is worth considering for ICU patients. Also, if an injury factor of 1.2 is incorporated in certain equations, patients may be given too many calories.

  2. ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

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

    Visel, Axel; Blow, Matthew J.; Li, Zirong

    2009-02-01

    A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. Wemore » tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.« less

  3. Patient preference for a racially or gender-concordant student dentist.

    PubMed

    Bender, Daniel J

    2007-06-01

    Disparities in health and health care due to race and ethnicity are a national problem. One commonly proposed method to address disparities is to increase the number of underrepresented minorities in the health professions to serve the needs of growing minority populations. This position is based in part on the racial concordance hypothesis, an untested assumption that minority patients prefer to be treated by providers of the same race as themselves. The purpose of this study was to test the racial concordance hypothesis. Gender preference of dental patients was also investigated. One hundred twenty male and female Caucasian, African American, Hispanic, and Asian dental patients over eighteen were recruited from the reception area of a private dental school clinic in Northern California. Participants were randomly assigned to a treatment condition that gave them a choice between two equally qualified fictitious dental students that varied on race and gender. Participants were initially blinded to the study's purpose to preserve the authenticity of the choice decision. Results showed that 58 percent of the participants had no preference for the race or gender of their student dentist, but that some black and Hispanic patients preferred a racially concordant student dentist and some female patients preferred a gender-concordant student dentist. Hispanic females were especially likely to prefer racial and gender concordance. The findings suggest that the racial concordance hypothesis may not apply to choosing a dentist and thus may not be as strong an argument to justify efforts to increase diversity in dental schools as previously thought.

  4. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    PubMed Central

    Noecker, Cecilia; Schaefer, Krista; Zaccheo, Kelly; Yang, Yiding; Day, Judy; Ganusov, Vitaly V.

    2015-01-01

    Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results

  5. Improving medical decisions for incapacitated persons: does focusing on "accurate predictions" lead to an inaccurate picture?

    PubMed

    Kim, Scott Y H

    2014-04-01

    The Patient Preference Predictor (PPP) proposal places a high priority on the accuracy of predicting patients' preferences and finds the performance of surrogates inadequate. However, the quest to develop a highly accurate, individualized statistical model has significant obstacles. First, it will be impossible to validate the PPP beyond the limit imposed by 60%-80% reliability of people's preferences for future medical decisions--a figure no better than the known average accuracy of surrogates. Second, evidence supports the view that a sizable minority of persons may not even have preferences to predict. Third, many, perhaps most, people express their autonomy just as much by entrusting their loved ones to exercise their judgment than by desiring to specifically control future decisions. Surrogate decision making faces none of these issues and, in fact, it may be more efficient, accurate, and authoritative than is commonly assumed.

  6. Does Repeated Testing Impact Concordance Between Genital and Self-Reported Sexual Arousal in Women?

    PubMed

    Velten, Julia; Chivers, Meredith L; Brotto, Lori A

    2018-04-01

    Women show a substantial variability in their genital and subjective responses to sexual stimuli. The level of agreement between these two aspects of response is termed sexual concordance and has been increasingly investigated because of its implications for understanding models of sexual response and as a potential endpoint in clinical trials of treatments to improve women's sexual dysfunction. However, interpreting changes in sexual concordance may be problematic because, to date, it still is unclear how repeated testing itself influences sexual concordance in women. We are aware of only one study that evaluated temporal stability of concordance in women, and it found no evidence of stability. However, time stability would be necessary for arguing that concordance is a stable individual difference. The main goal of this study was to investigate the test-retest reliability of sexual concordance in a sample of 30 women with sexual difficulties. Using hierarchical linear modeling, we found that sexual concordance was not influenced by repeated testing 12 weeks later, but showed test-retest reliability suggesting temporal stability. Our findings support the hypothesis that sexual concordance is a relatively stable individual difference and that changes in sexual concordance after treatment or experimental conditions could, therefore, be attributed to effects of those conditions.

  7. Rapid and accurate prediction of degradant formation rates in pharmaceutical formulations using high-performance liquid chromatography-mass spectrometry.

    PubMed

    Darrington, Richard T; Jiao, Jim

    2004-04-01

    Rapid and accurate stability prediction is essential to pharmaceutical formulation development. Commonly used stability prediction methods include monitoring parent drug loss at intended storage conditions or initial rate determination of degradants under accelerated conditions. Monitoring parent drug loss at the intended storage condition does not provide a rapid and accurate stability assessment because often <0.5% drug loss is all that can be observed in a realistic time frame, while the accelerated initial rate method in conjunction with extrapolation of rate constants using the Arrhenius or Eyring equations often introduces large errors in shelf-life prediction. In this study, the shelf life prediction of a model pharmaceutical preparation utilizing sensitive high-performance liquid chromatography-mass spectrometry (LC/MS) to directly quantitate degradant formation rates at the intended storage condition is proposed. This method was compared to traditional shelf life prediction approaches in terms of time required to predict shelf life and associated error in shelf life estimation. Results demonstrated that the proposed LC/MS method using initial rates analysis provided significantly improved confidence intervals for the predicted shelf life and required less overall time and effort to obtain the stability estimation compared to the other methods evaluated. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association.

  8. Decision-Making in Pediatric Transport Team Dispatch Using Script Concordance Testing.

    PubMed

    Rajapreyar, Prakadeshwari; Marcdante, Karen; Zhang, Liyun; Simpson, Pippa; Meyer, Michael T

    2017-11-01

    Our objective was to compare decision-making in dispatching pediatric transport teams by Medical Directors of pediatric transport teams (serving as experts) to that of Pediatric Intensivists and Critical Care fellows who often serve as Medical Control physicians. Understanding decision-making around team composition and dispatch could impact clinical management, cost effectiveness, and educational needs. Survey was developed using Script Concordance Testing guidelines. The survey contained 15 transport case vignettes covering 20 scenarios (45 questions). Eleven scenarios assessed impact of intrinsic patient factors (e.g., procedural needs), whereas nine assessed extrinsic factors (e.g., weather). Pediatric Critical Care programs accredited by the Accreditation Council for Graduate Medical Education (the United States). Pediatric Intensivists and senior Critical Care fellows at Pediatric Critical Care programs were the target population with Transport Medical Directors serving as the expert panel. None. Survey results were scored per Script Concordance Testing guidelines. Concordance within groups was assessed using simple percentage agreement. There was little concordance in decision-making by Transport Medical Directors (median Script Concordance Testing percentage score [interquartile range] of 33.9 [30.4-37.3]). In addition, there was no statistically significant difference between the median Script Concordance Testing scores among the senior fellows and Pediatric Intensivists (31.1 [29.6-33.2] vs 29.7 [28.3-32.3], respectively; p = 0.12). Transport Medical Directors were more concordant on reasoning involving intrinsic patient factors rather than extrinsic factors (10/21 vs 4/24). Our study demonstrates pediatric transport team dispatch decision-making discordance by pediatric critical care physicians of varying levels of expertise and experience. Script Concordance Testing at a local level may better elucidate standards in medical decision-making within

  9. Kinetic approach to degradation mechanisms in polymer solar cells and their accurate lifetime predictions

    NASA Astrophysics Data System (ADS)

    Arshad, Muhammad Azeem; Maaroufi, AbdelKrim

    2018-07-01

    A beginning has been made in the present study regarding the accurate lifetime predictions of polymer solar cells. Certain reservations about the conventionally employed temperature accelerated lifetime measurements test for its unworthiness of predicting reliable lifetimes of polymer solar cells are brought into light. Critical issues concerning the accelerated lifetime testing include, assuming reaction mechanism instead of determining it, and relying solely on the temperature acceleration of a single property of material. An advanced approach comprising a set of theoretical models to estimate the accurate lifetimes of polymer solar cells is therefore suggested in order to suitably alternate the accelerated lifetime testing. This approach takes into account systematic kinetic modeling of various possible polymer degradation mechanisms under natural weathering conditions. The proposed kinetic approach is substantiated by its applications on experimental aging data-sets of polymer solar materials/solar cells including, P3HT polymer film, bulk heterojunction (MDMO-PPV:PCBM) and dye-sensitized solar cells. Based on the suggested approach, an efficacious lifetime determination formula for polymer solar cells is derived and tested on dye-sensitized solar cells. Some important merits of the proposed method are also pointed out and its prospective applications are discussed.

  10. How Accurate are Self-Reports? An Analysis of Self-Reported Healthcare Utilization and Absence When Compared to Administrative Data

    PubMed Central

    Short, Meghan E.; Pei, Xiaofei; Tabrizi, Maryam J.; Ozminkowski, Ronald J.; Gibson, Teresa B.; DeJoy, Dave M.; Wilson, Mark G.

    2009-01-01

    Objective To determine the accuracy of self-reported healthcare utilization and absence reported on health risk assessments (HRAs) against administrative claims and human resource records. Methods Self-reported values of healthcare utilization and absenteeism were analyzed for concordance to administrative claims values. Percent agreement, Pearson’s correlations, and multivariate logistic regression models examined the level of agreement and characteristics of participants with concordance. Results Self-report and administrative data showed greater concordance for monthly compared to yearly healthcare utilization metrics. Percent agreement ranged from 30 to 99% with annual doctor visits having the lowest percent agreement. Younger people, males, those with higher education, and healthier individuals more accurately reported their healthcare utilization and absenteeism. Conclusions Self-reported healthcare utilization and absenteeism may be used as a proxy when medical claims and administrative data are unavailable, particularly for shorter recall periods. PMID:19528832

  11. Modeling methodology for the accurate and prompt prediction of symptomatic events in chronic diseases.

    PubMed

    Pagán, Josué; Risco-Martín, José L; Moya, José M; Ayala, José L

    2016-08-01

    Prediction of symptomatic crises in chronic diseases allows to take decisions before the symptoms occur, such as the intake of drugs to avoid the symptoms or the activation of medical alarms. The prediction horizon is in this case an important parameter in order to fulfill the pharmacokinetics of medications, or the time response of medical services. This paper presents a study about the prediction limits of a chronic disease with symptomatic crises: the migraine. For that purpose, this work develops a methodology to build predictive migraine models and to improve these predictions beyond the limits of the initial models. The maximum prediction horizon is analyzed, and its dependency on the selected features is studied. A strategy for model selection is proposed to tackle the trade off between conservative but robust predictive models, with respect to less accurate predictions with higher horizons. The obtained results show a prediction horizon close to 40min, which is in the time range of the drug pharmacokinetics. Experiments have been performed in a realistic scenario where input data have been acquired in an ambulatory clinical study by the deployment of a non-intrusive Wireless Body Sensor Network. Our results provide an effective methodology for the selection of the future horizon in the development of prediction algorithms for diseases experiencing symptomatic crises. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

    PubMed

    Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

    2014-07-01

    With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. © 2013 Wiley Periodicals, Inc.

  13. A novel nomogram accurately quantifies the risk of mortality in elderly patients undergoing colorectal surgery.

    PubMed

    Kiran, Ravi P; Attaluri, Vikram; Hammel, Jeff; Church, James

    2013-05-01

    The ability to accurately predict postoperative mortality is expected to improve preoperative decisions for elderly patients considered for colorectal surgery. Patients undergoing colorectal surgery were identified from the National Surgical Quality Improvement Program database (2005-2007) and stratified as elderly (>70 years) and nonelderly (<70 years). Univariate analysis of preoperative risk factors and 30-day mortality and morbidity were analyzed on 70% of the population. A nomogram for mortality was created and tested on the remaining 30%. Of 30,900 colorectal cases, 10,750 were elderly (>70 years). Mortality increased steadily with age (0.5% every 5 years) and at a faster rate (1.2% every 5 years) after 70 years, which defined "elderly" in this study. Elderly (mean age: 78.4 years) and nonelderly patients (52.8 years) had mortality of 7.6% versus 2.0% and a morbidity of 32.8% versus 25.7%, respectively. Elderly patients had greater preoperative comorbidities including chronic obstructive pulmonary disease (10.5% vs 3.8%), diabetes (18.7% vs 11.1%), and renal insufficiency (1.7% vs 1.3%). A multivariate model for 30-day mortality and nomogram were created. Increasing age was associated with mortality [age >70 years: odds ratio (OR) = 2.0 (95% confidence interval (CI): 1.7-2.4); >85 years: OR = 4.3 (95% CI: 3.3-5.5)]. The nomogram accurately predicted mortality, including very high-risk (>50% mortality) with a concordant index for this model of 0.89. Colorectal surgery in elderly patients is associated with significantly higher mortality. This novel nomogram that predicts postoperative mortality may facilitate preoperative treatment decisions.

  14. Parent and Teacher Concordance of Child Outcomes for Youth with Autism Spectrum Disorder

    PubMed Central

    Suhrheinrich, Jessica; Rieth, Sarah R.; Stahmer, Aubyn C.

    2017-01-01

    Cross-informant ratings of are considered gold standard for child behavioral assessment. To date, little work has examined informant ratings of adaptive functioning for youth with autism spectrum disorder (ASD). In a large, diverse sample of youth with ASD, this study evaluated parent–teacher concordance of ratings of adaptive functioning and ASD-specific symptomatology across time. The impact of child clinical characteristics on concordance was also examined. Participants included 246 children, their caregivers and teachers. Parent–teacher concordance was variable but generally consistent across time. Concordance was significantly impacted by autism severity and child cognitive abilities. Findings inform the broader concordance literature and support the need to consider child clinical factors when assessing child functioning in samples of children with ASD. PMID:29164440

  15. Determination of quantitative trait variants by concordance via application of the a posteriori granddaughter design to the U.S. Holstein population

    USDA-ARS?s Scientific Manuscript database

    Experimental designs that exploit family information can provide substantial predictive power in quantitative trait variant discovery projects. Concordance between quantitative trait locus genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 29 trai...

  16. Do dual-route models accurately predict reading and spelling performance in individuals with acquired alexia and agraphia?

    PubMed

    Rapcsak, Steven Z; Henry, Maya L; Teague, Sommer L; Carnahan, Susan D; Beeson, Pélagie M

    2007-06-18

    Coltheart and co-workers [Castles, A., Bates, T. C., & Coltheart, M. (2006). John Marshall and the developmental dyslexias. Aphasiology, 20, 871-892; Coltheart, M., Rastle, K., Perry, C., Langdon, R., & Ziegler, J. (2001). DRC: A dual route cascaded model of visual word recognition and reading aloud. Psychological Review, 108, 204-256] have demonstrated that an equation derived from dual-route theory accurately predicts reading performance in young normal readers and in children with reading impairment due to developmental dyslexia or stroke. In this paper, we present evidence that the dual-route equation and a related multiple regression model also accurately predict both reading and spelling performance in adult neurological patients with acquired alexia and agraphia. These findings provide empirical support for dual-route theories of written language processing.

  17. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

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

    Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys.more » 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.« less

  18. Evaluation of language concordant, patient-centered drug label instructions.

    PubMed

    Bailey, Stacy Cooper; Sarkar, Urmimala; Chen, Alice Hm; Schillinger, Dean; Wolf, Michael S

    2012-12-01

    Despite federal laws requiring language access in healthcare settings, most US pharmacies are unable to provide prescription (Rx) medication instructions to limited English proficient (LEP) patients in their native language. To evaluate the efficacy of health literacy-informed, multilingual Rx instructions (the ConcordantRx instructions) to improve Rx understanding, regimen dosing and regimen consolidation in comparison to standard, language-concordant Rx instructions. Randomized, experimental evaluation. Two hundred and two LEP adults speaking five non-English languages (Chinese, Korean, Russian, Spanish, Vietnamese), recruited from nine clinics and community organizations in San Francisco and Chicago. Subjects were randomized to review Rx bottles with either ConcordantRx or standard instructions. Proper demonstration of common prescription label instructions for single and multi-drug medication regimens. Regimen consolidation was assessed by determining how many times per day subjects would take medicine for a multi-drug regimen. Subjects receiving the ConcordantRx instructions demonstrated significantly greater Rx understanding, regimen dosing and regimen consolidation in comparison to those receiving standard instructions (incidence rate ratio [IRR]: 1.25, 95 % confidence interval [CI]: 1.06-1.48; P= 0.007 for Rx understanding, IRR: 1.19, 95 % CI: 1.03-1.39; P= 0.02 for regimen dosing and IRR: 0.76, 95 % CI: 0.64-0.90; P= 0.001 for regimen consolidation). In most cases, instruction type was the sole, independent predictor of outcomes in multivariate models controlling for relevant covariates. There is a need for standardized, multilingual Rx instructions that can be implemented in pharmacy practices to promote safe medication use among LEP patients. The ConcordantRx instructions represent an important step towards achieving this goal.

  19. CFHTLenS revisited: assessing concordance with Planck including astrophysical systematics

    NASA Astrophysics Data System (ADS)

    Joudaki, Shahab; Blake, Chris; Heymans, Catherine; Choi, Ami; Harnois-Deraps, Joachim; Hildebrandt, Hendrik; Joachimi, Benjamin; Johnson, Andrew; Mead, Alexander; Parkinson, David; Viola, Massimo; van Waerbeke, Ludovic

    2017-02-01

    We investigate the impact of astrophysical systematics on cosmic shear cosmological parameter constraints from the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS) and the concordance with cosmic microwave background measurements by Planck. We present updated CFHTLenS cosmic shear tomography measurements extended to degree scales using a covariance calibrated by a new suite of N-body simulations. We analyse these measurements with a new model fitting pipeline, accounting for key systematic uncertainties arising from intrinsic galaxy alignments, baryonic effects in the non-linear matter power spectrum, and photometric redshift uncertainties. We examine the impact of the systematic degrees of freedom on the cosmological parameter constraints, both independently and jointly. When the systematic uncertainties are considered independently, the intrinsic alignment amplitude is the only degree of freedom that is substantially preferred by the data. When the systematic uncertainties are considered jointly, there is no consistently strong preference in favour of the more complex models. We quantify the level of concordance between the CFHTLenS and Planck data sets by employing two distinct data concordance tests, grounded in Bayesian evidence and information theory. We find that the two data concordance tests largely agree with one another and that the level of concordance between the CFHTLenS and Planck data sets is sensitive to the exact details of the systematic uncertainties included in our analysis, ranging from decisive discordance to substantial concordance as the treatment of the systematic uncertainties becomes more conservative. The least conservative scenario is the one most favoured by the cosmic shear data, but it is also the one that shows the greatest degree of discordance with Planck. The data and analysis code are publicly available at https://github.com/sjoudaki/cfhtlens_revisited.

  20. ILT based defect simulation of inspection images accurately predicts mask defect printability on wafer

    NASA Astrophysics Data System (ADS)

    Deep, Prakash; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2016-05-01

    At advanced technology nodes mask complexity has been increased because of large-scale use of resolution enhancement technologies (RET) which includes Optical Proximity Correction (OPC), Inverse Lithography Technology (ILT) and Source Mask Optimization (SMO). The number of defects detected during inspection of such mask increased drastically and differentiation of critical and non-critical defects are more challenging, complex and time consuming. Because of significant defectivity of EUVL masks and non-availability of actinic inspection, it is important and also challenging to predict the criticality of defects for printability on wafer. This is one of the significant barriers for the adoption of EUVL for semiconductor manufacturing. Techniques to decide criticality of defects from images captured using non actinic inspection images is desired till actinic inspection is not available. High resolution inspection of photomask images detects many defects which are used for process and mask qualification. Repairing all defects is not practical and probably not required, however it's imperative to know which defects are severe enough to impact wafer before repair. Additionally, wafer printability check is always desired after repairing a defect. AIMSTM review is the industry standard for this, however doing AIMSTM review for all defects is expensive and very time consuming. Fast, accurate and an economical mechanism is desired which can predict defect printability on wafer accurately and quickly from images captured using high resolution inspection machine. Predicting defect printability from such images is challenging due to the fact that the high resolution images do not correlate with actual mask contours. The challenge is increased due to use of different optical condition during inspection other than actual scanner condition, and defects found in such images do not have correlation with actual impact on wafer. Our automated defect simulation tool predicts

  1. The c-index is not proper for the evaluation of $t$-year predicted risks.

    PubMed

    Blanche, Paul; Kattan, Michael W; Gerds, Thomas A

    2018-02-16

    We show that the widely used concordance index for time to event outcome is not proper when interest is in predicting a $t$-year risk of an event, for example 10-year mortality. In the situation with a fixed prediction horizon, the concordance index can be higher for a misspecified model than for a correctly specified model. Impropriety happens because the concordance index assesses the order of the event times and not the order of the event status at the prediction horizon. The time-dependent area under the receiver operating characteristic curve does not have this problem and is proper in this context.

  2. Sleep-Wake Concordance in Couples Is Inversely Associated With Cardiovascular Disease Risk Markers.

    PubMed

    Gunn, Heather E; Buysse, Daniel J; Matthews, Karen A; Kline, Christopher E; Cribbet, Matthew R; Troxel, Wendy M

    2017-01-01

    To determine whether interdependence in couples' sleep (sleep-wake concordance i.e., whether couples are awake or asleep at the same time throughout the night) is associated with two markers of cardiovascular disease (CVD) risk, ambulatory blood pressure (BP) and systemic inflammation. This community-based study is a cross-sectional analysis of 46 adult couples, aged 18-45 years, without known sleep disorders. Percent sleep-wake concordance, the independent variable, was calculated for each individual using actigraphy. Ambulatory BP monitors measured BP across 48 h. Dependent variables included mean sleep systolic BP (SBP) and diastolic BP (DBP), mean wake SBP and DBP, sleep-wake SBP and DBP ratios, and C-reactive protein (CRP). Mixed models were used and were adjusted for age, sex, education, race, and body mass index. Higher sleep-wake concordance was associated with lower sleep SBP (b = -.35, SE = .01) and DBP (b = -.22, SE = .10) and lower wake SBP (b = -.26, SE = .12; all p values < .05). Results were moderated by sex; for women, high concordance was associated with lower BP. Men and women with higher sleep-wake concordance also had lower CRP values (b = -.15, SE = .03, p < .05). Sleep-wake concordance was not associated with wake DBP or sleep/wake BP ratios. Significant findings remained after controlling for individual sleep quality, duration, and wake after sleep onset. Sleep-wake concordance was associated with sleep BP, and this association was stronger for women. Higher sleep-wake concordance was associated with lower systemic inflammation for men and women. Sleep-wake concordance may be a novel mechanism by which marital relationships are associated with long-term CVD outcomes. © Sleep Research Society 2016. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  3. Prediction of morbidity and mortality in patients with type 2 diabetes.

    PubMed

    Wells, Brian J; Roth, Rachel; Nowacki, Amy S; Arrigain, Susana; Yu, Changhong; Rosenkrans, Wayne A; Kattan, Michael W

    2013-01-01

    Introduction. The objective of this study was to create a tool that accurately predicts the risk of morbidity and mortality in patients with type 2 diabetes according to an oral hypoglycemic agent. Materials and Methods. The model was based on a cohort of 33,067 patients with type 2 diabetes who were prescribed a single oral hypoglycemic agent at the Cleveland Clinic between 1998 and 2006. Competing risk regression models were created for coronary heart disease (CHD), heart failure, and stroke, while a Cox regression model was created for mortality. Propensity scores were used to account for possible treatment bias. A prediction tool was created and internally validated using tenfold cross-validation. The results were compared to a Framingham model and a model based on the United Kingdom Prospective Diabetes Study (UKPDS) for CHD and stroke, respectively. Results and Discussion. Median follow-up for the mortality outcome was 769 days. The numbers of patients experiencing events were as follows: CHD (3062), heart failure (1408), stroke (1451), and mortality (3661). The prediction tools demonstrated the following concordance indices (c-statistics) for the specific outcomes: CHD (0.730), heart failure (0.753), stroke (0.688), and mortality (0.719). The prediction tool was superior to the Framingham model at predicting CHD and was at least as accurate as the UKPDS model at predicting stroke. Conclusions. We created an accurate tool for predicting the risk of stroke, coronary heart disease, heart failure, and death in patients with type 2 diabetes. The calculator is available online at http://rcalc.ccf.org under the heading "Type 2 Diabetes" and entitled, "Predicting 5-Year Morbidity and Mortality." This may be a valuable tool to aid the clinician's choice of an oral hypoglycemic, to better inform patients, and to motivate dialogue between physician and patient.

  4. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.

    PubMed

    Wang, Sheng; Sun, Siqi; Li, Zhen; Zhang, Renyu; Xu, Jinbo

    2017-01-01

    Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have

  5. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

    PubMed Central

    Li, Zhen; Zhang, Renyu

    2017-01-01

    Motivation Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. Method This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Results Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact

  6. Concordance between European and US case definitions of healthcare-associated infections

    PubMed Central

    2012-01-01

    Background Surveillance of healthcare-associated infections (HAI) is a valuable measure to decrease infection rates. Across Europe, inter-country comparisons of HAI rates seem limited because some countries use US definitions from the US Centers for Disease Control and Prevention (CDC/NHSN) while other countries use European definitions from the Hospitals in Europe Link for Infection Control through Surveillance (HELICS/IPSE) project. In this study, we analyzed the concordance between US and European definitions of HAI. Methods An international working group of experts from seven European countries was set up to identify differences between US and European definitions and then conduct surveillance using both sets of definitions during a three-month period (March 1st -May 31st, 2010). Concordance between case definitions was estimated with Cohen’s kappa statistic (κ). Results Differences in HAI definitions were found for bloodstream infection (BSI), pneumonia (PN), urinary tract infection (UTI) and the two key terms “intensive care unit (ICU)-acquired infection” and “mechanical ventilation”. Concordance was analyzed for these definitions and key terms with the exception of UTI. Surveillance was performed in 47 ICUs and 6,506 patients were assessed. One hundred and eighty PN and 123 BSI cases were identified. When all PN cases were considered, concordance for PN was κ = 0.99 [CI 95%: 0.98-1.00]. When PN cases were divided into subgroups, concordance was κ = 0.90 (CI 95%: 0.86-0.94) for clinically defined PN and κ = 0.72 (CI 95%: 0.63-0.82) for microbiologically defined PN. Concordance for BSI was κ = 0.73 [CI 95%: 0.66-0.80]. However, BSI cases secondary to another infection site (42% of all BSI cases) are excluded when using US definitions and concordance for BSI was κ = 1.00 when only primary BSI cases, i.e. Europe-defined BSI with ”catheter” or “unknown” origin and US-defined laboratory-confirmed BSI (LCBI), were

  7. Obtaining Accurate Probabilities Using Classifier Calibration

    ERIC Educational Resources Information Center

    Pakdaman Naeini, Mahdi

    2016-01-01

    Learning probabilistic classification and prediction models that generate accurate probabilities is essential in many prediction and decision-making tasks in machine learning and data mining. One way to achieve this goal is to post-process the output of classification models to obtain more accurate probabilities. These post-processing methods are…

  8. Concordance of Beta-papillomavirus across anogenital and oral anatomic sites of men: The HIM Study.

    PubMed

    Nunes, Emily M; López, Rossana V M; Sudenga, Staci L; Gheit, Tarik; Tommasino, Massimo; Baggio, Maria L; Ferreira, Silvaneide; Galan, Lenice; Silva, Roberto C; Lazcano-Ponce, Eduardo; Giuliano, Anna R; Villa, Luisa L; Sichero, Laura

    2017-10-01

    We evaluated the concordance between β-HPVs detected in external genital skin, anal canal, and oral cavity specimens collected simultaneously from 717 men that were participating in the multinational HIM Study. Viral genotyping was performed using the Luminex technology. Species- and type-specific concordance was measured using kappa statistics for agreement. Overall, concordance of β-HPVs across sites was low and mainly observed among paired genital/anal canal samples. When grouped by species, solely β-4 HPVs showed moderate concordance in genital/anal pairs (κ = 0.457), which could be attributed to the substantial concordance of HPV-92 in men from Brazil and Mexico (κ > 0.610). β-HPV type concordance was higher in Mexico, where HPV-19 was consistently concordant in all anatomic site combinations. Our analysis indicates that type-specific concordance across sites is limited to few viral types; however, these infections seem to occur more often than would be expected by chance, suggesting that although rare, there is agreement among sites. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. John M. Eisenberg Patient Safety Awards. System innovation: Concord Hospital.

    PubMed

    Uhlig, Paul N; Brown, Jeffrey; Nason, Anne K; Camelio, Addie; Kendall, Elise

    2002-12-01

    The Cardiac Surgery Program at Concord Hospital (Concord, NH) restructured clinical teamwork for improved safety and effectiveness on the basis of theory and practice from human factors science, aviation safety, and high-reliability organization theory. A team-based, collaborative rounds process--the Concord Collaborative Care Model--that involved use of a structured communications protocol was conducted daily at each patient's bedside. The entire care team agreed to meet at the same time each day (8:45 AM to 9:30 AM) to share information and develop a plan of care for each patient, with patient and family members as active participants. The cardiac surgery team developed a structured communications protocol adapted from human factors science. To provide a forum for discussion of team goals and progress and to address system-level concerns, a biweekly system rounds process was established. Following implementation of collaborative rounds, mortality of Concord Hospital's cardiac surgery patients declined significantly from expected rates. Satisfaction rates of open heart patients scores were consistently in the 97th-99th percentile nationally. A quality of work life survey indicated that in every category, providers expressed greater satisfaction with the collaborative care process than with the traditional rounds process. Practice patterns in the Cardiac Surgery Program at Concord Hospital have changed to a much more collaborative and participatory process, with improved outcomes, happier patients, and more satisfied practitioners. A culture of continuous program improvement has been implemented that continues to evolve and produce benefits.

  10. Individual characteristics, area social participation, and primary non-concordance with medication: a multilevel analysis.

    PubMed

    Johnell, Kristina; Lindström, Martin; Sundquist, Jan; Eriksson, Charli; Merlo, Juan

    2006-03-02

    Non-concordance with medication remains a major public health problem that imposes a considerable financial burden on the health care system, and there is still a need for studies on correlates of non-concordance. Our first aim is to analyse whether any of the individual characteristics age, educational level, financial strain, self-rated health, social participation, and trust in the health care system are associated with primary non-concordance with medication. Our second aim is to investigate whether people living in the same area have similar probability of primary non-concordance with medication, that relates to area social participation. We analysed cross sectional data from 9,070 women and 6,795 men aged 18 to 79 years, living in 78 areas in central Sweden, who participated in the Life & Health year 2000 survey, with multilevel logistic regression (individuals at the first level and areas at the second level). Younger age, financial strain, low self-rated health, and low trust in the health care system were associated with primary non-concordance with medication. However, area social participation was not related to primary non-concordance, and the variation in primary non-concordance between the areas was small. Our results indicate that people in central Sweden with younger age, financial difficulties, low self-rated health, and low trust in the health care system may have a higher probability of primary non-concordance with medication. However, the area of residence--as defined by administrative boundaries--seems to play a minor role for primary non-concordance.

  11. Individual characteristics, area social participation, and primary non-concordance with medication: a multilevel analysis

    PubMed Central

    Johnell, Kristina; Lindström, Martin; Sundquist, Jan; Eriksson, Charli; Merlo, Juan

    2006-01-01

    Background Non-concordance with medication remains a major public health problem that imposes a considerable financial burden on the health care system, and there is still a need for studies on correlates of non-concordance. Our first aim is to analyse whether any of the individual characteristics age, educational level, financial strain, self-rated health, social participation, and trust in the health care system are associated with primary non-concordance with medication. Our second aim is to investigate whether people living in the same area have similar probability of primary non-concordance with medication, that relates to area social participation. Methods We analysed cross sectional data from 9 070 women and 6 795 men aged 18 to 79 years, living in 78 areas in central Sweden, who participated in the Life & Health year 2000 survey, with multilevel logistic regression (individuals at the first level and areas at the second level). Results Younger age, financial strain, low self-rated health, and low trust in the health care system were associated with primary non-concordance with medication. However, area social participation was not related to primary non-concordance, and the variation in primary non-concordance between the areas was small. Conclusion Our results indicate that people in central Sweden with younger age, financial difficulties, low self-rated health, and low trust in the health care system may have a higher probability of primary non-concordance with medication. However, the area of residence – as defined by administrative boundaries – seems to play a minor role for primary non-concordance. PMID:16512907

  12. Degree-Day Prediction Models for the Flight Phenology of Western Bean Cutworm (Lepidoptera: Noctuidae) Assessed with the Concordance Correlation Coefficient.

    PubMed

    Hanson, A A; Moon, R D; Wright, R J; Hunt, T E; Hutchison, W D

    2015-08-01

    Western bean cutworm, Striacosta albicosta (Smith) (Lepidoptera: Noctuidae), is a native, univoltine pest of corn and dry beans in North America. The current degree-day model for predicting a specified percentage of yearly moth flight involves heat unit accumulation above 10°C after 1 May. However, because the moth's observed range has expanded into the northern and eastern United States, there is concern that suitable temperatures before May could allow for significant S. albicosta development. Daily blacklight moth catch and temperature data from four Nebraska locations were used to construct degree-day models using simple or sine-wave methods, starting dates between 1 January and 1 May, and lower (-5 to 15°C) and upper (20 to 43.3°C) developmental thresholds. Predicted dates of flight from these models were compared with observed flight dates using independent datasets to assess model performance. Model performance was assessed with the concordance correlation coefficient to concurrently evaluate precision and accuracy. The best model for predicting timing of S. albicosta flight used simple degree-day calculations beginning on 1 March, a 3.3°C (38°F) lower threshold, and a 23.9°C (75°F) upper threshold. The revised cumulative flight model indicated field scouting to estimate moth egg density at the time of 25% flight should begin when 1,432 degree-days (2,577 degree-days °F) have accumulated. These results underscore the importance of assessing multiple parameters in phenological models and utilizing appropriate assessment methods, which in this case may allow for improved timing of field scouting for S. albicosta. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

    DOE PAGES

    Monti, Remo; Barozzi, Iros; Osterwalder, Marco; ...

    2017-08-21

    Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo. However, reliance on single chromatin marks leads to high rates of false-positive predictions. More sophisticated, integrative methods have been described, but commonly suffer from limited accessibility to the resulting predictions and reduced biological interpretability. Here we present the Limb-Enhancer Genie (LEG), a collection of highly accurate, genome-wide predictions of enhancers in the developing limb, available through a user-friendly online interface. We predict limb enhancers using a combination of > 50 published limb-specific datasets and clusters of evolutionarily conserved transcription factor binding sites, taking advantage ofmore » the patterns observed at previously in vivo validated elements. By combining different statistical models, our approach outperforms current state-of-the-art methods and provides interpretable measures of feature importance. Our results indicate that including a previously unappreciated score that quantifies tissue-specific nuclease accessibility significantly improves prediction performance. We demonstrate the utility of our approach through in vivo validation of newly predicted elements. Moreover, we describe general features that can guide the type of datasets to include when predicting tissue-specific enhancers genome-wide, while providing an accessible resource to the general biological community and facilitating the functional interpretation of genetic studies of limb malformations.« less

  14. Prediction of non-biochemical recurrence rate after radical prostatectomy in a Japanese cohort: development of a postoperative nomogram.

    PubMed

    Okubo, Hidenori; Ohori, Makoto; Ohno, Yoshio; Nakashima, Jun; Inoue, Rie; Nagao, Toshitaka; Tachibana, Masaaki

    2014-05-01

    To develop a nomogram based on postoperative factors and prostate-specific antigen levels to predict the non-biochemical recurrence rate after radical prostatectomy ina Japanese cohort. A total of 606 Japanese patients with T1-3N0M0 prostate cancer who underwent radical prostatectomy and pelvic lymph node dissection at Tokyo Medical University hospital from 2000 to 2010 were studied. A nomogram was constructed based on Cox hazard regression analysis evaluating the prognostic significance of serum prostate-specific antigen and pathological factors in the radical prostatectomy specimens. The discriminating ability of the nomogram was assessed by the concordance index (C-index), and the predicted and actual outcomes were compared with a bootstrapped calibration plot. With a mean follow up of 60.0 months, a total of 187 patients (30.9%) experienced biochemical recurrence, with a 5-year non-biochemical recurrence rate of 72.3%. Based on a Cox hazard regression model, a nomogram was constructed to predict non-biochemical recurrence using serum prostate-specific antigen level and pathological features in radical prostatectomy specimens. The concordance index was 0.77, and the calibration plots appeared to be accurate. The postoperative nomogram described here can provide valuable information regarding the need for adjuvant/salvage radiation or hormonal therapy in patients after radical prostatectomy.

  15. Concordance of preclinical and clinical pharmacology and toxicology of therapeutic monoclonal antibodies and fusion proteins: cell surface targets

    PubMed Central

    Bugelski, Peter J; Martin, Pauline L

    2012-01-01

    Monoclonal antibodies (mAbs) and fusion proteins directed towards cell surface targets make an important contribution to the treatment of disease. The purpose of this review was to correlate the clinical and preclinical data on the 15 currently approved mAbs and fusion proteins targeted to the cell surface. The principal sources used to gather data were: the peer reviewed Literature; European Medicines Agency ‘Scientific Discussions’; and the US Food and Drug Administration ‘Pharmacology/Toxicology Reviews’ and package inserts (United States Prescribing Information). Data on the 15 approved biopharmaceuticals were included: abatacept; abciximab; alefacept; alemtuzumab; basiliximab; cetuximab; daclizumab; efalizumab; ipilimumab; muromonab; natalizumab; panitumumab; rituximab; tocilizumab; and trastuzumab. For statistical analysis of concordance, data from these 15 were combined with data on the approved mAbs and fusion proteins directed towards soluble targets. Good concordance with human pharmacodynamics was found for mice receiving surrogates or non-human primates (NHPs) receiving the human pharmaceutical. In contrast, there was poor concordance for human pharmacodynamics in genetically deficient mice and for human adverse effects in all three test systems. No evidence that NHPs have superior predictive value was found. PMID:22168282

  16. Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

    PubMed Central

    Garcia Lopez, Sebastian; Kim, Philip M.

    2014-01-01

    Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

  17. [Low concordance between primary care and hospital clinical information].

    PubMed

    Revilla-López, Concha; Calderón-Larrañaga, Amaia; Enríquez-Martín, Natalia; Prados-Torres, Alexandra

    2016-04-01

    To measure the diagnostic agreement between Primary Care (PC) and hospital information systems, in order to assess the usefulness of health care records for research purposes. Cross-sectional retrospective study integrating PC and hospital diagnostic information for the Aragon population admitted to hospital in 2010. 75.176 patients were analysed. Similarities, differences and the kappa index were calculated for each of the diagnoses recorded in both information systems. The studied diseases included COPD, diabetes, hypertension, cerebrovascular disease, ischaemic heart disease, asthma, epilepsy, and heart failure. Diagnostic concordance was higher in men and between 45 and 64 years. Diabetes was the condition showing the highest concordance (kappa index: 0.75), while asthma had the lowest values (kappa index: 0.34). The low concordance between the diagnostic information recorded in PC and in the hospital setting calls for urgent measures to ensure that healthcare professionals have a comprehensive picture of patient's health problems. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  18. Estrogen and progesterone receptor testing in breast carcinoma: concordance of results between local and reference laboratories in Brazil.

    PubMed

    Wludarski, Sheila Cristina Lordelo; Lopes, Lisandro Ferreira; Duarte, Ivison Xavier; Carvalho, Filomena Marino; Weiss, Lawrence; Bacchi, Carlos Eduardo

    2011-01-01

    Breast cancer accounts for approximately one quarter of all cancers in females. Estrogen and progesterone receptor testing has become an essential part of the clinical evaluation of breast carcinoma patients, and accurate results are critical in identifying patients who may benefit from hormone therapy. The present study had the aim of investigating the concordance of the results from hormone receptor tests between a reference laboratory and local (or community) laboratories in Brazil. Retrospective study at a reference pathology laboratory. The concordance in the results from hormone receptor tests between a reference laboratory and 146 local laboratories in Brazil was compared in relation to 500 invasive breast carcinoma cases, using immunohistochemistry. There was concordance in 89.4% (447/500 cases) and 85.0% (425/500 cases) of the results from estrogen (κ = 0.744, P < 0.001) and progesterone (κ = 0.688, P < 0.001) receptor tests, respectively, between local and reference laboratories. This was similar to findings in other countries. The false negative rates from estrogen and progesterone receptor tests in local laboratories were 8.7% and 14.4%, respectively. The false positive rates from estrogen and progesterone receptor tests in local laboratories were 15.5% and 16.0%, respectively. Technical and result interpretation issues may explain most of the discordances in hormone receptor testing in local laboratories. Validation of estrogen and progesterone receptor tests at local laboratories, with rigorous quality control measures, is strongly recommended in order to avoid erroneous treatment of breast cancer patients.

  19. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

    PubMed

    Wallace, Jason A; Wang, Yuhang; Shi, Chuanyin; Pastoor, Kevin J; Nguyen, Bao-Linh; Xia, Kai; Shen, Jana K

    2011-12-01

    Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy. Copyright © 2011 Wiley-Liss, Inc.

  20. Concordance Between Clinical Practice and Published Evidence: Findings From Virginia Commonwealth University School of Dentistry.

    PubMed

    Chiang, Harmeet K; Best, Al M; Sarrett, David C

    2017-09-01

    To evaluate the concordance between clinical practice and published evidence by dental faculty and graduating students of the Virginia Commonwealth University School of Dentistry. A questionnaire previously developed by the National Dental Practice-Based Research Network with 12 clinical scenarios was administered to VCU faculty and graduating students. Responses were scored as either consistent or inconsistent with published evidence and then analyzed for differences between dental faculty, graduating students, and the national results. There were 43 dental faculty members with at least half-time student contact who responded to the survey. Faculty concordance ranged from 33% to 100%, and general practice faculty had the highest concordance (82%). Eighty-five of the graduating class of 98 responded to the survey, and student concordance ranged from 18% to 92% and averaged 67%. General practice faculty had higher concordance with published evidence than recently graduated dental students. Graduating students and dental faculty demonstrated higher concordance with evidence-based practice than practitioners in the National Dental Practice-Based Research Network. General practice dental faculty demonstrated adequate concordance, but students demonstrated only a medium-level concordance. Practitioners involved in teaching dental students are better able to keep up with evolving evidence and are better able to demonstrate evidence-based practice. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. In vitro versus in vivo concordance: a case study of the replacement of an animal potency test with an immunochemical assay.

    PubMed

    Schofield, T

    2002-01-01

    Early in its development, the potency of Merck's recombinant hepatitis B vaccine, RECOMBIVAX HB, was monitored using an assay performed in mice. A specification was determined to be the lowest potency which induced acceptable response in clinical trials. As a post-licensing commitment, Merck was asked to replace its mouse potency assay with an in vitro procedure for product release in the US market. Early studies with a commercial enzyme immunoassay (EIA) yielded highly variable results. That assay, combined with a sample pretreatment step, proved more dependable and predictive of potency in the mouse assay. Based on measurements made on manufactured materials, combined with experiments contrived to yield a wide range of reactivity in the two assays, concordance was established between the EIA and the mouse potency assay. This concordance was used to calibrate a specification for the in vitro assay that is predictive of a satisfactory response in vivo. Data from clinical trials established a correspondence between human immunogenicity and these potency markers.

  2. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

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

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasetsmore » having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds

  3. Concordance and Transmission of Human Papillomavirus Within Heterosexual Couples Observed Over Short Intervals

    PubMed Central

    Widdice, Lea; Ma, Yifei; Jonte, Janet; Farhat, Sepideh; Breland, David; Shiboski, Stephen; Moscicki, Anna-Barbara

    2013-01-01

    Background. Because many human papillomavirus (HPV) infections are transient, rates of transmission may be miscalculated if the interval between testing spans several months. We examined rates of concordance and transmission in heterosexual couples over short intervals. Methods. Twenty-five adult couples were enrolled and sampled for HPV DNA from the genitals, hand, and mouth 5 times over a 6-week period, including 24 hours after sexual intercourse and after 48 hours of abstinence. Concordance and transmission patterns were described. Results. Concordance between the couple's genital sites ranged from 64% to 95% for at least 1 HPV type. The highest rates of concordance were observed 24 hours after sexual intercourse. A similar peak in concordance was not seen between genital and nongenital anatomic sites. Transmission rates for female genital to male genital ranged from 26.8 to 187.5 per 100 person-months and for male genital to female genital from 14.5 to 100 per 100 person-months. Conclusions. High rates of concordance shortly after intercourse suggest that some DNA detections in the genital area are contaminants from a partner and not established HPV infections. Female-to-male transmission appeared more common than male-to-female transmission. PMID:23319742

  4. Effects of Macroposthonia xenoplax on the growth of Concord grape.

    PubMed

    Santo, G S; Bolander, W J

    1977-07-01

    Concord grape (Vitis labrusca) plants were inoculated with Macroposthonia xenoplax at levels of 100, 1,000, and 10,000 nematodes. After 4 months, plants inoculated with 10,000 M. xenoplax were stunted, and root systems were darker and had fewer feeder roots than those in other treatments. The lower nematode inoculation levels suppressed top growth but did not affect root growth. M. xenoplax reproduced well on Concord grapes.

  5. Diagnostic Concordance Among Pathologists Interpreting Breast Biopsy Specimens

    PubMed Central

    Elmore, Joann G.; Longton, Gary M.; Carney, Patricia A.; Geller, Berta M.; Onega, Tracy; Tosteson, Anna N. A.; Nelson, Heidi D.; Pepe, Margaret S.; Allison, Kimberly H.; Schnitt, Stuart J.; O’Malley, Frances P.; Weaver, Donald L.

    2015-01-01

    IMPORTANCE A breast pathology diagnosis provides the basis for clinical treatment and management decisions; however, its accuracy is inadequately understood. OBJECTIVES To quantify the magnitude of diagnostic disagreement among pathologists compared with a consensus panel reference diagnosis and to evaluate associated patient and pathologist characteristics. DESIGN, SETTING, AND PARTICIPANTS Study of pathologists who interpret breast biopsies in clinical practices in 8 US states. EXPOSURES Participants independently interpreted slides between November 2011 and May 2014 from test sets of 60 breast biopsies (240 total cases, 1 slide per case), including 23 cases of invasive breast cancer, 73 ductal carcinoma in situ (DCIS), 72 with atypical hyperplasia (atypia), and 72 benign cases without atypia. Participants were blinded to the interpretations of other study pathologists and consensus panel members. Among the 3 consensus panel members, unanimous agreement of their independent diagnoses was 75%, and concordance with the consensus-derived reference diagnoses was 90.3%. MAIN OUTCOMES AND MEASURES The proportions of diagnoses overinterpreted and underinterpreted relative to the consensus-derived reference diagnoses were assessed. RESULTS Sixty-five percent of invited, responding pathologists were eligible and consented to participate. Of these, 91% (N = 115) completed the study, providing 6900 individual case diagnoses. Compared with the consensus-derived reference diagnosis, the overall concordance rate of diagnostic interpretations of participating pathologists was 75.3% (95% CI, 73.4%–77.0%; 5194 of 6900 interpretations). Consensus ReferenceDiagnosis Pathologist Interpretation vs Consensus-Derived Reference Diagnosis, % (95% CI) No. ofInterpretations Overall ConcordanceRate OverinterpretationRate UnderinterpretationRate Benign without atypia 2070 87 (85–89) 13 (11–15) Atypia 2070 48 (44–52) 17 (15–21) 35 (31–39) DCIS 2097 84 (82–86) 3 (2–4) 13 (12

  6. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

    PubMed

    Jones, David T; Singh, Tanya; Kosciolek, Tomasz; Tetchner, Stuart

    2015-04-01

    Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues. Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts-around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  7. Estimating the concordance probability in a survival analysis with a discrete number of risk groups.

    PubMed

    Heller, Glenn; Mo, Qianxing

    2016-04-01

    A clinical risk classification system is an important component of a treatment decision algorithm. A measure used to assess the strength of a risk classification system is discrimination, and when the outcome is survival time, the most commonly applied global measure of discrimination is the concordance probability. The concordance probability represents the pairwise probability of lower patient risk given longer survival time. The c-index and the concordance probability estimate have been used to estimate the concordance probability when patient-specific risk scores are continuous. In the current paper, the concordance probability estimate and an inverse probability censoring weighted c-index are modified to account for discrete risk scores. Simulations are generated to assess the finite sample properties of the concordance probability estimate and the weighted c-index. An application of these measures of discriminatory power to a metastatic prostate cancer risk classification system is examined.

  8. Interlaboratory comparison of autoradiographic DNA profiling measurements: precision and concordance.

    PubMed

    Duewer, D L; Lalonde, S A; Aubin, R A; Fourney, R M; Reeder, D J

    1998-05-01

    Knowledge of the expected uncertainty in restriction fragment length polymorphism (RFLP) measurements is required for confident exchange of such data among different laboratories. The total measurement uncertainty among all Technical Working Group for DNA Analysis Methods laboratories has previously been characterized and found to be acceptably small. Casework cell line control measurements provided by six Royal Canadian Mounted Police (RCMP) and 30 U.S. commercial, local, state, and Federal forensic laboratories enable quantitative determination of the within-laboratory precision and among-laboratory concordance components of measurement uncertainty typical of both sets of laboratories. Measurement precision is the same in the two countries for DNA fragments of size 1000 base pairs (bp) to 10,000 bp. However, the measurement concordance among the RCMP laboratories is clearly superior to that within the U.S. forensic community. This result is attributable to the use of a single analytical protocol in all RCMP laboratories. Concordance among U.S. laboratories cannot be improved through simple mathematical adjustments. Community-wide efforts focused on improved concordance may be the most efficient mechanism for further reduction of among-laboratory RFLP measurement uncertainty, should the resources required to fully evaluate potential cross-jurisdictional matches become burdensome as the number of RFLP profiles on record increases.

  9. The impact of non-concordant self-report of substance use in clinical trials research.

    PubMed

    Clark, C Brendan; Zyambo, Cosmas M; Li, Ye; Cropsey, Karen L

    2016-07-01

    Studies comparing self-report substance use data to biochemical verification generally demonstrate high rates of concordance. We argue that these rates are due to the relatively high true negative rate in the general population, and high degree of honestly in treatment seeking individuals. We hypothesized that high risk individuals not seeking treatment would demonstrate low concordance and a high false negative rate of self-reported substance use. A sample of 500 individuals from a smoking cessation clinical trial was assessed over 1 year. Assessments included semi-structured interviews, questionnaires (e.g. Addiction Severity Index, etc.), and urine drug screen assays (UDS). Generalized estimating equations (GEEs) were used to predict false negative reports for various substances across the study and determine the influence of substance use on the primary study outcome of smoking cessation. Participants demonstrated high false negative rates in reporting substances use, and the false negative rates increased as the study progressed. Established predictors of false negatives generalized to the current sample. High concordance and low false negative rates were found in self-report of nicotine use. A small but significant relationship was found in for effect of biochemically verified substance use on smoking cessation. Biochemical verification of substance use is needed in high risk populations involved in studies not directly related to the treatment of substance use, especially in populations with high threat of stigmatization. Testing should continue through the time period of the study for maximal identification of substance use. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.

    PubMed

    Brannon, A Rose; Vakiani, Efsevia; Sylvester, Brooke E; Scott, Sasinya N; McDermott, Gregory; Shah, Ronak H; Kania, Krishan; Viale, Agnes; Oschwald, Dayna M; Vacic, Vladimir; Emde, Anne-Katrin; Cercek, Andrea; Yaeger, Rona; Kemeny, Nancy E; Saltz, Leonard B; Shia, Jinru; D'Angelica, Michael I; Weiser, Martin R; Solit, David B; Berger, Michael F

    2014-08-28

    Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of response to anti-EGFR therapy has become standard practice in the treatment of metastatic colorectal cancer; however, the quantity and type of tissue available for testing is frequently limited. Further, the degree to which the primary tumor is a faithful representation of metastatic disease has been questioned. As next-generation sequencing technology becomes more widely available for clinical use and additional molecularly targeted agents are considered as treatment options in colorectal cancer, it is important to characterize the extent of tumor heterogeneity between primary and metastatic tumors. We performed deep coverage, targeted next-generation sequencing of 230 key cancer-associated genes for 69 matched primary and metastatic tumors and normal tissue. Mutation profiles were 100% concordant for KRAS, NRAS, and BRAF, and were highly concordant for recurrent alterations in colorectal cancer. Additionally, whole genome sequencing of four patient trios did not reveal any additional site-specific targetable alterations. Colorectal cancer primary tumors and metastases exhibit high genomic concordance. As current clinical practices in colorectal cancer revolve around KRAS, NRAS, and BRAF mutation status, diagnostic sequencing of either primary or metastatic tissue as available is acceptable for most patients. Additionally, consistency between targeted sequencing and whole genome sequencing results suggests that targeted sequencing may be a suitable strategy for clinical diagnostic applications.

  11. Quasi-closed phase forward-backward linear prediction analysis of speech for accurate formant detection and estimation.

    PubMed

    Gowda, Dhananjaya; Airaksinen, Manu; Alku, Paavo

    2017-09-01

    Recently, a quasi-closed phase (QCP) analysis of speech signals for accurate glottal inverse filtering was proposed. However, the QCP analysis which belongs to the family of temporally weighted linear prediction (WLP) methods uses the conventional forward type of sample prediction. This may not be the best choice especially in computing WLP models with a hard-limiting weighting function. A sample selective minimization of the prediction error in WLP reduces the effective number of samples available within a given window frame. To counter this problem, a modified quasi-closed phase forward-backward (QCP-FB) analysis is proposed, wherein each sample is predicted based on its past as well as future samples thereby utilizing the available number of samples more effectively. Formant detection and estimation experiments on synthetic vowels generated using a physical modeling approach as well as natural speech utterances show that the proposed QCP-FB method yields statistically significant improvements over the conventional linear prediction and QCP methods.

  12. WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms.

    PubMed

    Chi, Sang-Mun; Nam, Dougu

    2012-04-01

    We present an accurate and fast web server, WegoLoc for predicting subcellular localization of proteins based on sequence similarity and weighted Gene Ontology (GO) information. A term weighting method in the text categorization process is applied to GO terms for a support vector machine classifier. As a result, WegoLoc surpasses the state-of-the-art methods for previously used test datasets. WegoLoc supports three eukaryotic kingdoms (animals, fungi and plants) and provides human-specific analysis, and covers several sets of cellular locations. In addition, WegoLoc provides (i) multiple possible localizations of input protein(s) as well as their corresponding probability scores, (ii) weights of GO terms representing the contribution of each GO term in the prediction, and (iii) a BLAST E-value for the best hit with GO terms. If the similarity score does not meet a given threshold, an amino acid composition-based prediction is applied as a backup method. WegoLoc and User's guide are freely available at the website http://www.btool.org/WegoLoc smchiks@ks.ac.kr; dougnam@unist.ac.kr Supplementary data is available at http://www.btool.org/WegoLoc.

  13. Copula based prediction models: an application to an aortic regurgitation study

    PubMed Central

    Kumar, Pranesh; Shoukri, Mohamed M

    2007-01-01

    Background: An important issue in prediction modeling of multivariate data is the measure of dependence structure. The use of Pearson's correlation as a dependence measure has several pitfalls and hence application of regression prediction models based on this correlation may not be an appropriate methodology. As an alternative, a copula based methodology for prediction modeling and an algorithm to simulate data are proposed. Methods: The method consists of introducing copulas as an alternative to the correlation coefficient commonly used as a measure of dependence. An algorithm based on the marginal distributions of random variables is applied to construct the Archimedean copulas. Monte Carlo simulations are carried out to replicate datasets, estimate prediction model parameters and validate them using Lin's concordance measure. Results: We have carried out a correlation-based regression analysis on data from 20 patients aged 17–82 years on pre-operative and post-operative ejection fractions after surgery and estimated the prediction model: Post-operative ejection fraction = - 0.0658 + 0.8403 (Pre-operative ejection fraction); p = 0.0008; 95% confidence interval of the slope coefficient (0.3998, 1.2808). From the exploratory data analysis, it is noted that both the pre-operative and post-operative ejection fractions measurements have slight departures from symmetry and are skewed to the left. It is also noted that the measurements tend to be widely spread and have shorter tails compared to normal distribution. Therefore predictions made from the correlation-based model corresponding to the pre-operative ejection fraction measurements in the lower range may not be accurate. Further it is found that the best approximated marginal distributions of pre-operative and post-operative ejection fractions (using q-q plots) are gamma distributions. The copula based prediction model is estimated as: Post -operative ejection fraction = - 0.0933 + 0.8907 × (Pre

  14. Sex-specific lean body mass predictive equations are accurate in the obese paediatric population

    PubMed Central

    Jackson, Lanier B.; Henshaw, Melissa H.; Carter, Janet; Chowdhury, Shahryar M.

    2015-01-01

    Background The clinical assessment of lean body mass (LBM) is challenging in obese children. A sex-specific predictive equation for LBM derived from anthropometric data was recently validated in children. Aim The purpose of this study was to independently validate these predictive equations in the obese paediatric population. Subjects and methods Obese subjects aged 4–21 were analysed retrospectively. Predicted LBM (LBMp) was calculated using equations previously developed in children. Measured LBM (LBMm) was derived from dual-energy x-ray absorptiometry. Agreement was expressed as [(LBMm-LBMp)/LBMm] with 95% limits of agreement. Results Of 310 enrolled patients, 195 (63%) were females. The mean age was 11.8 ± 3.4 years and mean BMI Z-score was 2.3 ± 0.4. The average difference between LBMm and LBMp was −0.6% (−17.0%, 15.8%). Pearson’s correlation revealed a strong linear relationship between LBMm and LBMp (r=0.97, p<0.01). Conclusion This study validates the use of these clinically-derived sex-specific LBM predictive equations in the obese paediatric population. Future studies should use these equations to improve the ability to accurately classify LBM in obese children. PMID:26287383

  15. Accurate prediction of cation-π interaction energy using substituent effects.

    PubMed

    Sayyed, Fareed Bhasha; Suresh, Cherumuttathu H

    2012-06-14

    (M(+))' and ΔV(min). All the Φ-X···M(+) systems showed good agreement between the calculated and predicted E(M(+))() values, suggesting that the ΔV(min) approach to substituent effect is accurate and useful for predicting the interactive behavior of substituted π-systems with cations.

  16. RadNet Air Data From Concord, NH

    EPA Pesticide Factsheets

    This page presents radiation air monitoring and air filter analysis data for Concord, NH from EPA's RadNet system. RadNet is a nationwide network of monitoring stations that measure radiation in air, drinking water and precipitation.

  17. Surgical site infections among high-risk patients in clean-contaminated head and neck reconstructive surgery: concordance with preoperative oral flora.

    PubMed

    Yang, Ching-Hsiang; Chew, Khong-Yik; Solomkin, Joseph S; Lin, Pao-Yuan; Chiang, Yuan-Cheng; Kuo, Yur-Ren

    2013-12-01

    Salivary contamination of surgical wounds in clean-contaminated head and neck surgery with free flap reconstruction remains a major cause of infection and leads to significant morbidity. This study investigates the correlation between intraoral flora and surgical site infections (SSIs) among high-risk head and neck cancer patients undergoing resection and free flap reconstruction. One hundred twenty-nine patients were identified as being at high risk for infective complications based on cancer stage, tumor size, comorbid factors, and extent of reconstruction. All patients had intraoral swab cultures before surgery. Patients with culture-confirmed SSI after surgery were chosen for analysis, using the κ index and its 95% confidence interval for concordance analysis. All patients received clindamycin and gentamicin for antibiotic prophylaxis for 5 days. Antibiotic susceptibility testing of all isolates was obtained and analyzed. Thirty-seven patients experienced SSI, or an infection rate of 28.3%, occurring at a mean of 9.3 postoperative days. The overall concordance between oral flora and SSI was fair to moderate (κ index of 0.25), but detailed analysis shows a higher concordance for known and opportunistic pathogens, such as Pseudomonas aeruginosa and Enterococcus faecalis, compared to typical oral commensals. Antibiotic susceptibility tests show rapid and significant increases in resistance to clindamycin, indicating a need for a more effective alternative. Predicting pathogens in SSI using preoperative oral swabs did not demonstrate a good concordance in general for patients undergoing clean-contaminated head and neck surgery, although concordance for certain pathogenic species seem to be higher than for typical intraoral commensals. The rapid development of resistance to clindamycin precludes its use as a prophylactic agent.

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

    PubMed Central

    Hardison, Ross C.

    2017-01-01

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

  19. Is physician-patient concordance associated with greater trust for women of low socioeconomic status?

    PubMed

    Scheid, Teresa L; Smith, Galen H

    2017-07-01

    The authors examined the association between physician-patient concordance and patient trust for low socio-economic status women who were enrolled in Medicaid case management. The data were collected from October 2006 through March 2007 from a stratified random sample of 2,815 adult beneficiaries enrolled in North Carolina Medicaid's primary care case management delivery system. We limited our analyses to women enrolled in primary care, hence controlling for gender and social class as well as access to care. We were also able to control for the availability of minority providers. The findings revealed that the enrollee's race, education, and experiences seeking help with their health providers were significantly related to patient's trust of their physicians. Neither race concordance nor gender concordance improved trust. This may be because relatively few minority providers were included in the sample. These results extend research on physician-patient concordance by examining the relationship of both racial and gender concordance with patient trust while controlling for access and social class. Research on physician-patient concordance needs to account for multiple measures of social status, as well as differences in culture and communication styles between physicians and their patients.

  20. Accurate predictions of iron redox state in silicate glasses: A multivariate approach using X-ray absorption spectroscopy

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

    Dyar, M. Darby; McCanta, Molly; Breves, Elly

    2016-03-01

    Pre-edge features in the K absorption edge of X-ray absorption spectra are commonly used to predict Fe3+ valence state in silicate glasses. However, this study shows that using the entire spectral region from the pre-edge into the extended X-ray absorption fine-structure region provides more accurate results when combined with multivariate analysis techniques. The least absolute shrinkage and selection operator (lasso) regression technique yields %Fe3+ values that are accurate to ±3.6% absolute when the full spectral region is employed. This method can be used across a broad range of glass compositions, is easily automated, and is demonstrated to yield accurate resultsmore » from different synchrotrons. It will enable future studies involving X-ray mapping of redox gradients on standard thin sections at 1 × 1 μm pixel sizes.« less

  1. Accurate predictions of iron redox state in silicate glasses: A multivariate approach using X-ray absorption spectroscopy

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

    Dyar, M. Darby; McCanta, Molly; Breves, Elly

    2016-03-01

    Pre-edge features in the K absorption edge of X-ray absorption spectra are commonly used to predict Fe 3+ valence state in silicate glasses. However, this study shows that using the entire spectral region from the pre-edge into the extended X-ray absorption fine-structure region provides more accurate results when combined with multivariate analysis techniques. The least absolute shrinkage and selection operator (lasso) regression technique yields %Fe 3+ values that are accurate to ±3.6% absolute when the full spectral region is employed. This method can be used across a broad range of glass compositions, is easily automated, and is demonstrated to yieldmore » accurate results from different synchrotrons. It will enable future studies involving X-ray mapping of redox gradients on standard thin sections at 1 × 1 μm pixel sizes.« less

  2. Accuracy of a nomogram for prediction of lymph-node metastasis detected with conventional histopathology and ultrastaging in endometrial cancer

    PubMed Central

    Koskas, M; Chereau, E; Ballester, M; Dubernard, G; Lécuru, F; Heitz, D; Mathevet, P; Marret, H; Querleu, D; Golfier, F; Leblanc, E; Luton, D; Rouzier, R; Daraï, E

    2013-01-01

    Background: We developed a nomogram based on five clinical and pathological characteristics to predict lymph-node (LN) metastasis with a high concordance probability in endometrial cancer. Sentinel LN (SLN) biopsy has been suggested as a compromise between systematic lymphadenectomy and no dissection in patients with low-risk endometrial cancer. Methods: Patients with stage I–II endometrial cancer had pelvic SLN and systematic pelvic-node dissection. All LNs were histopathologically examined, and the SLNs were examined by immunohistochemistry. We compared the accuracy of the nomogram at predicting LN detected with conventional histopathology (macrometastasis) and ultrastaging procedure using SLN (micrometastasis). Results: Thirty-eight of the 187 patients (20%) had pelvic LN metastases, 20 had macrometastases and 18 had micrometastases. For the prediction of macrometastases, the nomogram showed good discrimination, with an area under the receiver operating characteristic curve (AUC) of 0.76, and was well calibrated (average error =2.1%). For the prediction of micro- and macrometastases, the nomogram showed poorer discrimination, with an AUC of 0.67, and was less well calibrated (average error =10.9%). Conclusion: Our nomogram is accurate at predicting LN macrometastases but less accurate at predicting micrometastases. Our results suggest that micrometastases are an ‘intermediate state' between disease-free LN and macrometastasis. PMID:23481184

  3. [Concordance and usefulness of a stratification system for clinical decision making].

    PubMed

    González González, Ana Isabel; Miquel Gómez, Ana María; Rodríguez Morales, David; Hernández Pascual, Montserrat; Sánchez Perruca, Luis; Mediavilla Herrera, Inmaculada

    2017-04-01

    1) To analyse concordance between the level of risk classification using the Adjusted Groups Morbidity (GMA) tool and the assigned level of intervention by general practitioners (GP). 2) To study the usefulness of the GMA tool as an aid in electronic medical records (EMR) for decision making. Cross-sectional observational study of concordance. Primary Care. Madrid Health Service. Twenty eight GPs. A sample of 840 patients assigned to participating GPs was selected by disproportionate stratified random sampling (0.65 kappa, 0.125 precision, 5% positive rate, 95% confidence level). Weighted Cohen Kappa index for the degree of concordance between the GMA tool and the GPs. The usefulness of the tool was assessed using an ad hoc developed questionnaire. Kappa weighted index obtained was 0.60 (95%CI: 0.55-0.65). In 3% of cases the disagreement was maximum. The GPs found that the grouping tool had been useful in 76% of cases. Moderate strength/good concordance; incorporating a grouping tool in the EMR helps as a reminder for taking more proactive/integrated decisions based on social and health needs of people with chronic diseases. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  4. Degree of concordance with DASH diet guidelines and incidence of hypertension and fatal cardiovascular disease.

    PubMed

    Folsom, Aaron R; Parker, Emily D; Harnack, Lisa J

    2007-03-01

    Guidelines to prevent and treat hypertension advocate the Dietary Approaches to Stop Hypertension (DASH) diet. We studied whether a greater concordance with the DASH diet is associated with reduced incidence of hypertension (self-reported) and mortality from cardiovascular disease in 20,993 women initially aged 55 to 69 years. We created a DASH diet concordance score using food frequency data in 1986 and followed the women for events through 2002. No woman had perfect concordance with the DASH diet. Adjusted for age and energy intake, incidence of hypertension was inversely associated with the degree of concordance with the DASH diet, with hazard ratios across quintiles of 1.0, 0.91, 0.95, 0.99, and 0.87 (P trend = .02). There also were inverse, but not monotonic, associations between better DASH diet concordance and mortality from coronary heart disease, stroke, and all cardiovascular disease (CVD). However, after adjustment for other risk factors, there was little evidence that any end point was associated with the DASH diet score. Our results suggest that greater concordance with DASH guidelines did not have an independent long-term association with hypertension or cardiovascular mortality in this cohort. This implies that very high concordance, as achieved in the DASH trials, may be necessary to achieve any benefits of the DASH diet.

  5. Accurate indel prediction using paired-end short reads

    PubMed Central

    2013-01-01

    Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/. PMID:23442375

  6. Patient-centered communication, ratings of care, and concordance of patient and physician race.

    PubMed

    Cooper, Lisa A; Roter, Debra L; Johnson, Rachel L; Ford, Daniel E; Steinwachs, Donald M; Powe, Neil R

    2003-12-02

    African-American patients who visit physicians of the same race rate their medical visits as more satisfying and participatory than do those who see physicians of other races. Little research has investigated the communication process in race-concordant and race-discordant medical visits. To compare patient-physician communication in race-concordant and race-discordant visits and examine whether communication behaviors explain differences in patient ratings of satisfaction and participatory decision making. Cohort study with follow-up using previsit and postvisit surveys and audiotape analysis. 16 urban primary care practices. 252 adults (142 African-American patients and 110 white patients) receiving care from 31 physicians (of whom 18 were African-American and 13 were white). Audiotape measures of patient-centeredness, patient ratings of physicians' participatory decision-making styles, and overall satisfaction. Race-concordant visits were longer (2.15 minutes [95% CI, 0.60 to 3.71]) and had higher ratings of patient positive affect (0.55 point, [95% CI, 0.04 to 1.05]) compared with race-discordant visits. Patients in race-concordant visits were more satisfied and rated their physicians as more participatory (8.42 points [95% CI, 3.23 to 13.60]). Audiotape measures of patient-centered communication behaviors did not explain differences in participatory decision making or satisfaction between race-concordant and race-discordant visits. Race-concordant visits are longer and characterized by more patient positive affect. Previous studies link similar communication findings to continuity of care. The association between race concordance and higher patient ratings of care is independent of patient-centered communication, suggesting that other factors, such as patient and physician attitudes, may mediate the relationship. Until more evidence is available regarding the mechanisms of this relationship and the effectiveness of intercultural communication skills programs

  7. 14 CFR 36.301 - Noise limits: Concorde.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Noise limits: Concorde. 36.301 Section 36.301 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION AIRCRAFT NOISE STANDARDS: AIRCRAFT TYPE AND AIRWORTHINESS CERTIFICATION Noise Limits for Supersonic Transport Category...

  8. 14 CFR 36.301 - Noise limits: Concorde.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Noise limits: Concorde. 36.301 Section 36.301 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION AIRCRAFT NOISE STANDARDS: AIRCRAFT TYPE AND AIRWORTHINESS CERTIFICATION Noise Limits for Supersonic Transport Category...

  9. Transitions from hospital to community care: the role of patient-provider language concordance.

    PubMed

    Rayan, Nosaiba; Admi, Hanna; Shadmi, Efrat

    2014-01-01

    Cultural and language discordance between patients and providers constitutes a significant challenge to provision of quality healthcare. This study aims to evaluate minority patients' discharge from hospital to community care, specifically examining the relationship between patient-provider language concordance and the quality of transitional care. This was a multi-method prospective study of care transitions of 92 patients: native Hebrew, Russian or Arabic speakers, with a pre-discharge questionnaire and structured observations examining discharge preparation from a large Israeli teaching hospital. Two weeks post-discharge patients were surveyed by phone, on the transition from hospital to community care (the Care Transition Measure (CTM-15, 0-100 scale)) and on the primary-care post-discharge visit. Overall, ratings on the CTM indicated fair quality of the transition process (scores of 51.8 to 58.8). Patient-provider language concordance was present in 49% of minority patients' discharge briefings. Language concordance was associated with higher CTM scores among minority groups (64.1 in language-concordant versus 49.8 in non-language-concordant discharges, P <0.001). Other aspects significantly associated with CTM scores: extent of discharge explanations (P <0.05), quality of discharge briefing (P <0.001), and post-discharge explanations by the primary care physician (P <0.01). Language-concordant care, coupled with extensive discharge briefings and post-discharge explanations for ongoing care, are important contributors to the quality of care transitions of ethnic minority patients.

  10. Transitions from hospital to community care: the role of patient–provider language concordance

    PubMed Central

    2014-01-01

    Background Cultural and language discordance between patients and providers constitutes a significant challenge to provision of quality healthcare. This study aims to evaluate minority patients’ discharge from hospital to community care, specifically examining the relationship between patient–provider language concordance and the quality of transitional care. Methods This was a multi-method prospective study of care transitions of 92 patients: native Hebrew, Russian or Arabic speakers, with a pre-discharge questionnaire and structured observations examining discharge preparation from a large Israeli teaching hospital. Two weeks post-discharge patients were surveyed by phone, on the transition from hospital to community care (the Care Transition Measure (CTM-15, 0–100 scale)) and on the primary-care post-discharge visit. Results Overall, ratings on the CTM indicated fair quality of the transition process (scores of 51.8 to 58.8). Patient–provider language concordance was present in 49% of minority patients’ discharge briefings. Language concordance was associated with higher CTM scores among minority groups (64.1 in language-concordant versus 49.8 in non-language-concordant discharges, P <0.001). Other aspects significantly associated with CTM scores: extent of discharge explanations (P <0.05), quality of discharge briefing (P <0.001), and post-discharge explanations by the primary care physician (P <0.01). Conclusion Language-concordant care, coupled with extensive discharge briefings and post-discharge explanations for ongoing care, are important contributors to the quality of care transitions of ethnic minority patients. PMID:25075273

  11. Accurate and robust genomic prediction of celiac disease using statistical learning.

    PubMed

    Abraham, Gad; Tye-Din, Jason A; Bhalala, Oneil G; Kowalczyk, Adam; Zobel, Justin; Inouye, Michael

    2014-02-01

    Practical application of genomic-based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-mediated illness, is strongly genetically determined and requires specific HLA haplotypes. HLA testing can exclude diagnosis but has low specificity, providing little information suitable for clinical risk stratification. Using six European cohorts, we provide a proof-of-concept that statistical learning approaches which simultaneously model all SNPs can generate robust and highly accurate predictive models of CD based on genome-wide SNP profiles. The high predictive capacity replicated both in cross-validation within each cohort (AUC of 0.87-0.89) and in independent replication across cohorts (AUC of 0.86-0.9), despite differences in ethnicity. The models explained 30-35% of disease variance and up to ∼43% of heritability. The GRS's utility was assessed in different clinically relevant settings. Comparable to HLA typing, the GRS can be used to identify individuals without CD with ≥99.6% negative predictive value however, unlike HLA typing, fine-scale stratification of individuals into categories of higher-risk for CD can identify those that would benefit from more invasive and costly definitive testing. The GRS is flexible and its performance can be adapted to the clinical situation by adjusting the threshold cut-off. Despite explaining a minority of disease heritability, our findings indicate a genomic risk score provides clinically relevant information to improve upon current diagnostic pathways for CD and support further studies evaluating the clinical utility of this approach in CD and other complex diseases.

  12. Concorde noise-induced building vibrations, Sully Plantation - Report no. 2, Chantilly, Virginia

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Noise-induced building vibrations associated with Concorde operations were studied. The approach is to record the levels of induced vibrations and associated indoor/outdoor noise levels in selected homes, historic and other buildings near Dulles International Airport. Representative data are presented which were recorded at Sully Plantation, Chantilly, Virginia during the periods of May 20 through May 28, 1976, and June 14 through June 17, 1976. Recorded data provide relationships between the vibration levels of windows, walls, floors, and the noise associated with Concorde operations, other aircraft, and nonaircraft events. The results presented are drawn from the combined May-June data base which is considerably larger than the May data base covered. The levels of window, wall and floor vibratory response resulting from Concorde operations are higher than the vibratory levels associated with conventional aircraft. Furthermore, the vibratory responses of the windows are considerably higher than those of the walls and floors. The window response is higher for aircraft than recorded nonaircraft events and exhibits a linear response relationship with the overall sound pressure level. For a given sound pressure level, the Concorde may cause more vibration than a conventional aircraft due to spectral or other differences. However, the responses associated with Concorde appear to be much more dependent upon sound pressure level than spectral or other characteristics of the noise.

  13. A concordance-based study to assess doctors’ and nurses’ mental models in Internal Medicine

    PubMed Central

    Chan, K. C. Gary; Muller-Juge, Virginie; Cullati, Stéphane; Hudelson, Patricia; Maître, Fabienne; Vu, Nu V.; Savoldelli, Georges L.; Nendaz, Mathieu R.

    2017-01-01

    Interprofessional collaboration between doctors and nurses is based on team mental models, in particular for each professional’s roles. Our objective was to identify factors influencing concordance on the expectations of doctors’ and nurses’ roles and responsibilities in an Internal Medicine ward. Using a dataset of 196 doctor-nurse pairs (14x14 = 196), we analyzed choices and prioritized management actions of 14 doctors and 14 nurses in six clinical nurse role scenarios, and in five doctor role scenarios (6 options per scenario). In logistic regression models with a non-nested correlation structure, we evaluated concordance among doctors and nurses, and adjusted for potential confounders (including prior experience in Internal Medicine, acuteness of case and gender). Concordance was associated with number of female professionals (adjusted OR 1.32, 95% CI 1.02 to 1.73), for acute situations (adjusted OR 2.02, 95% CI 1.13 to 3.62), and in doctor role scenarios (adjusted OR 2.19, 95% CI 1.32 to 3.65). Prior experience and country of training were not significant predictors of concordance. In conclusion, our concordance-based approach helped us identify areas of lower concordance in expected doctor-nurse roles and responsibilities, particularly in non-acute situations, which can be targeted by future interprofessional, educational interventions. PMID:28792524

  14. 76 FR 59167 - Siemens Medical Solutions USA, Inc., Oncology Care Systems Division, Concord, CA; Siemens Medical...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-23

    ... Medical Solutions USA, Inc., Oncology Care Systems Division, Concord, CA; Siemens Medical Solutions USA... Solutions USA, Inc. (Siemens), Oncology Care Systems Division, Concord, California (subject firm). The...., Oncology Care Systems Division, Concord, California (TA-W-73,158) and Siemens Medical Solutions USA, Inc...

  15. Concordant patterns of brain structure in mothers with recurrent depression and their never-depressed daughters

    PubMed Central

    Foland-Ross, Lara C.; Behzadian, Negin; LeMoult, Joelle; Gotlib, Ian H.

    2016-01-01

    Background A growing body of research has demonstrated that having a mother with a history of Major Depressive Disorder (MDD) is one of the strongest predictors of depression in adolescent offspring. Few studies, however, have assessed neural markers of this increased risk for depression, or examined whether risk-related anomalies in adolescents at maternal risk for depression are related to neural abnormalities in their depressed mothers. We addressed these questions by examining concordance in brain structure in two groups of participants: mothers with a history of depression and their never-depressed daughters, and never-depressed mothers and their never-depressed daughters. Method We scanned mothers with (remitted; RMD) and without (control; CTL) a history of recurrent episodes of depression and their never-depressed daughters, computed cortical gray matter thickness, and tested whether mothers’ thickness predicted daughters’ thickness. Results Both RMD mothers and their high-risk daughters exhibited focal areas of thinner cortical gray matter compared with their CTL / low-risk counterparts. Importantly, the extent of thickness anomalies in RMD mothers predicted analogous abnormalities in their daughters; this pattern was not present in CTL / low-risk dyads. Conclusions We identified neuroanatomical risk factors that may underlie the intergenerational transmission of risk for MDD. Our findings suggest that there is concordance in brain structure in dyads that is affected by maternal depression, and that the location, direction, and extent of neural anomalies in high-risk offspring mirror those of their recurrent depressed mothers. PMID:27198667

  16. Concordant Patterns of Brain Structure in Mothers with Recurrent Depression and Their Never-Depressed Daughters.

    PubMed

    Foland-Ross, Lara C; Behzadian, Negin; LeMoult, Joelle; Gotlib, Ian H

    2016-01-01

    A growing body of research has demonstrated that having a mother with a history of major depressive disorder (MDD) is one of the strongest predictors of depression in adolescent offspring. Few studies, however, have assessed neural markers of this increased risk for depression, or examined whether risk-related anomalies in adolescents at maternal risk for depression are related to neural abnormalities in their depressed mothers. We addressed these questions by examining concordance in brain structure in two groups of participants: mothers with a history of depression and their never-depressed daughters, and never-depressed mothers and their never-depressed daughters. We scanned mothers with (remitted; RMD) and without (control; CTL) a history of recurrent episodes of depression and their never-depressed daughters, computed cortical gray matter thickness, and tested whether mothers' thickness predicted daughters' thickness. Both RMD mothers and their high-risk daughters exhibited focal areas of thinner cortical gray matter compared with their CTL/low-risk counterparts. Importantly, the extent of thickness anomalies in RMD mothers predicted analogous abnormalities in their daughters; this pattern was not present in CTL/low-risk dyads. We identified neuroanatomical risk factors that may underlie the intergenerational transmission of risk for MDD. Our findings suggest that there is concordance in brain structure in dyads that is affected by maternal depression, and that the location, direction, and extent of neural anomalies in high-risk offspring mirror those of their recurrent depressed mothers. © 2016 S. Karger AG, Basel.

  17. Concordance between partners in desired waiting time to birth for newlyweds in India

    PubMed Central

    Singh, Abhishek; Becker, Stan

    2014-01-01

    Examining waiting time to birth among newlywed couples is likely to provide insights into the desire for spacing births among newlywed husbands and wives. Data from the Indian National Family Health Survey of 2005-06 is used to examine the desired waiting time (DWT) to birth among newlywed couples. The dependent variable is spousal concordance on desired times. Overall 65 % of couples have concordant DWTs. Among discordant couples, wives were more likely to want to wait longer than their husbands. Couples from richer wealth quintiles were more likely than couples from poorest quintile to have a concordant DWTs. Muslims were less likely than Hindus to have concordant desires. There is a need for spacing methods among newlyweds. This may have implications for the Indian Family Planning Programme which to date has largely focused on sterilization. Programmes need to include newlywed husbands to promote use of spacing methods. PMID:21933466

  18. CDX2 expression is concordant between primary colorectal cancer lesions and corresponding liver metastases independent of chemotherapy: a single-center retrospective study in Japan.

    PubMed

    Shigematsu, Yasuyuki; Inamura, Kentaro; Mise, Yoshihiro; Saiura, Akio; Rehnberg, Emil; Yamamoto, Noriko; Ishikawa, Yuichi; Takahashi, Shunji; Kanda, Hiroaki

    2018-03-30

    Loss of caudal-type homeobox transcription factor 2 (CDX2) expression in colorectal cancers (CRCs) has recently been proposed as a promising predictive biomarker for not only prognosis but also response to chemotherapy. However, the relationship between alterations in CDX2 expression during cancer progression and response to chemotherapy remains unclear. We herein aimed to determine the concordance of CDX2 expression between primary CRCs and corresponding liver metastases, in association with chemotherapy. Primary CRCs exhibited heterogeneous CDX2 expression. Seven of the 144 CRCs in the cohort (4.9%, 95% confidential interval, 2.0%-9.8%) were CDX2-negative. The concordance rate of the CDX2 expression status in patients who did not receive chemotherapy was 100% ( P = 0.041), whereas the concordance rate among patients who received chemotherapy only after primary resection was 96.3% ( P = 0.005). Moreover, the concordance rate in patients who received chemotherapy before both primary resection and liver metastasectomy was 100% ( P < 0.001). CDX2 expression status was highly concordant between primary CRCs and corresponding liver metastases, independent of chemotherapy, suggesting that the CDX2 expression status in CRCs was not affected by metastasis or chemotherapy. A total of 144 consecutive patients with CRC who were treated at a single center in Japan between 2006 and 2014 were included. Formalin-fixed paraffin-embedded whole sections of surgically resected primary CRCs and corresponding liver metastases were assessed for CDX2 expression by immunohistochemistry.

  19. Patient-clinician ethnic concordance and communication in mental health intake visits.

    PubMed

    Alegría, Margarita; Roter, Debra L; Valentine, Anne; Chen, Chih-nan; Li, Xinliang; Lin, Julia; Rosen, Daniel; Lapatin, Sheri; Normand, Sharon-Lise; Larson, Susan; Shrout, Patrick E

    2013-11-01

    This study examines how communication patterns vary across racial and ethnic patient-clinician dyads in mental health intake sessions and its relation to continuance in treatment, defined as attending the next scheduled appointment. Observational study of communication patterns among ethnically/racially concordant and discordant patient-clinician dyads. Primary analysis included 93 patients with 38 clinicians in race/ethnic concordant and discordant dyads. Communication was coded using the Roter Interaction Analysis System (RIAS) and the Working Alliance Inventory Observer (WAI-O) bond scale; continuance in care was derived from chart reviews. Latino concordant dyad patients were more verbally dominant (p<.05), engaged in more patient-centered communication (p<.05) and scored higher on the (WAI-O) bond scale (all p<.05) than other groups. Latino patients had higher continuance rates than other patients in models that adjusted for non-communication variables. When communication, global affect, and therapeutic process variables were adjusted for, differences were reversed and white dyad patients had higher continuance in care rates than other dyad patients. Communication patterns seem to explain the role of ethnic concordance for continuance in care. Improve intercultural communication in cross cultural encounters appears significant for retaining minorities in care. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  20. Concordance Between Administrator and Clinician Ratings of Organizational Culture and Climate.

    PubMed

    Beidas, Rinad S; Williams, Nathaniel J; Green, Philip D; Aarons, Gregory A; Becker-Haimes, Emily M; Evans, Arthur C; Rubin, Ronnie; Adams, Danielle R; Marcus, Steven C

    2018-01-01

    Organizational culture and climate are important determinants of behavioral health service delivery for youth. The Organizational Social Context measure is a well validated assessment of organizational culture and climate that has been developed and extensively used in public sector behavioral health service settings. The degree of concordance between administrators and clinicians in their reports of organizational culture and climate may have implications for research design, inferences, and organizational intervention. However, the extent to which administrators' and clinicians' reports demonstrate concordance is just beginning to garner attention in public behavioral health settings in the United States. We investigated the concordance between 73 administrators (i.e., supervisors, clinical directors, and executive directors) and 247 clinicians in 28 child-serving programs in a public behavioral health system. Findings suggest that administrators, compared to clinicians, reported more positive cultures and climates. Organizational size moderated this relationship such that administrators in small programs (<466 youth clients served annually) provided more congruent reports of culture and climate in contrast to administrators in large programs (≥466 youth clients served annually) who reported more positive cultures and climates than clinicians. We propose a research agenda that examines the effect of concordance between administrators and clinicians on organizational outcomes in public behavioral health service settings.

  1. Patient-Clinician Ethnic Concordance and Communication in Mental Health Intake Visits

    PubMed Central

    Alegría, Margarita; Roter, Debra L.; Valentine, Anne; Chen, Chih-nan; Li, Xinliang; Lin, Julia; Rosen, Daniel; Lapatin, Sheri; Normand, Sharon-Lise; Larson, Susan; Shrout, Patrick E.

    2013-01-01

    Objective This study examines how communication patterns vary across racial and ethnic patient-clinician dyads in mental health intake sessions and its relation to continuance in treatment, defined as attending the next scheduled appointment. Methods Observational study of communication patterns among ethnically/racially concordant and discordant patient-clinician dyads. Primary analysis included 93 patients with 38 clinicians in race/ethnic concordant and discordant dyads. Communication was coded using the Roter Interaction Analysis System (RIAS) and the Working Alliance Inventory Observer (WAI-O) bond scale; continuance in care was derived from chart reviews. Results Latino concordant dyad patients were more verbally dominant (p<.05), engaged in more patient-centered communication (p<.05) and scored higher on the (WAI-O) bond scale (all p<.05) than other groups. Latino patients had higher continuance rates than other patients in models that adjusted for non-communication variables. When communication, global affect, and therapeutic process variables were adjusted for, differences were reversed and white dyad patients had higher continuance in care rates than other dyad patients. Conclusion Communication patterns seem to explain the role of ethnic concordance for continuance in care. Practice Implications Improve intercultural communication in cross cultural encounters appears significant for retaining minorities in care. PMID:23896127

  2. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  3. An Interpretable Machine Learning Model for Accurate Prediction of Sepsis in the ICU.

    PubMed

    Nemati, Shamim; Holder, Andre; Razmi, Fereshteh; Stanley, Matthew D; Clifford, Gari D; Buchman, Timothy G

    2018-04-01

    Sepsis is among the leading causes of morbidity, mortality, and cost overruns in critically ill patients. Early intervention with antibiotics improves survival in septic patients. However, no clinically validated system exists for real-time prediction of sepsis onset. We aimed to develop and validate an Artificial Intelligence Sepsis Expert algorithm for early prediction of sepsis. Observational cohort study. Academic medical center from January 2013 to December 2015. Over 31,000 admissions to the ICUs at two Emory University hospitals (development cohort), in addition to over 52,000 ICU patients from the publicly available Medical Information Mart for Intensive Care-III ICU database (validation cohort). Patients who met the Third International Consensus Definitions for Sepsis (Sepsis-3) prior to or within 4 hours of their ICU admission were excluded, resulting in roughly 27,000 and 42,000 patients within our development and validation cohorts, respectively. None. High-resolution vital signs time series and electronic medical record data were extracted. A set of 65 features (variables) were calculated on hourly basis and passed to the Artificial Intelligence Sepsis Expert algorithm to predict onset of sepsis in the proceeding T hours (where T = 12, 8, 6, or 4). Artificial Intelligence Sepsis Expert was used to predict onset of sepsis in the proceeding T hours and to produce a list of the most significant contributing factors. For the 12-, 8-, 6-, and 4-hour ahead prediction of sepsis, Artificial Intelligence Sepsis Expert achieved area under the receiver operating characteristic in the range of 0.83-0.85. Performance of the Artificial Intelligence Sepsis Expert on the development and validation cohorts was indistinguishable. Using data available in the ICU in real-time, Artificial Intelligence Sepsis Expert can accurately predict the onset of sepsis in an ICU patient 4-12 hours prior to clinical recognition. A prospective study is necessary to determine the

  4. Concordance of parent proxy report and child self-report of posttraumatic stress in children with cancer and healthy children: influence of parental posttraumatic stress.

    PubMed

    Clawson, Ashley H; Jurbergs, Niki; Lindwall, Jennifer; Phipps, Sean

    2013-11-01

    This study examined the relationships between parental posttraumatic stress symptoms (PTSS), child PTSS, and parent-child concordance for child PTSS. Participants were children with cancer (n = 199), and healthy children (n = 108) and their parents. Children self-reported on PTSS and parents completed measures of child and parent PTSS. In the cancer group, child and parent reports of child PTSS were significantly correlated with no mean differences between reporters. In contrast, correlations were non-significant in the control group, and parents reported significantly lower levels of child PTSS than children. Increased parental PTSS was associated with better concordance in the cancer group but not in the control group. In fact, in the cancer group, parent-child concordance was strongest at the highest level of parental PTSS. Parents of children with cancer were found to be accurate reporters of their children's distress, even with high levels of reported personal distress. In contrast, parents of healthy children appear primarily influenced by personal distress when reporting child PTSS. Although multiple informant assessments are always desirable, it appears that utilization of a single informant may be reasonable in the cancer setting when access to informants is limited. Copyright © 2013 John Wiley & Sons, Ltd.

  5. Development and Validation of a Multidisciplinary Tool for Accurate and Efficient Rotorcraft Noise Prediction (MUTE)

    NASA Technical Reports Server (NTRS)

    Liu, Yi; Anusonti-Inthra, Phuriwat; Diskin, Boris

    2011-01-01

    A physics-based, systematically coupled, multidisciplinary prediction tool (MUTE) for rotorcraft noise was developed and validated with a wide range of flight configurations and conditions. MUTE is an aggregation of multidisciplinary computational tools that accurately and efficiently model the physics of the source of rotorcraft noise, and predict the noise at far-field observer locations. It uses systematic coupling approaches among multiple disciplines including Computational Fluid Dynamics (CFD), Computational Structural Dynamics (CSD), and high fidelity acoustics. Within MUTE, advanced high-order CFD tools are used around the rotor blade to predict the transonic flow (shock wave) effects, which generate the high-speed impulsive noise. Predictions of the blade-vortex interaction noise in low speed flight are also improved by using the Particle Vortex Transport Method (PVTM), which preserves the wake flow details required for blade/wake and fuselage/wake interactions. The accuracy of the source noise prediction is further improved by utilizing a coupling approach between CFD and CSD, so that the effects of key structural dynamics, elastic blade deformations, and trim solutions are correctly represented in the analysis. The blade loading information and/or the flow field parameters around the rotor blade predicted by the CFD/CSD coupling approach are used to predict the acoustic signatures at far-field observer locations with a high-fidelity noise propagation code (WOPWOP3). The predicted results from the MUTE tool for rotor blade aerodynamic loading and far-field acoustic signatures are compared and validated with a variation of experimental data sets, such as UH60-A data, DNW test data and HART II test data.

  6. Concordance of Parent- and Child-Reported Physical Abuse Following Child Protective Services Investigation.

    PubMed

    Kobulsky, Julia M; Kepple, Nancy Jo; Holmes, Megan R; Hussey, David L

    2017-02-01

    Knowledge about the concordance of parent- and child-reported child physical abuse is scarce, leaving researchers and practitioners with little guidance on the implications of selecting either informant. Drawing from a 2008-2009 sample of 11- to 17-year-olds ( N = 636) from Wave 1 of the second National Survey of Child and Adolescent Well-Being, this study first examined parent-child concordance in physical abuse reporting (Parent-Child Conflict Tactic Scale). Second, it applied multivariate regression analysis to relate parent-child agreement in physical abuse to parent-reported (Child Behavior Checklist) and child-reported (Youth Self Report) child behavioral problems. Results indicate low parent-child concordance of physical abuse (κ = .145). Coreporting of physical abuse was related to clinical-level parent-reported externalizing problems ([Formula: see text] = 64.57), whereas child-only reports of physical abuse were the only agreement category related to child-reported internalizing problems ( B = 4.17, p < .001). Attribution bias theory may further understanding of reporting concordance and its implications.

  7. Guideline concordance of treatment for depressive disorders in Canada.

    PubMed

    Duhoux, Arnaud; Fournier, Louise; Nguyen, Cat Tuong; Roberge, Pasquale; Beveridge, Rachelle

    2009-05-01

    Depression is one of the most prevalent mental health problems worldwide with considerable social and economic burdens. While practice guidelines exist, their adherence is inconsistent in clinical practice. To provide up-to-date national estimates of the adequacy of treatment received by Canadians having suffered a major depressive disorder (MDD) and examine factors associated with this adequacy. To evaluate the impact of different definitions of guideline-concordant treatment on the results. Data were drawn from the Canadian Community Health Survey, cycle 1.2: Mental Health and Well-Being (CCHS 1.2), a nationally representative survey conducted in 2002 and targetting persons aged 15 years or older living in private dwellings. In order to calculate the prevalence of treatment adequacy, we used a sample of 1,563 individuals meeting the criteria for MDD in the 12 months preceding the survey. A subset of 831 subjects who reported having used health services for mental health purposes at least once during that time served to identify the factors associated with treatment adequacy. Four definitions of minimally adequate treatment were considered and covariates were selected according to a well-known behavioral model. The analyses consisted of prevalence estimates and logistic regression models. Among selected subjects, 55% received guideline-concordant treatment according to the Canadian guidelines. Inadequacy was more prevalent in rural settings, for less complex cases, and in the general medical sector. Depending on the definition, prevalence of guideline-concordant treatment ranged between 48 and 71%, and factors associated with guideline-concordant treatment were mainly need factors and sector of care. A large proportion of people with a depressive disorder do not receive minimally adequate treatment. Improved access to and quality of treatment is required, especially in primary care settings.

  8. The effect of emotional distance on psychophysiologic concordance and perceived empathy between patient and interviewer.

    PubMed

    Marci, Carl D; Orr, Scott P

    2006-06-01

    This preliminary study investigated the effect of emotional distance on psychophysiologic concordance and perceived empathy in a clinical population. Participants included 20 adult outpatients from a mental health clinic that underwent a brief semi-structured interview with a trained psychiatrist in either an emotionally neutral or an emotionally distant condition. Simultaneous skin conductance (SC) levels of the patient and interviewer were recorded and used to calculate a measure of psychophysiologic concordance. Interviewer gaze was rated by an independent observer and used as a proxy indicator of emotional distance. Observer ratings of interviewer gaze, SC concordance, and patient ratings of perceived interviewer empathy were significantly lower in the emotionally distant condition compared with the emotionally neutral condition (p < 0.05). Results suggest that increased emotional distance is associated with decreased psychophysiologic concordance and reduced subjective ratings of perceived empathy. The observed differences in psychophysiologic concordance support the use of this measure as a potential marker of empathy in a clinical population in an interview setting.

  9. Concordance between local, institutional, and central pathology review in glioblastoma: implications for research and practice: a pilot study.

    PubMed

    Gupta, Tejpal; Nair, Vimoj; Epari, Sridhar; Pietsch, Torsten; Jalali, Rakesh

    2012-01-01

    There is significant inter-observer variation amongst the neuro-pathologists in the typing, subtyping, and grading of glial neoplasms for diagnosis. Centralized pathology review has been proposed to minimize this inter-observer variation and is now almost mandatory for accrual into multicentric trials. We sought to assess the concordance between neuro-pathologists on histopathological diagnosis of glioblastoma. Comparison of local, institutional, and central neuro-oncopathology reporting in a cohort of 34 patients with newly diagnosed supratentorial glioblastoma accrued consecutively at a tertiary-care institution on a prospective trial testing the addition of a new agent to standard chemo-radiation regimen. Concordance was sub-optimal between local histological diagnosis and central review, fair between local diagnosis and institutional review, and good between institutional and central review, with respect to histological typing/subtyping. Twelve (39%) of 31 patients with local histological diagnosis had identical tumor type, subtype and grade on central review. Overall agreement was modestly better (52%) between local diagnosis and institutional review. In contrast, 28 (83%) of 34 patients had completely concordant histopathologic diagnosis between institutional and central review. The inter-observer reliability test showed poor agreement between local and central review (kappa statistic=0.12, 95% confidence interval (CI): -0.03-0.32, P=0.043), but moderate agreement between institutional and central review (kappa statistic=0.51, 95%CI: 0.17-0.84, P=0.00003). Agreement between local diagnosis and institutional review was fair. There exists significant inter-observer variation regarding histopathological diagnosis of glioblastoma with significant implications for clinical research and practice. There is a need for more objective, quantitative, robust, and reproducible criteria for better subtyping for accurate diagnosis.

  10. Concorde noise-induced building vibrations for Sully Plantation, Chantilly, Virginia

    NASA Technical Reports Server (NTRS)

    Mayes, W. H.; Scholl, H. F.; Stephens, D. G.; Holliday, B. G.; Deloach, R.; Holmes, H. K.; Lewis, R. B.; Lynch, J. W.

    1976-01-01

    A study to assess the noise-induced building vibrations associated with Concorde operations is presented. The approach is to record the levels of induced vibrations and associated indoor/outdoor noise levels in selected homes, historic and other buildings near Dulles and Kennedy International Airports. Presented is a small, representative sample of data recorded at Sully Plantation, Chantilly, Virginia during the period of May 20 through May 28, 1976. Recorded data provide relationships between the vibration levels of walls, floors, windows, and the noise associated with Concorde operations (2 landings and 3 takeoffs), other aircraft, nonaircraft sources, and normal household activities. Results suggest that building vibrations resulting from aircraft operations were proportional to the overall sound pressure levels and relatively insensitive to spectral differences associated with the different types of aircraft. Furthermore, the maximum levels of vibratory response resulting from Concorde operations were higher than those associated with conventional aircraft. The vibrations of nonaircraft events were observed in some cases to exceed the levels resulting from aircraft operations. These nonaircraft events are currently being analyzed in greater detail.

  11. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

    PubMed Central

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

    2017-01-01

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

  12. Accurate First-Principles Spectra Predictions for Planetological and Astrophysical Applications at Various T-Conditions

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, V.

    2014-06-01

    Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical

  13. Accurate prediction of vaccine stability under real storage conditions and during temperature excursions.

    PubMed

    Clénet, Didier

    2018-04-01

    Due to their thermosensitivity, most vaccines must be kept refrigerated from production to use. To successfully carry out global immunization programs, ensuring the stability of vaccines is crucial. In this context, two important issues are critical, namely: (i) predicting vaccine stability and (ii) preventing product damage due to excessive temperature excursions outside of the recommended storage conditions (cold chain break). We applied a combination of advanced kinetics and statistical analyses on vaccine forced degradation data to accurately describe the loss of antigenicity for a multivalent freeze-dried inactivated virus vaccine containing three variants. The screening of large amounts of kinetic models combined with a statistical model selection approach resulted in the identification of two-step kinetic models. Predictions based on kinetic analysis and experimental stability data were in agreement, with approximately five percentage points difference from real values for long-term stability storage conditions, after excursions of temperature and during experimental shipments of freeze-dried products. Results showed that modeling a few months of forced degradation can be used to predict various time and temperature profiles endured by vaccines, i.e. long-term stability, short time excursions outside the labeled storage conditions or shipments at ambient temperature, with high accuracy. Pharmaceutical applications of the presented kinetics-based approach are discussed. Copyright © 2018 The Author. Published by Elsevier B.V. All rights reserved.

  14. Concord Grape Juice Supplementation Improves Memory Function In Older Adults with Mild Cognitive Impairment

    USDA-ARS?s Scientific Manuscript database

    Concord grape juice contains flavonoid polyphenol compounds, which have antioxidant and anti-inflammatory properties and influence neuronal signaling. Concord grape juice supplementation has been shown to reduce inflammation, blood pressure, and vascular pathology in individuals with cardiovascular...

  15. Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

    DOE PAGES

    Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.; ...

    2017-06-05

    Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

  16. Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

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

    Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.

    Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

  17. Spousal Concordance in Attitudes toward Violence and Reported Physical Abuse in African Couples

    ERIC Educational Resources Information Center

    Alio, Amina P.; Clayton, Heather B.; Garba, Madeleine; Mbah, Alfred K.; Daley, Ellen; Salihu, Hamisu M.

    2011-01-01

    Purpose: We examined the potential association between African couples' concordance on attitudes toward violence (ATV) and risk for intimate partner violence (IPV). Method: Analyses included 13,837 couples from Demographic and Health Surveys conducted between 2003 and 2007, from six African countries. Concordance on ATV was defined as both spouses…

  18. Concorde Noise-Induced Building Vibrations, Montgomery County, Maryland

    NASA Technical Reports Server (NTRS)

    Mayes, W. H.; Scholl, H. F.; Stephens, D. G.; Holliday, B. G.; Deloach, R.; Finley, T. D.; Holmes, H. K.; Lewis, R. B.; Lynch, J. W.

    1976-01-01

    A series of studies are reported to assess the noise induced building vibrations associated with Concorde operations. The levels of induced vibration and associated indoor/outdoor noise levels resulting from aircraft and nonaircraft events in selected homes, historic and other buildings near Dulles International Airport were recorded. The building response resulting from aircraft operations was found to be directly proportional to the overall sound pressure level and approximately independent of the aircraft type. The noise levels and, consequently, the response levels were observed to be higher for the Concorde operations than for the CTOL operations. Furthermore, the vibration could be closely reproduced by playing aircraft noise through a loudspeaker system located near the vibration measurement location. Nonaircraft events such as door closing were again observed to result in higher response levels than those induced by aircraft.

  19. Spousal Concordance of Diabetes Mellitus among Women in Ajman, United Arab Emirates.

    PubMed

    Al-Sharbatti, Shatha S; Abed, Yasmeen I; Al-Heety, Lujain M; Basha, Shaikh A

    2016-05-01

    Spousal concordance is defined as similar behaviours and associated health statuses between spouses. This study aimed to identify the concordance of diabetes mellitus (DM) and related variables among genetically unrelated couples in Ajman, United Arab Emirates (UAE). This cross-sectional study included 270 married women attending either the Mushairef Health Center or the Gulf Medical College Hospital in Ajman between May and November 2012. A validated questionnaire was designed to determine sociodemographic characteristics and a history or family history of DM, hypertension, coronary artery disease or dyslipidaemia among the women and their husbands. The weight, height, body mass index, waist circumference, fasting blood sugar and glycated haemoglobin (HbA1c) levels of all women were measured. Of the women, 39.3% of those with diabetic husbands and 39.9% of those with non-diabetic husbands were diabetic themselves (P >0.050). The prevalence of DM spousal concordance was 17.8%. A history of hypertension, coronary artery disease and dyslipidaemia was significantly more frequent among women whose husbands had a history of the same conditions (P = 0.001, 0.040 and 0.002, respectively). Spousal concordance of abnormal glycaemia among non-diabetic women with diabetic husbands was significant (P = 0.001). Having a diabetic husband (P = 0.006) and being obese (P = 0.009) were the only significant predictors of hyperglycaemia among non-diabetic women after controlling for confounding factors. There was significant concordance of abnormal glycaemia among non-diabetic women with diabetic husbands. The spouses of diabetic patients may therefore be a target population for regular hyperglycaemia and DM screening.

  20. Accurate and dynamic predictive model for better prediction in medicine and healthcare.

    PubMed

    Alanazi, H O; Abdullah, A H; Qureshi, K N; Ismail, A S

    2018-05-01

    Information and communication technologies (ICTs) have changed the trend into new integrated operations and methods in all fields of life. The health sector has also adopted new technologies to improve the systems and provide better services to customers. Predictive models in health care are also influenced from new technologies to predict the different disease outcomes. However, still, existing predictive models have suffered from some limitations in terms of predictive outcomes performance. In order to improve predictive model performance, this paper proposed a predictive model by classifying the disease predictions into different categories. To achieve this model performance, this paper uses traumatic brain injury (TBI) datasets. TBI is one of the serious diseases worldwide and needs more attention due to its seriousness and serious impacts on human life. The proposed predictive model improves the predictive performance of TBI. The TBI data set is developed and approved by neurologists to set its features. The experiment results show that the proposed model has achieved significant results including accuracy, sensitivity, and specificity.

  1. Dominant intraprostatic cancer confirmed by direct MRI-guided biopsy: Concordance with histopathological findings.

    PubMed

    Meermeier, Nicholas P; Turner, Kevin R; Foster, Bryan R; Várallyay, Csanád; Liu, Jen-Jane; Coakley, Fergus V

    2018-06-09

    To investigate the concordance between dominant intraprostatic cancer seen on endorectal multiparametric MRI and confirmed by MRI-targeted biopsy with histopathological findings at radical prostatectomy, since existing literature has emphasized the miss rather than the concordance rate of MRI. We retrospectively identified 20 patients who underwent radical prostatectomy after a dominant intraprostatic cancer focus was identified at endorectal multiparametric MRI and confirmed by MRI-targeted biopsy. Concordance was determined by comparing the location and Gleason grade group of dominant tumor at MRI with the location and Gleason grade group determined at histopathological review. Mean patient age was 65 years (range, 48 to 76) and median serum prostatic specific antigen level was 9.4 ng/mL (range, 4.6 to 58.0). In all 20 patients, the location of dominant tumor based on MRI and targeted biopsy corresponded with the dominant tumor location at histopathology. In 9 patients, Gleason grade group was the same at targeted biopsy and final histopathology. In 9 patients, final Gleason grade group was higher and in two patients it was lower. Our preliminary results suggest dominant tumor as determined by endorectal multiparametric MRI and confirmed by a positive MRI-targeted biopsy has high concordance with histopathological findings at radical prostatectomy for location, and reasonable concordance for Gleason grade group. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Multicenter Evaluation of a Commercial Cytomegalovirus Quantitative Standard: Effects of Commutability on Interlaboratory Concordance

    PubMed Central

    Shahbazian, M. D.; Valsamakis, A.; Boonyaratanakornkit, J.; Cook, L.; Pang, X. L.; Preiksaitis, J. K.; Schönbrunner, E. R.; Caliendo, A. M.

    2013-01-01

    Commutability of quantitative reference materials has proven important for reliable and accurate results in clinical chemistry. As international reference standards and commercially produced calibration material have become available to address the variability of viral load assays, the degree to which such materials are commutable and the effect of commutability on assay concordance have been questioned. To investigate this, 60 archived clinical plasma samples, which previously tested positive for cytomegalovirus (CMV), were retested by five different laboratories, each using a different quantitative CMV PCR assay. Results from each laboratory were calibrated both with lab-specific quantitative CMV standards (“lab standards”) and with common, commercially available standards (“CMV panel”). Pairwise analyses among laboratories were performed using mean results from each clinical sample, calibrated first with lab standards and then with the CMV panel. Commutability of the CMV panel was determined based on difference plots for each laboratory pair showing plotted values of standards that were within the 95% prediction intervals for the clinical specimens. Commutability was demonstrated for 6 of 10 laboratory pairs using the CMV panel. In half of these pairs, use of the CMV panel improved quantitative agreement compared to use of lab standards. Two of four laboratory pairs for which the CMV panel was noncommutable showed reduced quantitative agreement when that panel was used as a common calibrator. Commutability of calibration material varies across different quantitative PCR methods. Use of a common, commutable quantitative standard can improve agreement across different assays; use of a noncommutable calibrator can reduce agreement among laboratories. PMID:24025907

  3. Accurate prediction of severe allergic reactions by a small set of environmental parameters (NDVI, temperature).

    PubMed

    Notas, George; Bariotakis, Michail; Kalogrias, Vaios; Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions.

  4. Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

    PubMed Central

    Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

  5. A Machine Learned Classifier That Uses Gene Expression Data to Accurately Predict Estrogen Receptor Status

    PubMed Central

    Bastani, Meysam; Vos, Larissa; Asgarian, Nasimeh; Deschenes, Jean; Graham, Kathryn; Mackey, John; Greiner, Russell

    2013-01-01

    Background Selecting the appropriate treatment for breast cancer requires accurately determining the estrogen receptor (ER) status of the tumor. However, the standard for determining this status, immunohistochemical analysis of formalin-fixed paraffin embedded samples, suffers from numerous technical and reproducibility issues. Assessment of ER-status based on RNA expression can provide more objective, quantitative and reproducible test results. Methods To learn a parsimonious RNA-based classifier of hormone receptor status, we applied a machine learning tool to a training dataset of gene expression microarray data obtained from 176 frozen breast tumors, whose ER-status was determined by applying ASCO-CAP guidelines to standardized immunohistochemical testing of formalin fixed tumor. Results This produced a three-gene classifier that can predict the ER-status of a novel tumor, with a cross-validation accuracy of 93.17±2.44%. When applied to an independent validation set and to four other public databases, some on different platforms, this classifier obtained over 90% accuracy in each. In addition, we found that this prediction rule separated the patients' recurrence-free survival curves with a hazard ratio lower than the one based on the IHC analysis of ER-status. Conclusions Our efficient and parsimonious classifier lends itself to high throughput, highly accurate and low-cost RNA-based assessments of ER-status, suitable for routine high-throughput clinical use. This analytic method provides a proof-of-principle that may be applicable to developing effective RNA-based tests for other biomarkers and conditions. PMID:24312637

  6. Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

    PubMed

    Li, Fuyi; Li, Chen; Marquez-Lago, Tatiana T; Leier, André; Akutsu, Tatsuya; Purcell, Anthony W; Smith, A Ian; Lithgow, Trevor; Daly, Roger J; Song, Jiangning; Chou, Kuo-Chen

    2018-06-27

    Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary data are available at Bioinformatics online.

  7. A SNP panel and online tool for checking genotype concordance through comparing QR codes.

    PubMed

    Du, Yonghong; Martin, Joshua S; McGee, John; Yang, Yuchen; Liu, Eric Yi; Sun, Yingrui; Geihs, Matthias; Kong, Xuejun; Zhou, Eric Lingfeng; Li, Yun; Huang, Jie

    2017-01-01

    In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

  8. A SNP panel and online tool for checking genotype concordance through comparing QR codes

    PubMed Central

    Du, Yonghong; Martin, Joshua S.; McGee, John; Yang, Yuchen; Liu, Eric Yi; Sun, Yingrui; Geihs, Matthias; Kong, Xuejun; Zhou, Eric Lingfeng; Li, Yun

    2017-01-01

    In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine. PMID:28926565

  9. Molecular testing guidelines for lung adenocarcinoma: Utility of cell blocks and concordance between fine-needle aspiration cytology and histology samples

    PubMed Central

    Heymann, Jonas J.; Bulman, William A.; Maxfield, Roger A.; Powell, Charles A.; Halmos, Balazs; Sonett, Joshua; Beaubier, Nike T.; Crapanzano, John P.; Mansukhani, Mahesh M.; Saqi, Anjali

    2014-01-01

    Background: Lung cancer is a leading cause of mortality, and patients often present at a late stage. More recently, advances in screening, diagnosing, and treating lung cancer have been made. For instance, greater numbers of minimally invasive procedures are being performed, and identification of lung adenocarcinoma driver mutations has led to the implementation of targeted therapies. Advances in molecular techniques enable use of scant tissue, including cytology specimens. In addition, per recently published consensus guidelines, cytology-derived cell blocks (CBs) are preferred over direct smears. Yet, limited comparison of molecular testing of fine-needle aspiration (FNA) CBs and corresponding histology specimens has been performed. This study aimed to establish concordance of epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma (KRAS) virus homolog testing between FNA CBs and histology samples from the same patients. Materials and Methods: Patients for whom molecular testing for EGFR or KRAS was performed on both FNA CBs and histology samples containing lung adenocarcinoma were identified retrospectively. Following microdissection, when necessary, concordance of EGFR and KRAS molecular testing results between FNA CBs and histology samples was evaluated. Results: EGFR and/or KRAS testing was performed on samples obtained from 26 patients. Concordant results were obtained for all EGFR (22/22) and KRAS (17/17) mutation analyses performed. Conclusions: Identification of mutations in lung adenocarcinomas affects clinical decision-making, and it is important that results from small samples be accurate. This study demonstrates that molecular testing on cytology CBs is as sensitive and specific as that on histology. PMID:24987443

  10. 33 CFR 165.1198 - Safety zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Safety zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal Concord, CA. 165.1198 Section 165.1198... Limited Access Areas Eleventh Coast Guard District § 165.1198 Safety zone; Military Ocean Terminal Concord...

  11. 33 CFR 165.1198 - Safety zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Safety zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal Concord, CA. 165.1198 Section 165.1198... Limited Access Areas Eleventh Coast Guard District § 165.1198 Safety zone; Military Ocean Terminal Concord...

  12. A Place Called Home: Educational Reform in a Concord, Massachusetts School, 1897-1914

    ERIC Educational Resources Information Center

    Morice, Linda C.

    2012-01-01

    This paper examines the role of place in the reform efforts of two teachers who established Miss White's Home School in Concord, Massachusetts (USA). Flora and Mary White rebelled against the prevailing industrial model of instruction in tax-supported schools where they taught. As a solution, they moved to Concord--a nonconformist town with a…

  13. New body fat prediction equations for severely obese patients.

    PubMed

    Horie, Lilian Mika; Barbosa-Silva, Maria Cristina Gonzalez; Torrinhas, Raquel Susana; de Mello, Marco Túlio; Cecconello, Ivan; Waitzberg, Dan Linetzky

    2008-06-01

    Severe obesity imposes physical limitations to body composition assessment. Our aim was to compare body fat (BF) estimations of severely obese patients obtained by bioelectrical impedance (BIA) and air displacement plethysmography (ADP) for development of new equations for BF prediction. Severely obese subjects (83 female/36 male, mean age=41.6+/-11.6 years) had BF estimated by BIA and ADP. The agreement of the data was evaluated using Bland-Altman's graphic and concordance correlation coefficient (CCC). A multivariate regression analysis was performed to develop and validate new predictive equations. BF estimations from BIA (64.8+/-15 kg) and ADP (65.6+/-16.4 kg) did not differ (p>0.05, with good accuracy, precision, and CCC), but the Bland- Altman graphic showed a wide limit of agreement (-10.4; 8.8). The standard BIA equation overestimated BF in women (-1.3 kg) and underestimated BF in men (5.6 kg; p<0.05). Two BF new predictive equations were generated after BIA measurement, which predicted BF with higher accuracy, precision, CCC, and limits of agreement than the standard BIA equation. Standard BIA equations were inadequate for estimating BF in severely obese patients. Equations developed especially for this population provide more accurate BF assessment.

  14. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

    PubMed

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

    2017-01-09

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Spousal Concordance of Diabetes Mellitus among Women in Ajman, United Arab Emirates

    PubMed Central

    Al-Sharbatti, Shatha S.; Abed, Yasmeen I.; Al-Heety, Lujain M.; Basha, Shaikh A.

    2016-01-01

    Objectives: Spousal concordance is defined as similar behaviours and associated health statuses between spouses. This study aimed to identify the concordance of diabetes mellitus (DM) and related variables among genetically unrelated couples in Ajman, United Arab Emirates (UAE). Methods: This cross-sectional study included 270 married women attending either the Mushairef Health Center or the Gulf Medical College Hospital in Ajman between May and November 2012. A validated questionnaire was designed to determine sociodemographic characteristics and a history or family history of DM, hypertension, coronary artery disease or dyslipidaemia among the women and their husbands. The weight, height, body mass index, waist circumference, fasting blood sugar and glycated haemoglobin (HbA1c) levels of all women were measured. Results: Of the women, 39.3% of those with diabetic husbands and 39.9% of those with non-diabetic husbands were diabetic themselves (P >0.050). The prevalence of DM spousal concordance was 17.8%. A history of hypertension, coronary artery disease and dyslipidaemia was significantly more frequent among women whose husbands had a history of the same conditions (P = 0.001, 0.040 and 0.002, respectively). Spousal concordance of abnormal glycaemia among non-diabetic women with diabetic husbands was significant (P = 0.001). Having a diabetic husband (P = 0.006) and being obese (P = 0.009) were the only significant predictors of hyperglycaemia among non-diabetic women after controlling for confounding factors. Conclusion: There was significant concordance of abnormal glycaemia among non-diabetic women with diabetic husbands. The spouses of diabetic patients may therefore be a target population for regular hyperglycaemia and DM screening. PMID:27226911

  16. Concord, Convergence and Accommodation in Bilingual Children

    ERIC Educational Resources Information Center

    Radford, Andrew; Kupisch, Tanja; Koppe, Regina; Azzaro, Gabriele

    2007-01-01

    This paper examines the syntax of "GENDER CONCORD" in mixed utterances where bilingual children switch between a modifier in one language and a noun in another. Particular attention is paid to how children deal with potential gender mismatches between modifier and noun, i.e., if one of the languages has grammatical gender but the other does not,…

  17. Effects of Genital Response Measurement Device and Stimulus Characteristics on Sexual Concordance in Women.

    PubMed

    Bouchard, Katrina N; Chivers, Meredith L; Pukall, Caroline F

    2017-01-01

    Investigations of sexual concordance suggest that, on average, women exhibit a low, positive correlation between their subjective sexual arousal and genital response. However, this relationship appears to be stronger, on average, when genital response is measured via the external tissues of the vulva than within the vagina walls. Given the methodological variations, such as stimulus content and duration, in studies of vulvar and vaginal concordance, direct comparisons between individual studies are limited. In the current study, sexual concordance was examined using concurrent measures of vulvar blood flow (using laser Doppler imaging) and vaginal vasocongestion (using vaginal photoplethysmography) to investigate potential differences in vulvar and vaginal concordance. Twenty-five women viewed two erotic films that differed in sexual activity content (foreplay and intercourse) while their subjective sexual arousal and genital response was measured. In support of previous meta-analytic findings, results suggest that subjective sexual arousal is more strongly correlated with vulvar blood flow than with vaginal vasocongestion. Likewise, perceived genital response and actual vulvar blood flow are more strongly related than are vaginal vasocongestion and self-reported genital sensations. Practical implications for the study of women's sexual concordance as well as broader implications for the understanding of female sexuality are considered.

  18. Assessment of interobserver concordance in polysomnography scoring of sleep bruxism☆

    PubMed Central

    Ferraz, Otávio; de Moura Guimarães, Thais; Maluly Filho, Milton; Dal-Fabbro, Cibele; Abraão Crosara Cunha, Thays; Cristina Lotaif, Ana; Cristina Barros Schütz, Teresa; Santos-Silva, Rogério; Tufik, Sergio; Bittencourt, Lia

    2015-01-01

    Introduction Objective evaluation of sleep bruxism (SB) using whole-night polysomnography (PSG) is relevant for diagnostic confirmation. Nevertheless, the PSG electromyogram (EMG) scoring may give rise to controversy, particularly when audiovisual monitoring is not performed. Therefore, the present study assessed the concordance between two independent scorers to visual SB on a PSG performed without audiovisual monitoring. Methods Fifty-six PSG tests were scored from individuals with clinical history and polysomnography criteria of SB. In addition to the protocol of conventional whole-night PSG, electrodes were also placed bilaterally on the masseter and temporal muscles. Visual EMG scoring without audio video monitoring was scored by two independent scorers (Dentist 1 and Dentist 2) according the recommendations formulated in the AASM manual (2007). Kendall Tau correlation was used to assess interobserver concordance relative to variables “total duration of events (seconds), “shortest events”, “longest events” and index in each phasic, tonic or mixed event. Results The correlation was positive and significant relative to all the investigated variables, being T>0.54. Conclusion It was found a good inter-examiner concordance rate in SB scoring in absence of audio video monitoring. PMID:26779318

  19. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  20. Goal striving, need satisfaction, and longitudinal well-being: the self-concordance model.

    PubMed

    Sheldon, K M; Elliot, A J

    1999-03-01

    An integrative model of the conative process, which has important ramifications for psychological need satisfaction and hence for individuals' well-being, is presented. The self-concordance of goals (i.e., their consistency with the person's developing interests and core values) plays a dual role in the model. First, those pursuing self-concordant goals put more sustained effort into achieving those goals and thus are more likely to attain them. Second, those who attain self-concordant goals reap greater well-being benefits from their attainment. Attainment-to-well-being effects are mediated by need satisfaction, i.e., daily activity-based experiences of autonomy, competence, and relatedness that accumulate during the period of striving. The model is shown to provide a satisfactory fit to 3 longitudinal data sets and to be independent of the effects of self-efficacy, implementation intentions, avoidance framing, and life skills.

  1. Assessing risk prediction models using individual participant data from multiple studies.

    PubMed

    Pennells, Lisa; Kaptoge, Stephen; White, Ian R; Thompson, Simon G; Wood, Angela M

    2014-03-01

    Individual participant time-to-event data from multiple prospective epidemiologic studies enable detailed investigation into the predictive ability of risk models. Here we address the challenges in appropriately combining such information across studies. Methods are exemplified by analyses of log C-reactive protein and conventional risk factors for coronary heart disease in the Emerging Risk Factors Collaboration, a collation of individual data from multiple prospective studies with an average follow-up duration of 9.8 years (dates varied). We derive risk prediction models using Cox proportional hazards regression analysis stratified by study and obtain estimates of risk discrimination, Harrell's concordance index, and Royston's discrimination measure within each study; we then combine the estimates across studies using a weighted meta-analysis. Various weighting approaches are compared and lead us to recommend using the number of events in each study. We also discuss the calculation of measures of reclassification for multiple studies. We further show that comparison of differences in predictive ability across subgroups should be based only on within-study information and that combining measures of risk discrimination from case-control studies and prospective studies is problematic. The concordance index and discrimination measure gave qualitatively similar results throughout. While the concordance index was very heterogeneous between studies, principally because of differing age ranges, the increments in the concordance index from adding log C-reactive protein to conventional risk factors were more homogeneous.

  2. An Extrapolation of a Radical Equation More Accurately Predicts Shelf Life of Frozen Biological Matrices.

    PubMed

    De Vore, Karl W; Fatahi, Nadia M; Sass, John E

    2016-08-01

    Arrhenius modeling of analyte recovery at increased temperatures to predict long-term colder storage stability of biological raw materials, reagents, calibrators, and controls is standard practice in the diagnostics industry. Predicting subzero temperature stability using the same practice is frequently criticized but nevertheless heavily relied upon. We compared the ability to predict analyte recovery during frozen storage using 3 separate strategies: traditional accelerated studies with Arrhenius modeling, and extrapolation of recovery at 20% of shelf life using either ordinary least squares or a radical equation y = B1x(0.5) + B0. Computer simulations were performed to establish equivalence of statistical power to discern the expected changes during frozen storage or accelerated stress. This was followed by actual predictive and follow-up confirmatory testing of 12 chemistry and immunoassay analytes. Linear extrapolations tended to be the most conservative in the predicted percent recovery, reducing customer and patient risk. However, the majority of analytes followed a rate of change that slowed over time, which was fit best to a radical equation of the form y = B1x(0.5) + B0. Other evidence strongly suggested that the slowing of the rate was not due to higher-order kinetics, but to changes in the matrix during storage. Predicting shelf life of frozen products through extrapolation of early initial real-time storage analyte recovery should be considered the most accurate method. Although in this study the time required for a prediction was longer than a typical accelerated testing protocol, there are less potential sources of error, reduced costs, and a lower expenditure of resources. © 2016 American Association for Clinical Chemistry.

  3. SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

    PubMed Central

    2014-01-01

    Background Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. Results SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. Conclusions SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/. PMID:24980894

  4. Advanced Hepatocellular Carcinoma: Which Staging Systems Best Predict Prognosis?

    PubMed Central

    Huitzil-Melendez, Fidel-David; Capanu, Marinela; O'Reilly, Eileen M.; Duffy, Austin; Gansukh, Bolorsukh; Saltz, Leonard L.; Abou-Alfa, Ghassan K.

    2010-01-01

    Purpose The purpose of cancer staging systems is to accurately predict patient prognosis. The outcome of advanced hepatocellular carcinoma (HCC) depends on both the cancer stage and the extent of liver dysfunction. Many staging systems that include both aspects have been developed. It remains unknown, however, which of these systems is optimal for predicting patient survival. Patients and Methods Patients with advanced HCC treated over a 5-year period at Memorial Sloan-Kettering Cancer Center were identified from an electronic medical record database. Patients with sufficient data for utilization in all staging systems were included. TNM sixth edition, Okuda, Barcelona Clinic Liver Cancer (BCLC), Cancer of the Liver Italian Program (CLIP), Chinese University Prognostic Index (CUPI), Japan Integrated Staging (JIS), and Groupe d'Etude et de Traitement du Carcinome Hepatocellulaire (GETCH) systems were ranked on the basis of their accuracy at predicting survival by using concordance index (c-index). Other independent prognostic variables were also identified. Results Overall, 187 eligible patients were identified and were staged by using the seven staging systems. CLIP, CUPI, and GETCH were the three top-ranking staging systems. BCLC and TNM sixth edition lacked any meaningful prognostic discrimination. Performance status, AST, abdominal pain, and esophageal varices improved the discriminatory ability of CLIP. Conclusion In our selected patient population, CLIP, CUPI, and GETCH were the most informative staging systems in predicting survival in patients with advanced HCC. Prospective validation is required to determine if they can be accurately used to stratify patients in clinical trials and to direct the appropriate need for systemic therapy versus best supportive care. BCLC and TNM sixth edition were not helpful in predicting survival outcome, and their use is not supported by our data. PMID:20458042

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

    PubMed

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

    2017-08-01

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

  6. Achieving Goal-Concordant Care: A Conceptual Model and Approach to Measuring Serious Illness Communication and Its Impact.

    PubMed

    Sanders, Justin J; Curtis, J Randall; Tulsky, James A

    2018-03-01

    High-quality care for seriously ill patients aligns treatment with their goals and values. Failure to achieve "goal-concordant" care is a medical error that can harm patients and families. Because communication between clinicians and patients enables goal concordance and also affects the illness experience in its own right, healthcare systems should endeavor to measure communication and its outcomes as a quality assessment. Yet, little consensus exists on what should be measured and by which methods. To propose measurement priorities for serious illness communication and its anticipated outcomes, including goal-concordant care. We completed a narrative review of the literature to identify links between serious illness communication, goal-concordant care, and other outcomes. We used this review to identify gaps and opportunities for quality measurement in serious illness communication. Our conceptual model describes the relationship between communication, goal-concordant care, and other relevant outcomes. Implementation-ready measures to assess the quality of serious illness communication and care include (1) the timing and setting of serious illness communication, (2) patient experience of communication and care, and (3) caregiver bereavement surveys that include assessment of perceived goal concordance of care. Future measurement priorities include direct assessment of communication quality, prospective patient or family assessment of care concordance with goals, and assessment of the bereaved caregiver experience. Improving serious illness care necessitates ensuring that high-quality communication has occurred and measuring its impact. Measuring patient experience and receipt of goal-concordant care should be our highest priority. We have the tools to measure both.

  7. Modeling Concordance Correlation Coefficient for Longitudinal Study Data

    ERIC Educational Resources Information Center

    Ma, Yan; Tang, Wan; Yu, Qin; Tu, X. M.

    2010-01-01

    Measures of agreement are used in a wide range of behavioral, biomedical, psychosocial, and health-care related research to assess reliability of diagnostic test, psychometric properties of instrument, fidelity of psychosocial intervention, and accuracy of proxy outcome. The concordance correlation coefficient (CCC) is a popular measure of…

  8. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Concordance and acceptability of electric stimulation therapy: a randomised controlled trial.

    PubMed

    Miller, C; McGuiness, W; Wilson, S; Cooper, K; Swanson, T; Rooney, D; Piller, N; Woodward, M

    2017-08-02

    A pilot single-blinded randomised controlled trial (RCT) was conducted to examine concordance with and acceptability of electric stimulation therapy (EST) in patients with venous leg ulcers (VLUs) who had not tolerated moderate to high compression. Participants were randomised to the intervention group (n=15) or a placebo control group (n=8) in which EST was used four times daily for 20 minutes per session. Participants were monitored for eight weeks during which time concordance with the treatment and perceptions of the treatment were assessed. Concordance with the total recommended treatment time was 71.4% for the intervention group and 82.9% for the control group; a difference that was not statistically significant. Participants rated EST as acceptable (84.6% intervention; 83.3% control), only two participants, both from the placebo control group, would not be willing to use EST again. The majority considered EST easier to use than compression (68.4%). EST was a practical and acceptable treatment among people who have been unable to tolerate moderate to high compression therapy.

  10. International validation study for interim PET in ABVD-treated, advanced-stage hodgkin lymphoma: interpretation criteria and concordance rate among reviewers.

    PubMed

    Biggi, Alberto; Gallamini, Andrea; Chauvie, Stephane; Hutchings, Martin; Kostakoglu, Lale; Gregianin, Michele; Meignan, Michel; Malkowski, Bogdan; Hofman, Michael S; Barrington, Sally F

    2013-05-01

    At present, there are no standard criteria that have been validated for interim PET reporting in lymphoma. In 2009, an international workshop attended by hematologists and nuclear medicine experts in Deauville, France, proposed to develop simple and reproducible rules for interim PET reporting in lymphoma. Accordingly, an international validation study was undertaken with the primary aim of validating the prognostic role of interim PET using the Deauville 5-point score to evaluate images and with the secondary aim of measuring concordance rates among reviewers using the same 5-point score. This paper focuses on the criteria for interpretation of interim PET and on concordance rates. A cohort of advanced-stage Hodgkin lymphoma patients treated with doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) were enrolled retrospectively from centers worldwide. Baseline and interim scans were reviewed by an international panel of 6 nuclear medicine experts using the 5-point score. Complete scan datasets of acceptable diagnostic quality were available for 260 of 440 (59%) enrolled patients. Independent agreement among reviewers was reached on 252 of 260 patients (97%), for whom at least 4 reviewers agreed the findings were negative (score of 1-3) or positive (score of 4-5). After discussion, consensus was reached in all cases. There were 45 of 260 patients (17%) with positive interim PET findings and 215 of 260 patients (83%) with negative interim PET findings. Thirty-three interim PET-positive scans were true-positive, and 12 were false-positive. Two hundred three interim PET-negative scans were true-negative, and 12 were false-negative. Sensitivity, specificity, and accuracy were 0.73, 0.94, and 0.91, respectively. Negative predictive value and positive predictive value were 0.94 and 0.73, respectively. The 3-y failure-free survival was 83%, 28%, and 95% for the entire population and for interim PET-positive and -negative patients, respectively (P < 0.0001). The

  11. Merger of Multiple Accreting Black Holes Concordant with Gravitational-wave Events

    NASA Astrophysics Data System (ADS)

    Tagawa, Hiromichi; Umemura, Masayuki

    2018-03-01

    Recently, the advanced Laser Interferometer Gravitational-Wave Observatory (aLIGO) has detected black hole (BH) merger events, most of which are sourced by BHs more massive than 30 M ⊙. Especially, the observation of GW170104 suggests dynamically assembled binaries favoring a distribution of misaligned spins. It has been argued that mergers of unassociated BHs can be engendered through a chance meeting in a multiple BH system under gas-rich environments. In this paper, we consider the merger of unassociated BHs, concordant with the massive BH merger events. To that end, we simulate a multiple BH system with a post-Newtonian N-body code incorporating gas accretion and general relativistic effects. As a result, we find that gas dynamical friction effectively promotes a three-body interaction of BHs in dense gas of n gas ≳ 106 cm‑3, so that BH mergers can take place within 30 Myr. This scenario predicts an isotropic distribution of spin tilts. In the concordant models with GW150914, the masses of seed BHs are required to be ≳25 M ⊙. The potential sites of such chance meeting BH mergers are active galactic nucleus (AGN) disks and dense interstellar clouds. Assuming the LIGO O1, we roughly estimate the event rates for PopI BHs and PopIII BHs in AGN disks to be ≃1–2 yr‑1 and ≃1 yr‑1, respectively. Multiple episodes of AGNs may enhance the rates by roughly an order of magnitude. For massive PopI BHs in dense interstellar clouds the rate is ≃0.02 yr‑1. Hence, high-density AGN disks are a more plausible site for mergers of chance meeting BHs.

  12. [Diagnostic concordance between seven definitions of metabolic syndrome in overweight and obese adults].

    PubMed

    Cabrera-Rode, Eduardo; Stusser, Beatriz; Cálix, Wenny; Orlandi, Neraldo; Rodríguez, Janet; Cubas-Dueñas, Ileana; Echevarría, Ragmila; Álvarez, Aimee

    2017-01-01

    The aim of this study was to determine the level of diagnostic concordance between seven definitions of metabolic syndrome (MS) in a group of overweight and obese adults. 350 subjects aged from 19 to 70 years were recruited for study from a clinic for overweight and obese subjects. The definitions of MS used were those given by the WHO (World Health Organization), EGIR (European Group for the Study of Insulin Resistance), NCEP- ATPIII (Adult Treatment Panel), AHA/NHLBI (American Heart Association), IDF (International Diabetes Federation), and JIS (Joint Interim Statement) as well as the Szabo criteria. Concordance between the definitions was calculated with the Kappa coefficient. Insulin resistance (IR) was assessed using the HOMA-IR index. According to the Szabo, WHO, EGIR, NCEP-ATPIII, AHA/NHLBI, IDF, and JIS criteria, MS frequency was 74.3%, 42.0%, 46.8%, 56.0%, 52.9%, 58.6%, and 58.6%, respectively. The concordance between the Szabo and AHA/NHLBI criteria was 0.559, while the Kappa coefficient between the Szabo criteria and the rest of the guides (NCEP-ATPIII, IDF, and JIS) was from 0.612 to 0.657, respectively. The concordance of the WHO with the EGIR was 0.602, but it was between 0.358 and 0.422 with the other guidelines. IR was distributed similarly in all guidelines. There is a considerable concordance between the NCEP-ATPIII, IDF, and JIS guidelines and the Szabo criteria. The Szabo criteria could be an option for the active surveillance of MS in populations.

  13. Concord grape juice reverses the age-related impairment in latent learning in rats.

    PubMed

    Smith, Jessica M; Stouffer, Eric M

    2014-02-01

    Two experiments were conducted to determine if dietary supplementation with Concord grape juice could reverse the latent learning impairment normally observed in middle-aged male rats. Both experiments utilized the latent cue preference (LCP) task, in which water-replete rats sample water in one compartment of a three-compartment box, and are subsequently given a compartment preference test when water-deprived to determine if they remember the compartment cue previously associated with water. In the first experiment, 40 male Sprague-Dawley rats (9, 10, 11, or 12 months old) were used to determine the age of onset of the impairment. In the second experiment, 24 male Sprague-Dawley rats (11 months old) were given daily access (10 ml/day) to 50% Concord grape juice, 50% white grape juice, or a calorically-equivalent sugar solution daily for 5 weeks prior to training. The first experiment revealed that the latent learning impairment begins to manifest at 10 months of age in the male rats and is fully present at 11 months. The second experiment showed that rats that consumed the 50% Concord grape juice for 5 weeks beginning at 11 months of age showed intact latent learning in the LCP task, while rats that consumed the other two supplements showed the normal impairment on the LCP task. These results indicate that daily supplementation with Concord grape juice was able to reverse the latent learning impairment normally seen in middle-aged male rats. This reversal is most likely due to the presence of flavonoids in Concord grape juice.

  14. NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.

    PubMed

    Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp.

  15. Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease

    PubMed Central

    Owen, Joseph R.; Noyes, Noelle; Young, Amy E.; Prince, Daniel J.; Blanchard, Patricia C.; Lehenbauer, Terry W.; Aly, Sharif S.; Davis, Jessica H.; O’Rourke, Sean M.; Abdo, Zaid; Belk, Keith; Miller, Michael R.; Morley, Paul; Van Eenennaam, Alison L.

    2017-01-01

    Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease–associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis. While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease

  16. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-07

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  17. Prediction of appendicular skeletal and fat mass in children: excellent concordance of dual-energy X-ray absorptiometry and magnetic resonance imaging.

    PubMed

    Bridge, Pascale; Pocock, Nicholas A; Nguyen, Tuan; Munns, Craig; Cowell, Christopher T; Thompson, Martin W

    2009-09-01

    Body composition studies in children have great potential to help understand the aetiology and evolution of acute and chronic. diseases. To validate appendicular lean soft tissue mass (LSTM) and fat mass (FM) measured using dual energy X-ray absorptiometry (DXA), with magnetic resonance imaging (MRI) as the reference standard, in healthy peri-pubertal adolescents. Peri-pubertal Caucasian children (n = 74) aged 11-14 years were evaluated. DXA LSTM and FM of the mid third femur were measured and skeletal muscle mass (SM) and FM of the same region were measured on the same day by MRI. There was a strong correlation between MRI SM and DXA LSTM (r2 = 0.98, index of concordance [C] = 0.91). DXA estimation of LSTM exceeded MRI SM by a mean of 189 g, from 6-371 g (p < 0.0001). The discordance between DXA and MRI significantly increased with the absolute value (r = 0.27; p = 0.024). FM was highly correlated (r = 0.98) with a high index of concordance (C = 0.97). This study validates the use of DXA in LSTM measurement in children, confirming its potential in clinical and research roles in paediatric diseases affecting and related to body composition.

  18. A quality control study on cytotechnologist-cytopathologist concordance and its relationship to the number of dots on the slide.

    PubMed

    Bongiovanni, Massimo; De Saussure, Barbara; Kumar, Neeta; Pache, Jean-Claude; Cibas, Edmund S

    2009-01-01

    To study cytotechnologist (CT)-cytopathologist (CP) concordance for evaluating individual CTs' performance and for quality assurance and educational feedback. The interpretations of individual CTs were compared with the final interpretations (according to the 2001 Bethesda System) of the CP. Concordance percentages and kappa values were calculated for each CT and correlated with the numbers of dots on each slide, years of experience and percentage of work hours devoted to cytology. A total of 10,453 Pap tests were screened by 9 CTs during one year, out of which 993 (9.5%) were referred to one CP for a final interpretation. Mean concordance between the aggregate CT interpretations and those of the CP was 65.5%. Five CTs had good concordance, 3 had moderately good concordance, and one had surprisingly poor concordance that contrasted with good subjective impressions. No correlation was found between concordance and the average number of dots per slide, screening experience in cervicovaginal cytology or percentage of work hours devoted to cytology. Monitoring CT-CP concordance rates can unveil performance issues not detected by subjective impressions. An excessive number of dots per slide may not reflect poor diagnostic precision so much as a lack of confidence in interpretation.

  19. Does mesenteric venous imaging assessment accurately predict pathologic invasion in localized pancreatic ductal adenocarcinoma?

    PubMed

    Clanton, Jesse; Oh, Stephen; Kaplan, Stephen J; Johnson, Emily; Ross, Andrew; Kozarek, Richard; Alseidi, Adnan; Biehl, Thomas; Picozzi, Vincent J; Helton, William S; Coy, David; Dorer, Russell; Rocha, Flavio G

    2018-05-09

    Accurate prediction of mesenteric venous involvement in pancreatic ductal adenocarcinoma (PDAC) is necessary for adequate staging and treatment. A retrospective cohort study was conducted in PDAC patients at a single institution. All patients with resected PDAC and staging CT and EUS between 2003 and 2014 were included and sub-divided into "upfront resected" and "neoadjuvant chemotherapy (NAC)" groups. Independent imaging re-review was correlated to venous resection and venous invasion. Sensitivity, specificity, positive and negative predictive values were then calculated. A total of 109 patients underwent analysis, 60 received upfront resection, and 49 NAC. Venous resection (30%) and vein invasion (13%) was less common in patients resected upfront than those who received NAC (53% and 16%, respectively). Both CT and EUS had poor sensitivity (14-44%) but high specificity (75-95%) for detecting venous resection and vein invasion in patients resected upfront, whereas sensitivity was high (84-100%) and specificity was low (27-44%) after NAC. Preoperative CT and EUS in PDAC have similar efficacy but different predictive capacity in assessing mesenteric venous involvement depending on whether patients are resected upfront or received NAC. Both modalities appear to significantly overestimate true vascular involvement and should be interpreted in the appropriate clinical context. Copyright © 2018 International Hepato-Pancreato-Biliary Association Inc. Published by Elsevier Ltd. All rights reserved.

  20. Accurate load prediction by BEM with airfoil data from 3D RANS simulations

    NASA Astrophysics Data System (ADS)

    Schneider, Marc S.; Nitzsche, Jens; Hennings, Holger

    2016-09-01

    In this paper, two methods for the extraction of airfoil coefficients from 3D CFD simulations of a wind turbine rotor are investigated, and these coefficients are used to improve the load prediction of a BEM code. The coefficients are extracted from a number of steady RANS simulations, using either averaging of velocities in annular sections, or an inverse BEM approach for determination of the induction factors in the rotor plane. It is shown that these 3D rotor polars are able to capture the rotational augmentation at the inner part of the blade as well as the load reduction by 3D effects close to the blade tip. They are used as input to a simple BEM code and the results of this BEM with 3D rotor polars are compared to the predictions of BEM with 2D airfoil coefficients plus common empirical corrections for stall delay and tip loss. While BEM with 2D airfoil coefficients produces a very different radial distribution of loads than the RANS simulation, the BEM with 3D rotor polars manages to reproduce the loads from RANS very accurately for a variety of load cases, as long as the blade pitch angle is not too different from the cases from which the polars were extracted.

  1. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

    PubMed Central

    Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

    2015-01-01

    Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575

  2. Personal, Family, and Social Functioning among Older Couples Concordant and Discordant for High-Risk Alcohol Consumption

    PubMed Central

    Moos, Rudolf H.; Schutte, Kathleen K.; Brennan, Penny L.; Moos, Bernice S.

    2010-01-01

    Aims This study compares the personal, family, and social functioning of older husbands and wives concordant or discordant for high-risk alcohol consumption and identifies predictors of changes in concordance and high-risk consumption. Design, Participants, Measurements Three groups of couples were identified at baseline and followed 10 years later: (1) concordant couples in which husbands and wives engaged in low-risk alcohol consumption (N = 54), (2) concordant couples in which husbands and wives engaged in high-risk alcohol consumption (N = 38), and (3) discordant couples in which one partner engaged in high-risk alcohol consumption and the other partner did not (N = 75). At each follow-up, husbands and wives completed an inventory that assessed their personal, family, and social functioning. Findings Compared to the low-risk concordant group, husbands and wives in the high-risk concordant group were more likely to rely on tension-reduction coping, reported more friend approval of drinking, and were less involved in religious activities; however, they did not differ in the quality of the spousal relationship. The frequency of alcohol consumption declined among husbands in discordant couples, but not among husbands in concordant couples. Predictors of high-risk drinking included tension-reduction coping, friend approval of drinking, and, for husbands, their wives’ level of drinking. Conclusions High-risk and discordant alcohol consumption do not seem to be linked to decrements in family functioning among older couples in long-term stable marriages. The predictors of heavy alcohol consumption among older husbands and wives identify points of intervention that may help to reduce their high-risk drinking. PMID:20883458

  3. Personal, family and social functioning among older couples concordant and discordant for high-risk alcohol consumption.

    PubMed

    Moos, Rudolf H; Schutte, Kathleen K; Brennan, Penny L; Moos, Bernice S

    2011-02-01

    This study compares the personal, family and social functioning of older husbands and wives concordant or discordant for high-risk alcohol consumption and identifies predictors of changes in concordance and high-risk consumption. Three groups of couples were identified at baseline and followed 10 years later: (i) concordant couples in which husbands and wives engaged in low-risk alcohol consumption (n = 54); (ii) concordant couples in which husbands and wives engaged in high-risk alcohol consumption (n = 38); and (iii) discordant couples in which one partner engaged in high-risk alcohol consumption and the other partner did not (n = 75). At each follow-up, husbands and wives completed an inventory that assessed their personal, family and social functioning. Compared to the low-risk concordant group, husbands and wives in the high-risk concordant group were more likely to rely on tension-reduction coping, reported more friend approval of drinking, and were less involved in religious activities; however, they did not differ in the quality of the spousal relationship. The frequency of alcohol consumption declined among husbands in discordant couples, but not among husbands in concordant couples. Predictors of high-risk drinking included tension-reduction coping, friend approval of drinking and, for husbands, their wives' level of drinking. High-risk and discordant alcohol consumption do not seem to be linked to decrements in family functioning among older couples in long-term stable marriages. The predictors of heavy alcohol consumption among older husbands and wives identify points of intervention that may help to reduce their high-risk drinking. © 2010 Society for the Study of Addiction. No claim to US government works.

  4. Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles.

    PubMed

    Zou, Lingyun; Nan, Chonghan; Hu, Fuquan

    2013-12-15

    Various human pathogens secret effector proteins into hosts cells via the type IV secretion system (T4SS). These proteins play important roles in the interaction between bacteria and hosts. Computational methods for T4SS effector prediction have been developed for screening experimental targets in several isolated bacterial species; however, widely applicable prediction approaches are still unavailable In this work, four types of distinctive features, namely, amino acid composition, dipeptide composition, .position-specific scoring matrix composition and auto covariance transformation of position-specific scoring matrix, were calculated from primary sequences. A classifier, T4EffPred, was developed using the support vector machine with these features and their different combinations for effector prediction. Various theoretical tests were performed in a newly established dataset, and the results were measured with four indexes. We demonstrated that T4EffPred can discriminate IVA and IVB effectors in benchmark datasets with positive rates of 76.7% and 89.7%, respectively. The overall accuracy of 95.9% shows that the present method is accurate for distinguishing the T4SS effector in unidentified sequences. A classifier ensemble was designed to synthesize all single classifiers. Notable performance improvement was observed using this ensemble system in benchmark tests. To demonstrate the model's application, a genome-scale prediction of effectors was performed in Bartonella henselae, an important zoonotic pathogen. A number of putative candidates were distinguished. A web server implementing the prediction method and the source code are both available at http://bioinfo.tmmu.edu.cn/T4EffPred.

  5. The American College of Surgeons National Surgical Quality Improvement Program Surgical Risk Calculator Does Not Accurately Predict Risk of 30-Day Complications Among Patients Undergoing Microvascular Head and Neck Reconstruction.

    PubMed

    Arce, Kevin; Moore, Eric J; Lohse, Christine M; Reiland, Matthew D; Yetzer, Jacob G; Ettinger, Kyle S

    2016-09-01

    The American College of Surgeons (ACS) National Surgical Quality Improvement Program (NSQIP) Surgical Risk Calculator (SRC) is a novel universal risk calculator designed to aid in risk stratification of patients undergoing various types of major surgery. The purpose of this study was to assess the validity of the ACS NSQIP SRC in predicting postoperative complications in patients undergoing microvascular head and neck reconstruction. A retrospective cohort study of patients undergoing head and neck microvascular reconstruction with fibular free flaps at a single institution was completed. The NSQIP SRC was used to compute complication risk estimates and length of stay (LOS) estimates for all patients under study. Associations between complication risk estimates generated by the SRC and actual rates of observed complications were evaluated using logistic regression models. Logistic regression models also were used to evaluate the SRC estimates for LOS duration compared with the actual observed LOS after surgery. Of 153 patients under study, 46 (30%) developed a postoperative complication corresponding to those defined by NSQIP SRC. Thirty-eight patients (25%) developed a postoperative complication categorized as severe in the parameters of the NSQIP SRC. None of the SRC complication estimates showed a statistically relevant association with the corresponding observed rates of complications. The mean LOS predicted by the SRC was 8.0 days (median, 7.5 days; interquartile range [IQR], 6.5 to 9; range, 5.0 to 18.5 days). The mean observed LOS for the study group was 9.6 days (median, 7.0 days; IQR, 6 to 9; range, 5 to 67 days). Lin's (Biometrics 45:255, 1989) concordance correlation coefficient to measure agreement between observed and predicted LOS was 0.10, indicating only slight agreement between the 2 values. The ACS NSQIP SRC is not a useful risk-stratifying metric for patients undergoing major head and neck reconstruction with microvascular fibular free

  6. Towards accurate cosmological predictions for rapidly oscillating scalar fields as dark matter

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

    Ureña-López, L. Arturo; Gonzalez-Morales, Alma X., E-mail: lurena@ugto.mx, E-mail: alma.gonzalez@fisica.ugto.mx

    2016-07-01

    As we are entering the era of precision cosmology, it is necessary to count on accurate cosmological predictions from any proposed model of dark matter. In this paper we present a novel approach to the cosmological evolution of scalar fields that eases their analytic and numerical analysis at the background and at the linear order of perturbations. The new method makes use of appropriate angular variables that simplify the writing of the equations of motion, and which also show that the usual field variables play a secondary role in the cosmological dynamics. We apply the method to a scalar fieldmore » endowed with a quadratic potential and revisit its properties as dark matter. Some of the results known in the literature are recovered, and a better understanding of the physical properties of the model is provided. It is confirmed that there exists a Jeans wavenumber k {sub J} , directly related to the suppression of linear perturbations at wavenumbers k > k {sub J} , and which is verified to be k {sub J} = a √ mH . We also discuss some semi-analytical results that are well satisfied by the full numerical solutions obtained from an amended version of the CMB code CLASS. Finally we draw some of the implications that this new treatment of the equations of motion may have in the prediction of cosmological observables from scalar field dark matter models.« less

  7. Patient factors associated with guideline-concordant treatment of anxiety and depression in primary care.

    PubMed

    Prins, Marijn A; Verhaak, Peter F M; Smolders, Mirrian; Laurant, Miranda G H; van der Meer, Klaas; Spreeuwenberg, Peter; van Marwijk, Harm W J; Penninx, Brenda W J H; Bensing, Jozien M

    2010-07-01

    To identify associations of patient characteristics (predisposing, enabling and need factors) with guideline-concordant care for anxiety and depression in primary care. Analysis of data from the Netherlands Study of Depression and Anxiety (NESDA). Seven hundred and twenty-one patients with a current anxiety or depressive disorder, recruited from 67 general practitioners (GPs), were included. Diagnoses according to the Diagnostic and Statistic Manual of Mental Disorders, fourth edition (DSM-IV) were made using a structured and widely validated assessment. Socio-demographic and enabling characteristics, severity of symptoms, disability, (under treatment for) chronic somatic conditions, perceived need for care, beliefs and evaluations of care were measured by questionnaires. Actual care data were derived from electronic medical records. Criteria for guideline-concordant care were based on general practice guidelines, issued by the Dutch College of General Practitioners. Two hundred and eighty-one (39%) patients received guideline-concordant care. High education level, accessibility of care, comorbidity of anxiety and depression, and severity and disability scores were positively associated with receiving guideline-concordant care in univariate analyses. In multivariate multi-level logistic regression models, significant associations with the clinical need factors disappeared. Positive evaluations of accessibility of care increased the chance (OR = 1.31; 95%-CI = 1.05-1.65; p = 0.02) of receiving guideline-concordant care, as well as perceiving any need for medication (OR = 2.99; 95%-CI = 1.84-4.85; p < 0.001), counseling (OR = 2.25; 95%-CI = 1.29-3.95; p = 0.005) or a referral (OR = 1.83; 95%-CI = 1.09-3.09; p = 0.02). A low educational level decreased the odds (OR = 0.33; 95%-CI = 0.11-0.98; p = 0.04) of receiving guideline-concordant care. This study shows that education level, accessibility of care and patients' perceived needs for care are more strongly associated

  8. Assessing Risk Prediction Models Using Individual Participant Data From Multiple Studies

    PubMed Central

    Pennells, Lisa; Kaptoge, Stephen; White, Ian R.; Thompson, Simon G.; Wood, Angela M.; Tipping, Robert W.; Folsom, Aaron R.; Couper, David J.; Ballantyne, Christie M.; Coresh, Josef; Goya Wannamethee, S.; Morris, Richard W.; Kiechl, Stefan; Willeit, Johann; Willeit, Peter; Schett, Georg; Ebrahim, Shah; Lawlor, Debbie A.; Yarnell, John W.; Gallacher, John; Cushman, Mary; Psaty, Bruce M.; Tracy, Russ; Tybjærg-Hansen, Anne; Price, Jackie F.; Lee, Amanda J.; McLachlan, Stela; Khaw, Kay-Tee; Wareham, Nicholas J.; Brenner, Hermann; Schöttker, Ben; Müller, Heiko; Jansson, Jan-Håkan; Wennberg, Patrik; Salomaa, Veikko; Harald, Kennet; Jousilahti, Pekka; Vartiainen, Erkki; Woodward, Mark; D'Agostino, Ralph B.; Bladbjerg, Else-Marie; Jørgensen, Torben; Kiyohara, Yutaka; Arima, Hisatomi; Doi, Yasufumi; Ninomiya, Toshiharu; Dekker, Jacqueline M.; Nijpels, Giel; Stehouwer, Coen D. A.; Kauhanen, Jussi; Salonen, Jukka T.; Meade, Tom W.; Cooper, Jackie A.; Cushman, Mary; Folsom, Aaron R.; Psaty, Bruce M.; Shea, Steven; Döring, Angela; Kuller, Lewis H.; Grandits, Greg; Gillum, Richard F.; Mussolino, Michael; Rimm, Eric B.; Hankinson, Sue E.; Manson, JoAnn E.; Pai, Jennifer K.; Kirkland, Susan; Shaffer, Jonathan A.; Shimbo, Daichi; Bakker, Stephan J. L.; Gansevoort, Ron T.; Hillege, Hans L.; Amouyel, Philippe; Arveiler, Dominique; Evans, Alun; Ferrières, Jean; Sattar, Naveed; Westendorp, Rudi G.; Buckley, Brendan M.; Cantin, Bernard; Lamarche, Benoît; Barrett-Connor, Elizabeth; Wingard, Deborah L.; Bettencourt, Richele; Gudnason, Vilmundur; Aspelund, Thor; Sigurdsson, Gunnar; Thorsson, Bolli; Kavousi, Maryam; Witteman, Jacqueline C.; Hofman, Albert; Franco, Oscar H.; Howard, Barbara V.; Zhang, Ying; Best, Lyle; Umans, Jason G.; Onat, Altan; Sundström, Johan; Michael Gaziano, J.; Stampfer, Meir; Ridker, Paul M.; Michael Gaziano, J.; Ridker, Paul M.; Marmot, Michael; Clarke, Robert; Collins, Rory; Fletcher, Astrid; Brunner, Eric; Shipley, Martin; Kivimäki, Mika; Ridker, Paul M.; Buring, Julie; Cook, Nancy; Ford, Ian; Shepherd, James; Cobbe, Stuart M.; Robertson, Michele; Walker, Matthew; Watson, Sarah; Alexander, Myriam; Butterworth, Adam S.; Angelantonio, Emanuele Di; Gao, Pei; Haycock, Philip; Kaptoge, Stephen; Pennells, Lisa; Thompson, Simon G.; Walker, Matthew; Watson, Sarah; White, Ian R.; Wood, Angela M.; Wormser, David; Danesh, John

    2014-01-01

    Individual participant time-to-event data from multiple prospective epidemiologic studies enable detailed investigation into the predictive ability of risk models. Here we address the challenges in appropriately combining such information across studies. Methods are exemplified by analyses of log C-reactive protein and conventional risk factors for coronary heart disease in the Emerging Risk Factors Collaboration, a collation of individual data from multiple prospective studies with an average follow-up duration of 9.8 years (dates varied). We derive risk prediction models using Cox proportional hazards regression analysis stratified by study and obtain estimates of risk discrimination, Harrell's concordance index, and Royston's discrimination measure within each study; we then combine the estimates across studies using a weighted meta-analysis. Various weighting approaches are compared and lead us to recommend using the number of events in each study. We also discuss the calculation of measures of reclassification for multiple studies. We further show that comparison of differences in predictive ability across subgroups should be based only on within-study information and that combining measures of risk discrimination from case-control studies and prospective studies is problematic. The concordance index and discrimination measure gave qualitatively similar results throughout. While the concordance index was very heterogeneous between studies, principally because of differing age ranges, the increments in the concordance index from adding log C-reactive protein to conventional risk factors were more homogeneous. PMID:24366051

  9. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    PubMed Central

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-01-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally—a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process. PMID:26887592

  10. A New Weighted Injury Severity Scoring System: Better Predictive Power for Pediatric Trauma Mortality.

    PubMed

    Shi, Junxin; Shen, Jiabin; Caupp, Sarah; Wang, Angela; Nuss, Kathryn E; Kenney, Brian; Wheeler, Krista K; Lu, Bo; Xiang, Henry

    2018-05-02

    An accurate injury severity measurement is essential for the evaluation of pediatric trauma care and outcome research. The traditional Injury Severity Score (ISS) does not consider the differential risks of the Abbreviated Injury Scale (AIS) from different body regions nor is it pediatric specific. The objective of this study was to develop a weighted injury severity scoring (wISS) system for pediatric blunt trauma patients with better predictive power than ISS. Based on the association between mortality and AIS from each of the six ISS body regions, we generated different weights for the component AIS scores used in the calculation of ISS. The weights and wISS were generated using the National Trauma Data Bank (NTDB). The Nationwide Emergency Department Sample (NEDS) was used to validate our main results. Pediatric blunt trauma patients less than 16 years were included, and mortality was the outcome. Discrimination (areas under the receiver operating characteristic curve, sensitivity, specificity, positive predictive value, negative predictive value, concordance) and calibration (Hosmer-Lemeshow statistic) were compared between the wISS and ISS. The areas under the receiver operating characteristic curves from the wISS and ISS are 0.88 vs. 0.86 in ISS=1-74 and 0.77 vs. 0.64 in ISS=25-74 (p<0.0001). The wISS showed higher specificity, positive predictive value, negative predictive value, and concordance when they were compared at similar levels of sensitivity. The wISS had better calibration (smaller Hosmer-Lemeshow statistic) than the ISS (11.6 versus 19.7 for ISS=1-74 and 10.9 versus 12.6 for ISS= 25-74). The wISS showed even better discrimination with the NEDS. By weighting the AIS from different body regions, the wISS had significantly better predictive power for mortality than the ISS, especially in critically injured children.Level of Evidence and study typeLevel IV Prognostic/Epidemiological.

  11. Radiology Reports With Hyperlinks Improve Target Lesion Selection and Measurement Concordance in Cancer Trials.

    PubMed

    Machado, Laura B; Apolo, Andrea B; Steinberg, Seth M; Folio, Les R

    2017-02-01

    Radiology reports often lack the measurements of target lesions that are needed for oncology clinical trials. When available, the measurements in the radiology reports often do not match those in the records used to calculate therapeutic response. This study assessed the clinical value of hyperlinked tumor measurements in multimedia-enhanced radiology reports in the PACS and the inclusion of a radiologist assistant in the process of assessing tumor burden. We assessed 489 target lesions in 232 CT examinations of 71 patients with metastatic genitourinary cancer enrolled in two therapeutic trials. We analyzed target lesion selection and measurement concordance between oncology records (used to calculate therapeutic response) and two types of radiology reports in the PACS: multimedia-enhanced radiology reports and text-only reports. For statistical tests, we used the Wilcoxon signed rank, Wilcoxon rank sum test, and Fisher method to combine p values from the paired and unpaired results. The Fisher exact test was used to compare overall measurement concordance. Concordance on target lesion selection was greater for multimedia-enhanced radiology reports (78%) than the text-only reports (52%) (p = 0.0050). There was also improved overall measurement concordance with the multimedia-enhanced radiology reports (68%) compared with the text-only reports (38%) (p < 0.0001). Compared with text-only reports, hyperlinked multimedia-enhanced radiology reports improved concordance of target lesion selection and measurement with the measurements used to calculate therapeutic response.

  12. Concordance analysis of paired cancer antigen (CA) 15-3 and 27.29 testing.

    PubMed

    Lin, David C; Genzen, Jonathan R

    2018-01-01

    Cancer antigens (CA) 15-3 and 27.29 are used in the clinical management of many breast cancer patients. Given that immunoassays for CA 15-3 and CA 27.29 target epitopes on the same glycoprotein-Mucin 1 (MUC1)-the present analysis was conducted to evaluate the potential concordance of tumor marker results when both tests were ordered by providers on the same specimens. A retrospective limited dataset of paired CA 15-3 (Roche Diagnostics) and CA 27.29 (Siemens Diagnostics) test results was obtained from a national clinical reference laboratory. Concordance according to reference interval (RI) status and percent (%) change between consecutive test results was analyzed. 37,652 paired results from 12,470 distinct patients were obtained. The correlation between CA 15-3 and CA 27.29 results was high (correlation coefficient: Pearson, 0.967), although across the dataset a significant difference between CA 15-3 and CA 27.29 results was observed (P < 0.05). RI concordance between CA 15-3 and CA 27.29 results was observed in 93.7% of pairs (35,280 of 37,652). Correlation was also observed in the % change of CA 15-3 and CA 27.29 results between consecutive specimens for individual patients. Using doubling or halving thresholds (i.e., 100% increase or 50% decrease), concordance in % change was observed between CA 15-3 and CA 27.29 in approximately 90% of cases. Individual patient results trended similarly across both markers over time. While generally concordant, CA 15-3 and CA 27.29 results should not be used interchangeably. The present report provides no evidence for added value in performing both tests routinely for individual patients.

  13. The concordance between self-reported medication use and pharmacy records in pregnant women.

    PubMed

    Cheung, K; El Marroun, H; Elfrink, M E; Jaddoe, V W V; Visser, L E; Stricker, B H Ch

    2017-09-01

    Several studies have been conducted to assess determinants affecting the performance or accuracy of self-reports. These studies are often not focused on pregnant women, or medical records were used as a data source where it is unclear if medications have been dispensed. Therefore, our objective was to evaluate the concordance between self-reported medication data and pharmacy records among pregnant women and its determinants. We conducted a population-based cohort study within the Generation R study, in 2637 pregnant women. The concordance between self-reported medication data and pharmacy records was calculated for different therapeutic classes using Yule's Y. We evaluated a number of variables as determinant of discordance between both sources through univariate and multivariate logistic regression analysis. The concordance between self-reports and pharmacy records was moderate to good for medications used for chronic conditions, such as selective serotonin reuptake inhibitors or anti-asthmatic medications (0.88 and 0.68, respectively). Medications that are used occasionally, such as antibiotics, had a lower concordance (0.51). Women with a Turkish or other non-Western background were more likely to demonstrate discordance between pharmacy records and self-reported data compared with women with a Dutch background (Turkish: odds ratio, 1.63; 95% confidence interval, 1.16-2.29; other non-Western: odds ratio, 1.33; 95% confidence interval, 1.03-1.71). Further research is needed to assess how the cultural or ethnic differences may affect the concordance or discordance between both medication sources. The results of this study showed that the use of multiple sources is needed to have a good estimation of the medication use during pregnancy. Copyright © 2017 John Wiley & Sons, Ltd.

  14. Concordance of Mother-Daughter Diurnal Cortisol Production: Understanding the Intergenerational Transmission of Risk for Depression

    PubMed Central

    LeMoult, Joelle; Chen, Michael C.; Foland-Ross, Lara C.; Burley, Hannah W.; Gotlib, Ian H.

    2015-01-01

    A growing body of research is demonstrating concordance between mother and child diurnal cortisol production. In the context of maternal history of depression, intergenerational concordance of cortisol production could contribute to hypercortisolemia in children of depressed mothers, which has been shown to increase risk for MDD. The current study is the first to examine concordance in diurnal cortisol production between mothers with a history of depression and their never-depressed, but high-risk, children. We collected salivary cortisol across two days from mothers with (remitted; RMD) and without (CTL) a history of recurrent episodes of depression and their never-depressed daughters. As expected, RMD mothers and their daughters both exhibited higher cortisol production than did their CTL counterparts. Moreover, both across and within groups, mothers’ and daughters’ cortisol production was directly coupled. These findings suggest that there is an intergenerational concordance in cortisol dysregulation that may contribute to hypercortisolemia in girls at familial risk for depression. PMID:25862380

  15. Concordance of mother-daughter diurnal cortisol production: Understanding the intergenerational transmission of risk for depression.

    PubMed

    LeMoult, Joelle; Chen, Michael C; Foland-Ross, Lara C; Burley, Hannah W; Gotlib, Ian H

    2015-05-01

    A growing body of research is demonstrating concordance between mother and child diurnal cortisol production. In the context of maternal history of depression, intergenerational concordance of cortisol production could contribute to hypercortisolemia in children of depressed mothers, which has been shown to increase risk for MDD. The current study is the first to examine concordance in diurnal cortisol production between mothers with a history of depression and their never-depressed, but high-risk, children. We collected salivary cortisol across 2 days from mothers with (remitted; RMD) and without (CTL) a history of recurrent episodes of depression and their never-depressed daughters. As expected, RMD mothers and their daughters both exhibited higher cortisol production than did their CTL counterparts. Moreover, both across and within groups, mothers' and daughters' cortisol production were directly coupled. These findings suggest that there is an intergenerational concordance in cortisol dysregulation that may contribute to hypercortisolemia in girls at familial risk for depression. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. A gene expression biomarker accurately predicts estrogen ...

    EPA Pesticide Factsheets

    The EPA’s vision for the Endocrine Disruptor Screening Program (EDSP) in the 21st Century (EDSP21) includes utilization of high-throughput screening (HTS) assays coupled with computational modeling to prioritize chemicals with the goal of eventually replacing current Tier 1 screening tests. The ToxCast program currently includes 18 HTS in vitro assays that evaluate the ability of chemicals to modulate estrogen receptor α (ERα), an important endocrine target. We propose microarray-based gene expression profiling as a complementary approach to predict ERα modulation and have developed computational methods to identify ERα modulators in an existing database of whole-genome microarray data. The ERα biomarker consisted of 46 ERα-regulated genes with consistent expression patterns across 7 known ER agonists and 3 known ER antagonists. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression data sets from experiments in MCF-7 cells. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% or 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) OECD ER reference chemicals including “very weak” agonists and replicated predictions based on 18 in vitro ER-associated HTS assays. For 114 chemicals present in both the HTS data and the MCF-7 c

  17. Particulate Matter Resuspension in Mississippi Bight Evaluated with CONCORDE's Synthesis Model

    NASA Astrophysics Data System (ADS)

    O'Brien, S. J.; Quas, L. M.; Miles, T. N.; Pan, C.; Cambazoglu, M. K.; Soto Ramos, I. M.; Greer, A. T.; Church, I.; Wiggert, J. D.

    2017-12-01

    The CONsortium for oil spill exposure pathways in COastal River-Dominated Ecosystems (CONCORDE) was established to investigate the complex fine-scale biological, chemical and physical interactions in a marine system controlled by pulsed-river plume dynamics. During CONCORDE's spring 2016 field campaign, the In Situ Ichthyoplankton Imaging System (ISIIS) on the R/V Point Sur and the Scanfish on the R/V Pelican comprehensively characterized the physical and biological structure in the region. Increased suspended particulate matter was observed by the ISIIS, with concentrations at depth sufficient to completely occlude the in situ images of planktonic organisms. Data was also collected on the continental shelf during the spring cruise by the RU31 glider in the proximity of the Mississippi River Delta, east of the ISIIS / Scanfish transects. Backscatter and salinity observed by the Scanfish and glider showed elevated suspended particulate matter and increased salinity, suggesting a linkage to shoreward advection from the continental shelf of oceanic waters that are sufficiently energetic to drive sediment resuspension. As part of the CONCORDE research effort, a four-dimensional biogeochemical/lower trophic level synthesis model for Mississippi Sound and Bight has been developed, based on the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System. This study utilizes CONCORDE's synthesis model to investigate the physical forcing mechanisms affecting the increased suspended particulate matter concentration observed in the Mississippi Bight during spring 2016, and advection pathways between estuarine and shelf waters in the northern Gulf of Mexico. The results show that episodic, advection-driven resuspension is a critical aspect controlling suspended sediment distributions in Mississippi Bight, which has implications for observed spatio-temporal patterns of planktonic species.

  18. Is There Concordance in Attitudes and Beliefs between Parents and Scientists about Autism Spectrum Disorder?

    ERIC Educational Resources Information Center

    Fischbach, Ruth L.; Harris, Mark J.; Ballan, Michelle S.; Fischbach, Gerald D.; Link, Bruce G.

    2016-01-01

    There is no reported investigation comparing concordance in attitudes and beliefs about autism spectrum disorder between parents of children with autism spectrum disorder and scientists who research autism spectrum disorder. To investigate the level of concordance between these groups on causes of autism, priorities of research, perceived stigma,…

  19. The proposed 'concordance-statistic for benefit' provided a useful metric when modeling heterogeneous treatment effects.

    PubMed

    van Klaveren, David; Steyerberg, Ewout W; Serruys, Patrick W; Kent, David M

    2018-02-01

    Clinical prediction models that support treatment decisions are usually evaluated for their ability to predict the risk of an outcome rather than treatment benefit-the difference between outcome risk with vs. without therapy. We aimed to define performance metrics for a model's ability to predict treatment benefit. We analyzed data of the Synergy between Percutaneous Coronary Intervention with Taxus and Cardiac Surgery (SYNTAX) trial and of three recombinant tissue plasminogen activator trials. We assessed alternative prediction models with a conventional risk concordance-statistic (c-statistic) and a novel c-statistic for benefit. We defined observed treatment benefit by the outcomes in pairs of patients matched on predicted benefit but discordant for treatment assignment. The 'c-for-benefit' represents the probability that from two randomly chosen matched patient pairs with unequal observed benefit, the pair with greater observed benefit also has a higher predicted benefit. Compared to a model without treatment interactions, the SYNTAX score II had improved ability to discriminate treatment benefit (c-for-benefit 0.590 vs. 0.552), despite having similar risk discrimination (c-statistic 0.725 vs. 0.719). However, for the simplified stroke-thrombolytic predictive instrument (TPI) vs. the original stroke-TPI, the c-for-benefit (0.584 vs. 0.578) was similar. The proposed methodology has the potential to measure a model's ability to predict treatment benefit not captured with conventional performance metrics. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides.

    PubMed

    Islam, S M Ashiqul; Sajed, Tanvir; Kearney, Christopher Michel; Baker, Erich J

    2015-07-05

    Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides includes a tri-disulfide domain arrangement that offers toxicity and high stability. Sequential tri-disulfide connectivity variants create highly compact disulfide folds capable of withstanding a variety of environmental stresses. Their combination of toxicity and stability make these peptides remarkably valuable for their potential as bio-insecticides, antimicrobial peptides and peptide drug candidates. However, the wide sequence variation, sources and modalities of group members impose serious limitations on our ability to rapidly identify potential members. As a result, there is a need for automated high-throughput member classification approaches that leverage their demonstrated tertiary and functional homology. We developed an SVM-based model to predict sequential tri-disulfide peptide (STP) toxins from peptide sequences. One optimized model, called PredSTP, predicted STPs from training set with sensitivity, specificity, precision, accuracy and a Matthews correlation coefficient of 94.86%, 94.11%, 84.31%, 94.30% and 0.86, respectively, using 200 fold cross validation. The same model outperforms existing prediction approaches in three independent out of sample testsets derived from PDB. PredSTP can accurately identify a wide range of cystine stabilized peptide toxins directly from sequences in a species-agnostic fashion. The ability to rapidly filter sequences for potential bioactive peptides can greatly compress the time between peptide identification and testing structural and functional properties for possible antimicrobial and insecticidal candidates. A web interface is freely available to predict STP toxins from http://crick.ecs.baylor.edu/.

  1. Occupation and industry on death certificates of long-term chemical workers: concordance with work history records.

    PubMed

    Olsen, G W; Brondum, J; Bodner, K M; Kravat, B A; Mandel, J S; Mandel, J H; Bond, G G

    1990-01-01

    This study evaluated the concordance between occupation and industry listed on death certificates with actual work history information for a group (n = 5,882) of long-term (10 years or more) workers at a chemical company. Match rates were calculated as the percent of death certificate occupation and company entries that were confirmed by work history data using 3-digit 1980 U.S. Census Bureau group codes. The concordance rate for industry differed by employment status at death: employed, 94.9%; inactive, 30.8%; and retired, 91.1%. Concordance on occupation was analyzed for employed (n = 467) and retired (n = 932) subjects who had computerized work histories (randomly done prior to the study) and who had matched on the company on the death certificate. Concordance ranged from 0 to 50% for the first job, to 50 to 70% for the last job, longest job, and longest job in the last 10 years of company employment. The most consistent predictor of concordance was job duration. Misclassification was reviewed by occupational category. Results from this and other investigations lead to the inevitable conclusion that usual occupation data from death certificates are grossly inadequate for studies of occupational risks.

  2. Achieving Goal-Concordant Care: A Conceptual Model and Approach to Measuring Serious Illness Communication and Its Impact

    PubMed Central

    Curtis, J. Randall; Tulsky, James A.

    2018-01-01

    Abstract Background: High-quality care for seriously ill patients aligns treatment with their goals and values. Failure to achieve “goal-concordant” care is a medical error that can harm patients and families. Because communication between clinicians and patients enables goal concordance and also affects the illness experience in its own right, healthcare systems should endeavor to measure communication and its outcomes as a quality assessment. Yet, little consensus exists on what should be measured and by which methods. Objectives: To propose measurement priorities for serious illness communication and its anticipated outcomes, including goal-concordant care. Methods: We completed a narrative review of the literature to identify links between serious illness communication, goal-concordant care, and other outcomes. We used this review to identify gaps and opportunities for quality measurement in serious illness communication. Results: Our conceptual model describes the relationship between communication, goal-concordant care, and other relevant outcomes. Implementation-ready measures to assess the quality of serious illness communication and care include (1) the timing and setting of serious illness communication, (2) patient experience of communication and care, and (3) caregiver bereavement surveys that include assessment of perceived goal concordance of care. Future measurement priorities include direct assessment of communication quality, prospective patient or family assessment of care concordance with goals, and assessment of the bereaved caregiver experience. Conclusion: Improving serious illness care necessitates ensuring that high-quality communication has occurred and measuring its impact. Measuring patient experience and receipt of goal-concordant care should be our highest priority. We have the tools to measure both. PMID:29091522

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

    PubMed

    Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

  4. Medication discrepancy: a concordance problem between dialysis patients and caregivers.

    PubMed

    Lindberg, Magnus; Lindberg, Per; Wikström, Björn

    2007-01-01

    Extensive drug utilization, and non-concordance between the patient and the caregiver about prescriptions and actual medicine intake, are associated with the risk of non-adherence to medication as well as medication-related illness. To achieve reliable estimates of drug use, it is important to consider the patient's self-reported drug utilization as well as to consult his/her medical record. The present multicentre study was conducted with the aim of examining the self-reported drug consumption of dialysis patients and its congruence with medical records. Consumption of pharmaceutical agents was recorded by 204 patients undergoing haemo- or peritoneal dialysis at 10 Swedish clinics. Drug record discrepancies were identified by comparing the self-reported use of prescribed medicines with the subsequently obtained medication lists. The median drug intake was 11 prescribed medicines and by including on-demand drugs this increased to 12. Discrepancies between the self-reported use of prescribed drugs and the medical record were prevalent in 80.4% of cases, with a median of three discrepancies per patient. Dialysis patients have an extensive need for medication but there is an undesirable deviation between consumption and prescription. A single medication list, accessible for the patient and for all prescribers, is a possible solution to achieve concordance but other measures, such as analysis of the reasons for discrepancy and tailored measures, would also benefit concordant medicine-taking.

  5. Prediction of Individual Serum Infliximab Concentrations in Inflammatory Bowel Disease by a Bayesian Dashboard System.

    PubMed

    Eser, Alexander; Primas, Christian; Reinisch, Sieglinde; Vogelsang, Harald; Novacek, Gottfried; Mould, Diane R; Reinisch, Walter

    2018-01-30

    Despite a robust exposure-response relationship of infliximab in inflammatory bowel disease (IBD), attempts to adjust dosing to individually predicted serum concentrations of infliximab (SICs) are lacking. Compared with labor-intensive conventional software for pharmacokinetic (PK) modeling (eg, NONMEM) dashboards are easy-to-use programs incorporating complex Bayesian statistics to determine individual pharmacokinetics. We evaluated various infliximab detection assays and the number of samples needed to precisely forecast individual SICs using a Bayesian dashboard. We assessed long-term infliximab retention in patients being dosed concordantly versus discordantly with Bayesian dashboard recommendations. Three hundred eighty-two serum samples from 117 adult IBD patients on infliximab maintenance therapy were analyzed by 3 commercially available assays. Data from each assay was modeled using NONMEM and a Bayesian dashboard. PK parameter precision and residual variability were assessed. Forecast concentrations from both systems were compared with observed concentrations. Infliximab retention was assessed by prediction for dose intensification via Bayesian dashboard versus real-life practice. Forecast precision of SICs varied between detection assays. At least 3 SICs from a reliable assay are needed for an accurate forecast. The Bayesian dashboard performed similarly to NONMEM to predict SICs. Patients dosed concordantly with Bayesian dashboard recommendations had a significantly longer median drug survival than those dosed discordantly (51.5 versus 4.6 months, P < .0001). The Bayesian dashboard helps to assess the diagnostic performance of infliximab detection assays. Three, not single, SICs provide sufficient information for individualized dose adjustment when incorporated into the Bayesian dashboard. Treatment adjusted to forecasted SICs is associated with longer drug retention of infliximab. © 2018, The American College of Clinical Pharmacology.

  6. Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease.

    PubMed

    Owen, Joseph R; Noyes, Noelle; Young, Amy E; Prince, Daniel J; Blanchard, Patricia C; Lehenbauer, Terry W; Aly, Sharif S; Davis, Jessica H; O'Rourke, Sean M; Abdo, Zaid; Belk, Keith; Miller, Michael R; Morley, Paul; Van Eenennaam, Alison L

    2017-09-07

    Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease-associated bacterial isolates ( Histophilus somni , Mycoplasma bovis , Mannheimia haemolytica , and Pasteurella multocida ) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni , M. haemolytica , and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% ( P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease

  7. Concordance between the quality of maternal and paternal parenting behavior within couples.

    PubMed

    Deschênes, Marie; Bernier, Annie; Jarry-Boileau, Véronique; St-Laurent, Diane

    2014-01-01

    There is compelling evidence that the quality of maternal and paternal parenting behavior bears critical importance for child development. Yet, less is known of the degree of similarity between maternal and paternal parenting behavior in families, and especially little is known about the factors that may explain variation in degrees of similarity. This article aims to examine (a) the concordance (similarity) between the quality of mothers' and fathers' interactive behavior with their child and (b) the sociodemographic determinants of this concordance. The sample included 74 families (mother, father, and their child). The quality of maternal and paternal interactive behavior was assessed independently, and rated with the Maternal Behavior Q-Sort (mother-infant, 12 months; D. R. Pederson et al., 1990) or the Mutually Responsive Orientation scale (father-toddler, 18 months; N. Aksan et al., 2006). The results indicated that the overall correlation between the quality of mothers' and fathers' behavior was moderate. The concordance was greater among higher socioeconomic status families or when interacting with a boy, but did not differ according to the presence or absence of siblings in the family.

  8. Development and validation of a nomogram predicting recurrence risk in women with symptomatic urinary tract infection.

    PubMed

    Cai, Tommaso; Mazzoli, Sandra; Migno, Serena; Malossini, Gianni; Lanzafame, Paolo; Mereu, Liliana; Tateo, Saverio; Wagenlehner, Florian M E; Pickard, Robert S; Bartoletti, Riccardo

    2014-09-01

    To develop and externally validate a novel nomogram predicting recurrence risk probability at 12 months in women after an episode of urinary tract infection. The study included 768 women from Santa Maria Annunziata Hospital, Florence, Italy, affected by urinary tract infections from January 2005 to December 2009. Another 373 women with the same criteria enrolled at Santa Chiara Hospital, Trento, Italy, from January 2010 to June 2012 were used to externally validate and calibrate the nomogram. Univariate and multivariate Cox regression models tested the relationship between urinary tract infection recurrence risk, and patient clinical and laboratory characteristics. The nomogram was evaluated by calculating concordance probabilities, as well as testing calibration of predicted urinary tract infection recurrence with observed urinary tract infections. Nomogram variables included: number of partners, bowel function, type of pathogens isolated (Gram-positive/negative), hormonal status, number of previous urinary tract infection recurrences and previous treatment of asymptomatic bacteriuria. Of the original development data, 261 out of 768 women presented at least one episode of recurrence of urinary tract infection (33.9%). The nomogram had a concordance index of 0.85. The nomogram predictions were well calibrated. This model showed high discrimination accuracy and favorable calibration characteristics. In the validation group (373 women), the overall c-index was 0.83 (P = 0.003, 95% confidence interval 0.51-0.99), whereas the area under the receiver operating characteristic curve was 0.85 (95% confidence interval 0.79-0.91). The present nomogram accurately predicts the recurrence risk of urinary tract infection at 12 months, and can assist in identifying women at high risk of symptomatic recurrence that can be suitable candidates for a prophylactic strategy. © 2014 The Japanese Urological Association.

  9. Accuracy of pre-operative hysteroscopic guided biopsy for predicting final pathology in uterine malignancies.

    PubMed

    Martinelli, Fabio; Ditto, Antonino; Bogani, Giorgio; Signorelli, Mauro; Chiappa, Valentina; Lorusso, Domenica; Haeusler, Edward; Raspagliesi, Francesco

    2017-07-01

    To evaluate concordance (C) between pre-operative hysteroscopic-directed sampling and final pathology in uterine cancers. A retrospective cross-sectional evaluation of prospectively collected data of women who underwent hysterectomy for uterine malignancies and a previous hysteroscopic-guided biopsy was performed. Diagnostic concordance between pre-operative (hysteroscopic biopsy) and postoperative (uterine specimen) histology was evaluated. In endometrioid-endometrial cancers cases Kappa (k) statistics was applied to evaluate agreement for grading (G) between the preoperative and final pathology. A total 101 hysterectomies for uterine malignancies were evaluated. There were 23 non-endometrioid cancers: 7 serous (C:5/7, 71.4%); 10 carcinosarcomas (C:7/10, 70%, remaining 3 cases only epithelial component diagnosed); 3 clear cell (C:3/3, 100%); 3 sarcomas (C:3/3, 100%). In 78 cases an endometrioid endometrial cancer was found. In 63 cases there was a histological C (63/78, 80.8%) between hysteroscopic-guided biopsy and final pathology, while in 15 cases (19.2%) only hyperplasia (with/without atypia) was found preoperatively. Overall accuracy to detect endometrial cancer was 80.2%. In 50 out of 63 endometrial cancers (79.4%) grading was concordant. The overall level of agreement between preoperative and postoperative grading was "substantial" according to Kappa (k) statistics (k 0.64; 95% CI: 0.449-0.83; p < 0.001), as well as for G1 (0.679; 95% CI: 0.432-0.926; p < 0.001) and G3 (0.774; 94% CI: 0.534-1; p < 0.001), while for G2 (0.531; 95% CI: 0.286-0.777; p < 0.001) it was moderate. In our series we found an 80% C between pre-operative hysteroscopic-guided biopsy and final pathology, in uterine malignancies. Moreover, hysteroscopic biopsy accurately predicted endometrial cancer in 80% of cases and "substantially" predicted histological grading. Hysteroscopic-guided uterine sampling could be a useful tool to tailor treatment in patients with uterine

  10. Accurate multimodal probabilistic prediction of conversion to Alzheimer's disease in patients with mild cognitive impairment.

    PubMed

    Young, Jonathan; Modat, Marc; Cardoso, Manuel J; Mendelson, Alex; Cash, Dave; Ourselin, Sebastien

    2013-01-01

    Accurately identifying the patients that have mild cognitive impairment (MCI) who will go on to develop Alzheimer's disease (AD) will become essential as new treatments will require identification of AD patients at earlier stages in the disease process. Most previous work in this area has centred around the same automated techniques used to diagnose AD patients from healthy controls, by coupling high dimensional brain image data or other relevant biomarker data to modern machine learning techniques. Such studies can now distinguish between AD patients and controls as accurately as an experienced clinician. Models trained on patients with AD and control subjects can also distinguish between MCI patients that will convert to AD within a given timeframe (MCI-c) and those that remain stable (MCI-s), although differences between these groups are smaller and thus, the corresponding accuracy is lower. The most common type of classifier used in these studies is the support vector machine, which gives categorical class decisions. In this paper, we introduce Gaussian process (GP) classification to the problem. This fully Bayesian method produces naturally probabilistic predictions, which we show correlate well with the actual chances of converting to AD within 3 years in a population of 96 MCI-s and 47 MCI-c subjects. Furthermore, we show that GPs can integrate multimodal data (in this study volumetric MRI, FDG-PET, cerebrospinal fluid, and APOE genotype with the classification process through the use of a mixed kernel). The GP approach aids combination of different data sources by learning parameters automatically from training data via type-II maximum likelihood, which we compare to a more conventional method based on cross validation and an SVM classifier. When the resulting probabilities from the GP are dichotomised to produce a binary classification, the results for predicting MCI conversion based on the combination of all three types of data show a balanced accuracy

  11. [Validity and concordance of electronic health records in primary care (AP-Madrid) for surveillance of diabetes mellitus. PREDIMERC study].

    PubMed

    Gil Montalbán, Elisa; Ortiz Marrón, Honorato; López-Gay Lucio-Villegas, Dulce; Zorrilla Torrás, Belén; Arrieta Blanco, Francisco; Nogales Aguado, Pedro

    2014-01-01

    To assess the validity and concordance of diabetes data in the electronic health records of primary care (Madrid-PC) by comparing with those from the PREDIMERC study. The sensitivity, specificity, positive predictive value, negative predictive value and kappa index of diabetes cases recorded in the health records of Madrid-PC were calculated by using data from PREDIMERC as the gold standard. The prevalence of diabetes was also determined according to each data source. The sensitivity of diabetes recorded in Madrid-PC was 74%, the specificity was 98.8%, the positive predictive value was 87.9%, the negative predictive value was 97.3%, and the kappa index was 0.78. The prevalence of diabetes recorded in Madrid-PC was 6.7% versus 8.1% by PREDIMERC, where known diabetes was 6.3%. The electronic health records of primary care are a valid source for epidemiological surveillance of diabetes in Madrid. Copyright © 2013 SESPAS. Published by Elsevier Espana. All rights reserved.

  12. Dyadic Concordance in Mother and Preschooler Resting Cardiovascular Function Varies by Risk Status

    PubMed Central

    Skowron, Elizabeth A.; Hughes, Brian M.; Howard, Siobhán; Loken, Eric

    2014-01-01

    This study examined concordance in heart rate (HR) and respiratory sinus arrhythmia (RSA) in a sample of 104 child-maltreating (CM) and nonCM mother–preschooler dyads (208 individuals). In a laboratory setting, mother and child cardiac physiology was simultaneously monitored via ECG in a 5-min resting period. Mothers ranged in age from 20 to 49 years; children ranged in age from 3 to 5 years. Significant within-dyad (WD) and between-dyad (BD) associations were observed for mother HR and both child HR and RSA, and the associations were moderated by CM status. Only CM dyads exhibited BD associations: Higher average maternal HR was associated with higher child HR and lower child RSA. By contrast, when the time interval was divided into 30 s epochs, nonCM dyads exhibited positive WD (dynamic) associations in mother and child HR, and both CM and nonCM dyads showed negative WD associations in mother HR and child RSA. Further, mothers’ mean HR levels moderated the extent of epoch-by-epoch WD concordance observed in mother and child, such that elevated average maternal HR was associated with lower levels of WD (dynamic) concordance. No BD or WD concordance in maternal and child RSA was observed. The findings suggest that measures of intraindividual variation provide useful, alternate perspectives in the study of dyadic processes in at-risk families. PMID:24022469

  13. Attitudes toward concordance and self-efficacy in decision making: a cross-sectional study on pharmacist–patient consultations

    PubMed Central

    Ng, Yew Keong; Shah, Noraida Mohamed; Loong, Ly Sia; Pee, Lay Ting; Hidzir, Sarina Anim M; Chong, Wei Wen

    2018-01-01

    Purpose This study investigated patients’ and pharmacists’ attitudes toward concordance in a pharmacist–patient consultation and how patients’ attitudes toward concordance relate to their involvement and self-efficacy in decision making associated with medication use. Subjects and methods A cross-sectional study was conducted among patients with chronic diseases and pharmacists from three public hospitals in Malaysia. The Revised United States Leeds Attitudes toward Concordance (RUS-LATCon) was used to measure attitudes toward concordance in both patients and pharmacists. Patients also rated their perceived level of involvement in decision making and completed the Decision Self-Efficacy scale. One-way analysis of variance (ANOVA) and independent t-test were used to determine significant differences between different subgroups on attitudes toward concordance, and multiple linear regression was performed to find the predictors of patients’ self-efficacy in decision making. Results A total of 389 patients and 93 pharmacists participated in the study. Pharmacists and patients scored M=3.92 (SD=0.37) and M=3.84 (SD=0.46) on the RUS-LATCon scale, respectively. Seven items were found to be significantly different between pharmacists and patients on the subscale level. Patients who felt fully involved in decision making (M=3.94, SD=0.462) scored significantly higher on attitudes toward concordance than those who felt partially involved (M=3.82, SD=0.478) and not involved at all (M=3.68, SD=0.471; p<0.001). Patients had an average score of 76.7% (SD=14.73%) on the Decision Self-Efficacy scale. In multiple linear regression analysis, ethnicity, number of medications taken by patients, patients’ perceived level of involvement, and attitudes toward concordance are significant predictors of patients’ self-efficacy in decision making (p<0.05). Conclusion Patients who felt involved in their consultations had more positive attitudes toward concordance and higher

  14. Attitudes toward concordance and self-efficacy in decision making: a cross-sectional study on pharmacist-patient consultations.

    PubMed

    Ng, Yew Keong; Shah, Noraida Mohamed; Loong, Ly Sia; Pee, Lay Ting; Hidzir, Sarina Anim M; Chong, Wei Wen

    2018-01-01

    This study investigated patients' and pharmacists' attitudes toward concordance in a pharmacist-patient consultation and how patients' attitudes toward concordance relate to their involvement and self-efficacy in decision making associated with medication use. A cross-sectional study was conducted among patients with chronic diseases and pharmacists from three public hospitals in Malaysia. The Revised United States Leeds Attitudes toward Concordance (RUS-LATCon) was used to measure attitudes toward concordance in both patients and pharmacists. Patients also rated their perceived level of involvement in decision making and completed the Decision Self-Efficacy scale. One-way analysis of variance (ANOVA) and independent t -test were used to determine significant differences between different subgroups on attitudes toward concordance, and multiple linear regression was performed to find the predictors of patients' self-efficacy in decision making. A total of 389 patients and 93 pharmacists participated in the study. Pharmacists and patients scored M=3.92 (SD=0.37) and M=3.84 (SD=0.46) on the RUS-LATCon scale, respectively. Seven items were found to be significantly different between pharmacists and patients on the subscale level. Patients who felt fully involved in decision making (M=3.94, SD=0.462) scored significantly higher on attitudes toward concordance than those who felt partially involved (M=3.82, SD=0.478) and not involved at all (M=3.68, SD=0.471; p <0.001). Patients had an average score of 76.7% (SD=14.73%) on the Decision Self-Efficacy scale. In multiple linear regression analysis, ethnicity, number of medications taken by patients, patients' perceived level of involvement, and attitudes toward concordance are significant predictors of patients' self-efficacy in decision making ( p <0.05). Patients who felt involved in their consultations had more positive attitudes toward concordance and higher confidence in making an informed decision. Further study is

  15. Brief report: parent-adolescent child concordance in social norms related to gender equity in marriage - findings from rural India.

    PubMed

    Raj, Anita; Ghule, Mohan; Battala, Madhusudana; Dasgupta, Anindita; Ritter, Julie; Nair, Saritha; Saggurti, Niranjan; Silverman, Jay G; Balaiah, Donta

    2014-10-01

    The purpose of this exploratory study was to assess parent-adolescent child concordance on social norms related to gender equity in marriage in rural Maharashtra, India. Survey data on marital norms related to girl's marital age and choice, contraception, and marital violence (MV) were collected from unmarried adolescents (n = 113 girls, 116 boys) and their parents (n = 227 mothers, 203 fathers). Concordance was assessed using a Cohen's unweighted Kappa statistic, with analyses stratified by sex of parent and child. Analyses revealed fair (K = .25-.27) mother-daughter concordance on girls' right to choose when to marry, contraception use, and acceptability of MV. Father-son concordance was seen on girls' right to choose when (K = .22, slight) and who (K = .20, fair) to marry and MV acceptability (K = .53, moderate). No opposite sex parent-child concordance was revealed. Results indicate same but not opposite sex parent-child concordance on gender equity social norms related to marriage, suggesting same sex transfer of these norms. Copyright © 2014 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

  16. Colonic catabolism of dietary phenolic and polyphenolic compounds from Concord grape juice.

    PubMed

    Stalmach, Angelique; Edwards, Christine A; Wightman, Jolynne D; Crozier, Alan

    2013-01-01

    After acute ingestion of 350 ml of Concord grape juice, containing 528 μmol of (poly)phenolic compounds, by healthy volunteers, a wide array of phase I and II metabolites were detected in the circulation and excreted in urine. Ingestion of the juice by ileostomists resulted in 40% of compounds being recovered intact in ileal effluent. The current study investigated the fate of these undigested (poly)phenolic compounds on reaching the colon. This was achieved through incubation of the juice using an in vitro model of colonic fermentation and through quantification of catabolites produced after colonic degradation and their subsequent absorption prior to urinary excretion by healthy subjects and ileostomy volunteers. A total of 16 aromatic and phenolic compounds derived from colonic metabolism of Concord grape juice (poly)phenolic compounds were identified by GC-MS in the faecal incubation samples. Thirteen urinary phenolic acids and aromatic compounds were excreted in significantly increased amounts after intake of the juice by healthy volunteers, whereas only two of these compounds were excreted in elevated amounts by ileostomists. The production of phenolic acids and aromatic compounds by colonic catabolism contributed to the bioavailability of Concord grape (poly)phenolic compounds to a much greater extent than phase I and II metabolites originating from absorption in the upper gastrointestinal tract. Catabolic pathways are proposed, highlighting the impact of colonic microbiota and subsequent phase II metabolism prior to excretion of phenolic compounds derived from (poly)phenolic compounds in Concord grape juice, which pass from the small to the large intestine.

  17. Impact of Patient-Provider Race, Ethnicity, and Gender Concordance on Cancer Screening: Findings from Medical Expenditure Panel Survey.

    PubMed

    Malhotra, Jyoti; Rotter, David; Tsui, Jennifer; Llanos, Adana A M; Balasubramanian, Bijal A; Demissie, Kitaw

    2017-12-01

    Background: Racial and ethnic minorities experience lower rates of cancer screening compared with non-Hispanic whites (NHWs). Previous studies evaluating the role of patient-provider race, ethnicity, or gender concordance in cancer screening have been inconclusive. Methods: In a cross-sectional analysis using the Medical Expenditure Panel Survey (MEPS), data from 2003 to 2010 were assessed for associations between patient-provider race, ethnicity, and/or gender concordance and, screening (American Cancer Society guidelines) for breast, cervical, and colorectal cancer. Multivariable logistic analyses were conducted to examine associations of interest. Results: Of the 32,041 patient-provider pairs in our analysis, more than 60% of the patients were NHW, 15% were non-Hispanic black (NHB), and 15% were Hispanic. Overall, patients adherent to cancer screening were more likely to be non-Hispanic, better educated, married, wealthier, and privately insured. Patient-provider gender discordance was associated with lower rates of breast [OR, 0.83; 95% confidence interval (CI), 0.76-0.90], cervical (OR, 0.83; 95% CI, 0.76-0.91), and colorectal cancer (OR, 0.84; 95% CI, 0.79-0.90) screening in all patients. This association was also significant after adjusting for racial and/or ethnic concordance. Conversely, among NHWs and NHBs, patient-provider racial and/or ethnic concordance was not associated with screening. Among Hispanics, patient-provider ethnic discordant pairs had higher breast (58% vs. 52%) and colorectal cancer (45% vs. 39%) screening rates compared with concordant pairs. Conclusions: Patient-provider gender concordance positively affected cancer screening. Patient-provider ethnic concordance was inversely associated with receipt of cancer screening among Hispanics. This counter-intuitive finding requires further study. Impact: Our findings highlight the importance of gender concordance in improving cancer screening rates. Cancer Epidemiol Biomarkers Prev; 26

  18. Concordance between macrophytes and macroinvertebrates in a Mediterranean river of central Apennine region.

    PubMed

    Traversetti, Lorenzo; Scalici, Massimiliano; Ginepri, Valeria; Manfrin, Alessandro; Ceschin, Simona

    2014-05-01

    The main aim of this study was to improve the knowledge about the concordance among macrophytes and macroinvertebrates to provide complementary information and facilitate the procedures for quality assessment of river ecosystems. Macrophytes and macroinvertebrates were collected in 11 sampling sites along a central Apennine calcareous river in October 2008 and June 2009. The concordance between the two biomonitoring groups was tested according to several environmental parameters. The comparison of data matrix similarities by Mantel test showed differences in the assemblage of macrophytes and macroinvertebrates along the river since correlation values were 0.04, p > 0.05 in October 2008 and 0.39, p > 0.05 in June 2009. The study revealed lack of concordance between the two groups, emphasizing that the information provided by macrophytes and macroinvertebrates does not overlap in terms of response to environmental parameters. Indeed, the two different biological groups resulted useful descriptors of different parameters. Together, they could represent a complementary tool to reflect the river environmental quality.

  19. A novel fibrosis index comprising a non-cholesterol sterol accurately predicts HCV-related liver cirrhosis.

    PubMed

    Ydreborg, Magdalena; Lisovskaja, Vera; Lagging, Martin; Brehm Christensen, Peer; Langeland, Nina; Buhl, Mads Rauning; Pedersen, Court; Mørch, Kristine; Wejstål, Rune; Norkrans, Gunnar; Lindh, Magnus; Färkkilä, Martti; Westin, Johan

    2014-01-01

    Diagnosis of liver cirrhosis is essential in the management of chronic hepatitis C virus (HCV) infection. Liver biopsy is invasive and thus entails a risk of complications as well as a potential risk of sampling error. Therefore, non-invasive diagnostic tools are preferential. The aim of the present study was to create a model for accurate prediction of liver cirrhosis based on patient characteristics and biomarkers of liver fibrosis, including a panel of non-cholesterol sterols reflecting cholesterol synthesis and absorption and secretion. We evaluated variables with potential predictive significance for liver fibrosis in 278 patients originally included in a multicenter phase III treatment trial for chronic HCV infection. A stepwise multivariate logistic model selection was performed with liver cirrhosis, defined as Ishak fibrosis stage 5-6, as the outcome variable. A new index, referred to as Nordic Liver Index (NoLI) in the paper, was based on the model: Log-odds (predicting cirrhosis) = -12.17+ (age × 0.11) + (BMI (kg/m(2)) × 0.23) + (D7-lathosterol (μg/100 mg cholesterol)×(-0.013)) + (Platelet count (x10(9)/L) × (-0.018)) + (Prothrombin-INR × 3.69). The area under the ROC curve (AUROC) for prediction of cirrhosis was 0.91 (95% CI 0.86-0.96). The index was validated in a separate cohort of 83 patients and the AUROC for this cohort was similar (0.90; 95% CI: 0.82-0.98). In conclusion, the new index may complement other methods in diagnosing cirrhosis in patients with chronic HCV infection.

  20. Towards more accurate vegetation mortality predictions

    DOE PAGES

    Sevanto, Sanna Annika; Xu, Chonggang

    2016-09-26

    Predicting the fate of vegetation under changing climate is one of the major challenges of the climate modeling community. Here, terrestrial vegetation dominates the carbon and water cycles over land areas, and dramatic changes in vegetation cover resulting from stressful environmental conditions such as drought feed directly back to local and regional climate, potentially leading to a vicious cycle where vegetation recovery after a disturbance is delayed or impossible.

  1. Concordance with dietary and lifestyle population goals for cancer prevention in Dutch, Scottish, Mexican, and Guatemalan population samples.

    PubMed

    Vossenaar, Marieke; Solomons, Noel W; Valdés-Ramos, Roxana; Anderson, Annie S

    2010-01-01

    We assessed concordance with selected population goal components of the 1997 World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) diet and lifestyle recommendations to decrease cancer risk across four population samples. This was a prospectively designed survey examining concordance with the population goals of the WCRF/AICR recommendations using target criteria across sites. Population samples were from the Netherlands, Scotland, Mexico, and Guatemala. A total of 3564 men and women aged 18 to 70 y were recruited in equal proportions by site and gender. None of the four pooled samples met the target population average criteria for body mass index or refined sugar intake. The Guatemalan sample had concordance with the largest number of recommended cancer-prevention goals (10 of 12 selected WCRF/AICR components). Successively, Mexican, Scottish, and Dutch samples were concordant with seven, four, and three selected components, respectively. A prospectively designed research instrument and exhaustive prior examination of operative criteria allow for the assessment of group-level concordance with cancer-prevention goals. To the extent that the study samples reflect the respective national situations, geographic variance in concordance exists, with conditions and behaviors in Guatemala bringing that nation into more general compliance with the 1997 WCRF/AICR goals.

  2. Correlates of non-concordance between perceived and objective measures of walkability.

    PubMed

    Gebel, Klaus; Bauman, Adrian; Owen, Neville

    2009-04-01

    Objective and self-reported physical environmental attributes have been related to physical activity. We examined the characteristics of adults who are resident in objectively identified high walkable neighborhoods but whose perceptions of neighborhood attributes are not concordant with objective attributes relating to high walkability. Neighborhood built-environment attributes relating to walkability (dwelling density, intersection density, land use mix, and net retail area) were determined objectively, using Geographic Information System databases; data on corresponding perceptions of local environment attributes (from the Neighborhood Environment Walkability Scale) were derived from a self-completion survey of a socially diverse sample of 2,650 adults aged 19 to 65. Objective and perceived walkability attributes were categorized using median splits, and correlates of non-concordance were determined using multiple logistic regression models. There was a fair overall agreement between objectively determined walkability and perceived walkability (Kappa = 0.35, 95% CI = 0.31-0.39). Among those resident in objectively assessed high walkable areas (n = 1,063), 32.1% perceived them to be low walkable; conversely, 32.7% (n = 1,021) resident in objectively determined low walkability areas perceived them to be high. For residents of objectively determined high walkable areas, the characteristics that differentiated those with perceptions of low walkability (non-concordant perceptions) from those with concordant perceptions of high walkability were: not being university-educated (OR = 1.47, 95% CI = 1.06-2.04); having lower household incomes (OR = 1.54, 95% CI = 1.09-2.17); being overweight (OR = 1.46, 95% CI = 1.03-2.07); and walking fewer days per week for transport (OR = 1.75, 95% CI = 1.11-2.70). Higher walking times and more positive cognitive variables were noted among participants who lived in a neighborhood with low walkability that was perceived as high compared

  3. Weak Concordance between Fish and Macroinvertebrates in Mediterranean Streams

    PubMed Central

    Larsen, Stefano; Mancini, Laura; Pace, Giorgio; Scalici, Massimiliano; Tancioni, Lorenzo

    2012-01-01

    Although anthropogenic degradation of riverine systems stimulated a multi-taxon bioassessment of their ecological integrity in EU countries, specific responses of different taxonomic groups to human pressure are poorly investigated in Mediterranean rivers. Here, we assess if richness and composition of macroinvertebrate and fish assemblages show concordant variation along a gradient of anthropogenic pressure in 31 reaches across 13 wadeable streams in central Italy. Fish and invertebrate taxonomic richness was not correlated across sites. However, Mantel test showed that the two groups were significantly, albeit weakly, correlated even after statistically controlling for the effect of environmental variables and site proximity. Variance partitioning with partial Canonical Correspondence Analysis showed that the assemblages of the two groups were influenced by different set of environmental drivers: invertebrates were influenced by water organic content, channel and substratum features, while fish were related to stream temperature (mirroring elevation) and local land-use. Variance partitioning revealed the importance of biotic interactions between the two groups as a possible mechanisms determining concordance. Although significant, the congruence between the groups was weak, indicating that they should not be used as surrogate of each other for environmental assessments in these Mediterranean catchments. Indeed, both richness and patterns in nestedness (i.e. where depauperate locations host only a subset of taxa found in richer locations) appeared influenced by different environmental drivers suggesting that the observed concordance did not result from a co-loss of taxa along similar environmental gradients. As fish and macroinvertebrates appeared sensitive to different environmental factors, we argue that monitoring programmes should consider a multi-assemblage assessment, as also required by the Water Framework Directive. PMID:23251432

  4. Concordance of Commercial Data Sources for Neighborhood-Effects Studies

    PubMed Central

    Schootman, Mario

    2010-01-01

    Growing evidence supports a relationship between neighborhood-level characteristics and important health outcomes. One source of neighborhood data includes commercial databases integrated with geographic information systems to measure availability of certain types of businesses or destinations that may have either favorable or adverse effects on health outcomes; however, the quality of these data sources is generally unknown. This study assessed the concordance of two commercial databases for ascertaining the presence, locations, and characteristics of businesses. Businesses in the St. Louis, Missouri area were selected based on their four-digit Standard Industrial Classification (SIC) codes and classified into 14 business categories. Business listings in the two commercial databases were matched by standardized business name within specified distances. Concordance and coverage measures were calculated using capture–recapture methods for all businesses and by business type, with further stratification by census-tract-level population density, percent below poverty, and racial composition. For matched listings, distance between listings and agreement in four-digit SIC code, sales volume, and employee size were calculated. Overall, the percent agreement was 32% between the databases. Concordance and coverage estimates were lowest for health-care facilities and leisure/entertainment businesses; highest for popular walking destinations, eating places, and alcohol/tobacco establishments; and varied somewhat by population density. The mean distance (SD) between matched listings was 108.2 (179.0) m with varying levels of agreement in four-digit SIC (percent agreement = 84.6%), employee size (weighted kappa = 0.63), and sales volume (weighted kappa = 0.04). Researchers should cautiously interpret findings when using these commercial databases to yield measures of the neighborhood environment. PMID:20480397

  5. A high order accurate finite element algorithm for high Reynolds number flow prediction

    NASA Technical Reports Server (NTRS)

    Baker, A. J.

    1978-01-01

    A Galerkin-weighted residuals formulation is employed to establish an implicit finite element solution algorithm for generally nonlinear initial-boundary value problems. Solution accuracy, and convergence rate with discretization refinement, are quantized in several error norms, by a systematic study of numerical solutions to several nonlinear parabolic and a hyperbolic partial differential equation characteristic of the equations governing fluid flows. Solutions are generated using selective linear, quadratic and cubic basis functions. Richardson extrapolation is employed to generate a higher-order accurate solution to facilitate isolation of truncation error in all norms. Extension of the mathematical theory underlying accuracy and convergence concepts for linear elliptic equations is predicted for equations characteristic of laminar and turbulent fluid flows at nonmodest Reynolds number. The nondiagonal initial-value matrix structure introduced by the finite element theory is determined intrinsic to improved solution accuracy and convergence. A factored Jacobian iteration algorithm is derived and evaluated to yield a consequential reduction in both computer storage and execution CPU requirements while retaining solution accuracy.

  6. Reliable and accurate point-based prediction of cumulative infiltration using soil readily available characteristics: A comparison between GMDH, ANN, and MLR

    NASA Astrophysics Data System (ADS)

    Rahmati, Mehdi

    2017-08-01

    Developing accurate and reliable pedo-transfer functions (PTFs) to predict soil non-readily available characteristics is one of the most concerned topic in soil science and selecting more appropriate predictors is a crucial factor in PTFs' development. Group method of data handling (GMDH), which finds an approximate relationship between a set of input and output variables, not only provide an explicit procedure to select the most essential PTF input variables, but also results in more accurate and reliable estimates than other mostly applied methodologies. Therefore, the current research was aimed to apply GMDH in comparison with multivariate linear regression (MLR) and artificial neural network (ANN) to develop several PTFs to predict soil cumulative infiltration point-basely at specific time intervals (0.5-45 min) using soil readily available characteristics (RACs). In this regard, soil infiltration curves as well as several soil RACs including soil primary particles (clay (CC), silt (Si), and sand (Sa)), saturated hydraulic conductivity (Ks), bulk (Db) and particle (Dp) densities, organic carbon (OC), wet-aggregate stability (WAS), electrical conductivity (EC), and soil antecedent (θi) and field saturated (θfs) water contents were measured at 134 different points in Lighvan watershed, northwest of Iran. Then, applying GMDH, MLR, and ANN methodologies, several PTFs have been developed to predict cumulative infiltrations using two sets of selected soil RACs including and excluding Ks. According to the test data, results showed that developed PTFs by GMDH and MLR procedures using all soil RACs including Ks resulted in more accurate (with E values of 0.673-0.963) and reliable (with CV values lower than 11 percent) predictions of cumulative infiltrations at different specific time steps. In contrast, ANN procedure had lower accuracy (with E values of 0.356-0.890) and reliability (with CV values up to 50 percent) compared to GMDH and MLR. The results also revealed

  7. Parent-Youth Rating Concordance for Hair Pulling Variables, Functional Impairment, and Anxiety Scale Scores in Trichotillomania

    ERIC Educational Resources Information Center

    Keuthen, Nancy J.; Flessner, Christopher A.; Woods, Douglas W.; Franklin, Martin E.; Piacentini, John A.; Khanna, Muniya; Moore, Phoebe; Cashin, Susan

    2008-01-01

    Knowledge of cross-informant rating concordance is critical for the assessment of child and adolescent problems in clinical and research settings. We explored parent-youth rating concordance for hair pulling variables, functional impairment, and anxiety symptoms in a sample of child and adolescent hair pullers (n = 133) satisfying conservative…

  8. 78 FR 5717 - Safety Zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-28

    ...-AA00 Safety Zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal... Guard is establishing a safety zone in the navigable waters of Suisun Bay near Military Ocean Terminal Concord, CA in support of military onload and offload operations. This safety zone is established to...

  9. Monozygotic male twins concordant for Beckwith-Wiedemann syndrome

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

    Clemens, M.; McPherson, E.; Sherer, C.

    1994-09-01

    The Beckwith-Wiedemann syndrome (BWS) is a multiple congenital anomaly syndrome characterized by macrosomia, macro glossia, visceromegaly, characteristic facies, and in some cases omphalocele, hypoglycemia, hemihypertrophy, and risk of embryonal tumors. Most cases occur sporadically in chromosomally normal individuals, but a few BWS patients have anomalies of 11p and others have evidence of microduplications or paternal isodisomy in this region. In some families with autosomal dominant transmission, BWS maps to 11p15.5, but the mechanism of transmission is not fully understood. BWS has been reported in 11 sets of MZ twins, including 10 female pairs (9 discordant and 1 partially concordant) andmore » one male pair concordant for both BWS & dup 15q11.2-q13. We report a pair of premature male MZ twins with macroglossia, postnatal overgrowth, characteristic BWS facies, and mild developmental delay. One twin had hypoglycemia, but neither had omphalocele or hemihypertrophy and serial abdominal ultrasounds have been normal. DNA fingerprinting confirmed monozygosity. Chromosome studies showed a marker 11p14.2 in one twin only, and molecular genetic studies of the 11p15.5 region showed no evidence of duplication or isodisomy in either twin.« less

  10. Perceived Physician-informed Weight Status Predicts Accurate Weight Self-Perception and Weight Self-Regulation in Low-income, African American Women.

    PubMed

    Harris, Charlie L; Strayhorn, Gregory; Moore, Sandra; Goldman, Brian; Martin, Michelle Y

    2016-01-01

    Obese African American women under-appraise their body mass index (BMI) classification and report fewer weight loss attempts than women who accurately appraise their weight status. This cross-sectional study examined whether physician-informed weight status could predict weight self-perception and weight self-regulation strategies in obese women. A convenience sample of 118 low-income women completed a survey assessing demographic characteristics, comorbidities, weight self-perception, and weight self-regulation strategies. BMI was calculated during nurse triage. Binary logistic regression models were performed to test hypotheses. The odds of obese accurate appraisers having been informed about their weight status were six times greater than those of under-appraisers. The odds of those using an "approach" self-regulation strategy having been physician-informed were four times greater compared with those using an "avoidance" strategy. Physicians are uniquely positioned to influence accurate weight self-perception and adaptive weight self-regulation strategies in underserved women, reducing their risk for obesity-related morbidity.

  11. Lack of concordance between a rapid bedside and conventional laboratory method of cardiac troponin testing: impact on risk stratification of patients suspected of acute coronary syndrome.

    PubMed

    Cramer, G Etienne; Kievit, Peter C; Brouwer, Marc A; de Keijzer, Marinus H; Luijten, Hans E; Verheugt, Freek W A

    2007-06-01

    This study was designed to test the usefulness of a bedside assay as compared to a laboratory method of troponin testing to predict adverse cardiac outcome of chest pain patients. We studied 358 ER visits of patients suspected of a non ST-elevation acute coronary syndrome. cTnI (Immulite, DPC) on a lab analyser and cTnT (Cardiac Reader, Roche) at bedside were measured at baseline. The between-assay level of concordance, reporting turnaround times and clinical outcomes during 180 days of follow-up were assessed. Death and myocardial infarction were then evaluated according to troponin result, either concordant negative, discordant or concordant positive. Discordance occurred in 11.4% (41/358) of cases. The proportion of patients with a positive cTnI and negative cTnT result (8.9%) versus the reverse (2.5%) differed significantly (p<0.001). The median time gained using the rapid test was 72 min. The rate of death and/or MI was 25% (10/40) among patients with discordant results as compared to 7.5% (17/228) with a concordant negative result (p<0.001). All patients from the discordant group with an event had a positive cTnI result, while cTnT was negative. Patients with a discordant reading were at high risk of adverse cardiac outcome, which was only identified by the laboratory cTnI assay. Markedly, the use of the rapid assay saved time at the expense of clinical sensitivity.

  12. Concordance of HPV-DNA in cervical dysplasia or genital warts in women and their monogamous long-term male partners.

    PubMed

    Rob, Filip; Tachezy, Ruth; Pichlík, Tomáš; Škapa, Petr; Rob, Lukáš; Hamšíková, Eva; Šmahelová, Jana; Hercogová, Jana

    2017-09-01

    Transmission of human papillomavirus (HPV) is a premise for development of cervical dysplasia and genital warts (GWs). This cross-sectional study assesses concordance of HPV types present in GWs or cervical dysplasia in women and genital infection of their monogamous male partners in conjunction with seroprevalence of HPV-6, -11, -16, and -18 antibodies. Blood was taken from both women and men, as well a smear of the urogenital area of men. HPV DNA detection in women was done in fixed paraffin embedded tissues under histological control. Of 143 couples who agreed to participate in the study, 68 met inclusion criteria. Type-specific concordance was observed in 32.5% (13/40) of couples in which women had genital warts and in 32.1% (9/28) of couples in which women had cervical dysplasia. In multivariate analysis only smoking in women was associated with concordance (P < 0.05). Prevalence of HPV-specific antibodies was high in male partners, but was not associated with presence of the same HPV type on their genitals. The same type-specific HPV antibodies were detected in 81.8% of men in couples with HPV-6 concordant genital warts, but only in 14.3% of men in couples with HPV-16 concordant cervical dysplasia (P < 0.01). These results suggest that type-specific HPV concordance in genital warts and cervical dysplasia lesions of women and genital infection of their male partners is common and similar. Higher seroconversion in couples with HPV-6 concordant genital warts compared with couples with HPV-16 concordant cervical dysplasia may be explained by viral load exposure. © 2017 Wiley Periodicals, Inc.

  13. He Said, She Said: Examining Parental Concordance on Home Environment Factors and Adolescent Health Behaviors and Weight Status.

    PubMed

    Berge, Jerica M; MacLehose, Richard F; Meyer, Craig; Didericksen, Katharine; Loth, Katie A; Neumark-Sztainer, Dianne

    2016-01-01

    Few studies have examined concordance/discordance between caregivers to identify whether caregivers see familial and parental factors in the home environment similarly or differently and whether the agreement or disagreement is related to adolescent obesity risk. Answers to these questions are important and may inform whether family-based childhood obesity interventions need to target both parents. The main objective of the study was to examine whether and how parental concordance/discordance on factors in the home environment (eg, importance of family meals, parent feeding practices, encouraging child physical activity, and limit setting on child screen time) are associated with adolescent health behaviors and weight status. Data from two linked population-based studies were used in cross-sectional analyses. Linear regression models examined associations between parental concordance/discordance on home environment factors and adolescents' health behaviors and weight status. Racially/ethnically and socioeconomically diverse adolescents (n=1,052; 54% girls; mean age=14.3 years) and their parents (n=2,104; 52% women; mean age=41.0 years) from Minneapolis and St Paul, MN, participated in the study. Anthropometric assessments and surveys were completed at school by adolescents and surveys were completed at home by parents. Parental concordance on home environment factors was high for some factors (eg, 68% concordance on not pressuring adolescent to eat) and low for other factors (eg, 2% concordance on parent engaging in physically activity with child 4+ hours per week). Parental concordance on positive home environment factors (eg, frequency of family meals) was associated with more adolescent healthful eating patterns and hours of physical activity (P<0.05), but not consistently. When parents were discordant, adolescents had higher consumption of fast food and more unhealthy weight control behaviors (P<0.05), but not consistently. Results suggest there is some degree

  14. He Said, She Said: Examining Parental Concordance on Home Environment Factors and Adolescent Health Behaviors and Weight Status

    PubMed Central

    Berge, Jerica M.; MacLehose, Richard F; Meyer, Craig; Didericksen, Katharine; Loth, Katie A.; Neumark-Sztainer, Dianne

    2015-01-01

    Introduction Few studies have examined concordance/discordance between caregivers to identify whether caregivers see familial and parental factors in the home environment similarly or differently and whether the agreement or disagreement is related to adolescent obesity risk. Answers to these questions are important and may inform whether family-based childhood obesity interventions need to target both parents. Objective The main objective of the study is to examine whether and how parental concordance/discordance on factors in the home environment (e.g., importance of family meals, parent feeding practices, encouraging child physical activity, limit setting on child screen time) are associated with adolescent health behaviors and weight status. Design Data from two linked population-based studies were used in cross-sectional analyses. Linear regression models examined associations between parental concordance/discordance on home environment factors and adolescents’ health behaviors and weight status. Participant/Settings Racially/ethnically and socioeconomically diverse adolescents (n=1,052; 54% girls; mean age = 14.3 years) and their parents (n=2,104; 52% female; mean age = 41.0 years) from Minneapolis and St. Paul, Minnesota participated in the study. Anthropometric assessments and surveys were completed at school by adolescents and surveys were completed at home by parents. Results Parental concordance on home environment factors was high for some factors (e.g., 68% concordance on not pressuring adolescent to eat) and low for other factors (e.g., 2% concordance on parent engaging in physically activity with child 4+ hours/week). Parental concordance on positive home environment factors (e.g., frequency of family meals) was associated with more adolescent healthful eating patterns and hours of physical activity (p < 0.05), but not consistently. When parents were discordant, adolescents had higher consumption of fast food and more unhealthy weight control

  15. Predicted osteotomy planes are accurate when using patient-specific instrumentation for total knee arthroplasty in cadavers: a descriptive analysis.

    PubMed

    Kievit, A J; Dobbe, J G G; Streekstra, G J; Blankevoort, L; Schafroth, M U

    2018-06-01

    Malalignment of implants is a major source of failure during total knee arthroplasty. To achieve more accurate 3D planning and execution of the osteotomy cuts during surgery, the Signature (Biomet, Warsaw) patient-specific instrumentation (PSI) was used to produce pin guides for the positioning of the osteotomy blocks by means of computer-aided manufacture based on CT scan images. The research question of this study is: what is the transfer accuracy of osteotomy planes predicted by the Signature PSI system for preoperative 3D planning and intraoperative block-guided pin placement to perform total knee arthroplasty procedures? The transfer accuracy achieved by using the Signature PSI system was evaluated by comparing the osteotomy planes predicted preoperatively with the osteotomy planes seen intraoperatively in human cadaveric legs. Outcomes were measured in terms of translational and rotational errors (varus, valgus, flexion, extension and axial rotation) for both tibia and femur osteotomies. Average translational errors between the osteotomy planes predicted using the Signature system and the actual osteotomy planes achieved was 0.8 mm (± 0.5 mm) for the tibia and 0.7 mm (± 4.0 mm) for the femur. Average rotational errors in relation to predicted and achieved osteotomy planes were 0.1° (± 1.2°) of varus and 0.4° (± 1.7°) of anterior slope (extension) for the tibia, and 2.8° (± 2.0°) of varus and 0.9° (± 2.7°) of flexion and 1.4° (± 2.2°) of external rotation for the femur. The similarity between osteotomy planes predicted using the Signature system and osteotomy planes actually achieved was excellent for the tibia although some discrepancies were seen for the femur. The use of 3D system techniques in TKA surgery can provide accurate intraoperative guidance, especially for patients with deformed bone, tailored to individual patients and ensure better placement of the implant.

  16. Predicting early cognitive decline in newly-diagnosed Parkinson's patients: A practical model.

    PubMed

    Hogue, Olivia; Fernandez, Hubert H; Floden, Darlene P

    2018-06-19

    To create a multivariable model to predict early cognitive decline among de novo patients with Parkinson's disease, using brief, inexpensive assessments that are easily incorporated into clinical flow. Data for 351 drug-naïve patients diagnosed with idiopathic Parkinson's disease were obtained from the Parkinson's Progression Markers Initiative. Baseline demographic, disease history, motor, and non-motor features were considered as candidate predictors. Best subsets selection was used to determine the multivariable baseline symptom profile that most accurately predicted individual cognitive decline within three years. Eleven per cent of the sample experienced cognitive decline. The final logistic regression model predicting decline included five baseline variables: verbal memory retention, right-sided bradykinesia, years of education, subjective report of cognitive impairment, and REM behavior disorder. Model discrimination was good (optimism-adjusted concordance index = .749). The associated nomogram provides a tool to determine individual patient risk of meaningful cognitive change in the early stages of the disease. Through the consideration of easily-implemented or routinely-gathered assessments, we have identified a multidimensional baseline profile and created a convenient, inexpensive tool to predict cognitive decline in the earliest stages of Parkinson's disease. The use of this tool would generate prediction at the individual level, allowing clinicians to tailor medical management for each patient and identify at-risk patients for clinical trials aimed at disease modifying therapies. Copyright © 2018. Published by Elsevier Ltd.

  17. Influence knowledge and behavior of TB medical personnels’ concordance principle based communications skill at primary healthcare, Medan, Indonesia

    NASA Astrophysics Data System (ADS)

    Wahyuni, A. S.; Soeroso, N. N.; Alona, I.; Yunanda, Y.; Siregar, I.

    2018-03-01

    Concordance behavior of TB management is a form of collaboration among doctors, personnel, and patients in treating TB. Approvalamong them could be achieved if credibility and policy occur. This study is aimed to analyze the influence of TB medical personnel’s concordance behaviour principle to patient obedience at primary health care in Medan.The design of this study was quasi experimental, focusing on interventional primary health care, which is those who applied concordance behaviour principle to non-interventionalprimary health care. The population is TB patients, starting from 18 years old, TB category I with positive Acid Fast Bacilli Smear Test (AFBST), and taking TB regimens at Medan. Seventy- four patients were selected to be samples. They had undergone interview based on validated concordance principle, knowledge, behavior, and treatment. Data were analyzed using chi- square. The percentage of knowledge, behavior of TB patient to the treatment is higher on interventional primary health care than noninterventional ones. Treatment awareness based on concordance principle is expected to planish DOTS-based TB programs.

  18. CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.

    PubMed

    Testa, Alison C; Hane, James K; Ellwood, Simon R; Oliver, Richard P

    2015-03-11

    The impact of gene annotation quality on functional and comparative genomics makes gene prediction an important process, particularly in non-model species, including many fungi. Sets of homologous protein sequences are rarely complete with respect to the fungal species of interest and are often small or unreliable, especially when closely related species have not been sequenced or annotated in detail. In these cases, protein homology-based evidence fails to correctly annotate many genes, or significantly improve ab initio predictions. Generalised hidden Markov models (GHMM) have proven to be invaluable tools in gene annotation and, recently, RNA-seq has emerged as a cost-effective means to significantly improve the quality of automated gene annotation. As these methods do not require sets of homologous proteins, improving gene prediction from these resources is of benefit to fungal researchers. While many pipelines now incorporate RNA-seq data in training GHMMs, there has been relatively little investigation into additionally combining RNA-seq data at the point of prediction, and room for improvement in this area motivates this study. CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. RNA-seq data informs annotations both during gene-model training and in prediction. Our approach capitalises on the high quality of fungal transcript assemblies by incorporating predictions made directly from transcript sequences. Correct predictions are made despite transcript assembly problems, including those caused by overlap between the transcripts of adjacent gene loci. Stringent benchmarking against high-confidence annotation subsets showed CodingQuarry predicted 91.3% of Schizosaccharomyces pombe genes and 90.4% of Saccharomyces cerevisiae genes perfectly. These results are 4-5% better than those of AUGUSTUS, the next best performing RNA-seq driven gene predictor tested. Comparisons against

  19. Deformation, Failure, and Fatigue Life of SiC/Ti-15-3 Laminates Accurately Predicted by MAC/GMC

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2002-01-01

    NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) (ref.1) has been extended to enable fully coupled macro-micro deformation, failure, and fatigue life predictions for advanced metal matrix, ceramic matrix, and polymer matrix composites. Because of the multiaxial nature of the code's underlying micromechanics model, GMC--which allows the incorporation of complex local inelastic constitutive models--MAC/GMC finds its most important application in metal matrix composites, like the SiC/Ti-15-3 composite examined here. Furthermore, since GMC predicts the microscale fields within each constituent of the composite material, submodels for local effects such as fiber breakage, interfacial debonding, and matrix fatigue damage can and have been built into MAC/GMC. The present application of MAC/GMC highlights the combination of these features, which has enabled the accurate modeling of the deformation, failure, and life of titanium matrix composites.

  20. Development and Validation of a Weather-Based Model for Predicting Infection of Loquat Fruit by Fusicladium eriobotryae

    PubMed Central

    González-Domínguez, Elisa; Armengol, Josep; Rossi, Vittorio

    2014-01-01

    A mechanistic, dynamic model was developed to predict infection of loquat fruit by conidia of Fusicladium eriobotryae, the causal agent of loquat scab. The model simulates scab infection periods and their severity through the sub-processes of spore dispersal, infection, and latency (i.e., the state variables); change from one state to the following one depends on environmental conditions and on processes described by mathematical equations. Equations were developed using published data on F. eriobotryae mycelium growth, conidial germination, infection, and conidial dispersion pattern. The model was then validated by comparing model output with three independent data sets. The model accurately predicts the occurrence and severity of infection periods as well as the progress of loquat scab incidence on fruit (with concordance correlation coefficients >0.95). Model output agreed with expert assessment of the disease severity in seven loquat-growing seasons. Use of the model for scheduling fungicide applications in loquat orchards may help optimise scab management and reduce fungicide applications. PMID:25233340

  1. Concordance between Preservice Teachers' Personal Responsibilities and Intended Instructional Practices

    ERIC Educational Resources Information Center

    Daniels, Lia M.; Radil, Amanda; Wagner, Amanda K.

    2016-01-01

    During their education, preservice teachers begin to assume professional responsibilities and gain pedagogical knowledge. However, the question remains whether preservice teachers intend to use instructional practices that are effective in meeting their assumed responsibilities. Thus, we examined the concordance between preservice teachers'…

  2. [Comparison of predictive models for the selection of high-complexity patients].

    PubMed

    Estupiñán-Ramírez, Marcos; Tristancho-Ajamil, Rita; Company-Sancho, María Consuelo; Sánchez-Janáriz, Hilda

    2017-08-18

    To compare the concordance of complexity weights between Clinical Risk Groups (CRG) and Adjusted Morbidity Groups (AMG). To determine which one is the best predictor of patient admission. To optimise the method used to select the 0.5% of patients of higher complexity that will be included in an intervention protocol. Cross-sectional analytical study in 18 Canary Island health areas, 385,049 citizens were enrolled, using sociodemographic variables from health cards; diagnoses and use of healthcare resources obtained from primary health care electronic records (PCHR) and the basic minimum set of hospital data; the functional status recorded in the PCHR, and the drugs prescribed through the electronic prescription system. The correlation between stratifiers was estimated from these data. The ability of each stratifier to predict patient admissions was evaluated and prediction optimisation models were constructed. Concordance between weights complexity stratifiers was strong (rho = 0.735) and the correlation between categories of complexity was moderate (weighted kappa = 0.515). AMG complexity weight predicts better patient admission than CRG (AUC: 0.696 [0.695-0.697] versus 0.692 [0.691-0.693]). Other predictive variables were added to the AMG weight, obtaining the best AUC (0.708 [0.707-0.708]) the model composed by AMG, sex, age, Pfeiffer and Barthel scales, re-admissions and number of prescribed therapeutic groups. strong concordance was found between stratifiers, and higher predictive capacity for admission from AMG, which can be increased by adding other dimensions. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  3. Accurate prediction of cardiorespiratory fitness using cycle ergometry in minimally disabled persons with relapsing-remitting multiple sclerosis.

    PubMed

    Motl, Robert W; Fernhall, Bo

    2012-03-01

    To examine the accuracy of predicting peak oxygen consumption (VO(2peak)) primarily from peak work rate (WR(peak)) recorded during a maximal, incremental exercise test on a cycle ergometer among persons with relapsing-remitting multiple sclerosis (RRMS) who had minimal disability. Cross-sectional study. Clinical research laboratory. Women with RRMS (n=32) and sex-, age-, height-, and weight-matched healthy controls (n=16) completed an incremental exercise test on a cycle ergometer to volitional termination. Not applicable. Measured and predicted VO(2peak) and WR(peak). There were strong, statistically significant associations between measured and predicted VO(2peak) in the overall sample (R(2)=.89, standard error of the estimate=127.4 mL/min) and subsamples with (R(2)=.89, standard error of the estimate=131.3 mL/min) and without (R(2)=.85, standard error of the estimate=126.8 mL/min) multiple sclerosis (MS) based on the linear regression analyses. Based on the 95% confidence limits for worst-case errors, the equation predicted VO(2peak) within 10% of its true value in 95 of every 100 subjects with MS. Peak VO(2) can be accurately predicted in persons with RRMS who have minimal disability as it is in controls by using established equations and WR(peak) recorded from a maximal, incremental exercise test on a cycle ergometer. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  4. Glutamate quantification by PRESS or MEGA-PRESS: Validation, repeatability, and concordance.

    PubMed

    van Veenendaal, Tamar M; Backes, Walter H; van Bussel, Frank C G; Edden, Richard A E; Puts, Nicolaas A J; Aldenkamp, Albert P; Jansen, Jacobus F A

    2018-05-01

    While PRESS is often employed to measure glutamate concentrations, MEGA-PRESS enables simultaneous Glx (glutamate and glutamine) and GABA measurements. This study aimed to compare validation, repeatability, and concordance of different approaches for glutamate quantification at 3T to aid future studies in their selection of the appropriate sequence and quantification method. Nine phantoms with different glutamate and glutamine concentrations and five healthy participants were scanned twice to assess respectively the validation and repeatability of measurements with PRESS and MEGA-PRESS. To assess concordance between the different methods, results from 95 human participants were compared. PRESS, MEGA-PRESS (i.e. difference), and the MEGA-PRESS OFF spectra were analyzed with both LCModel and Gannet. In vitro, excellent agreement was shown between actual and measured glutamate concentrations for all measurements (r>0.98). In vivo CVs were better for PRESS (2.9%) than MEGA-PRESS (4.9%) and MEGA-PRESS OFF (4.2%). However, the concordance between the sequences was low (PRESS and MEGA-PRESS OFF, r=0.3) to modest (MEGA-PRESS versus MEGA-PRESS OFF, r=0.8). Both PRESS and MEGA-PRESS can be employed to measure in vivo glutamate concentrations, although PRESS shows a better repeatability. Comparisons between in vivo glutamate measures of different sequences however need to be interpreted cautiously. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. A test of concordance between patient and psychiatrist valuations of multiple treatment goals for schizophrenia

    PubMed Central

    Bridges, John F. P.; Slawik, Lara; Schmeding, Annette; Reimer, Jens; Naber, Dieter; Kuhnigk, Olaf

    2011-01-01

    Abstract Background  While much discussion has been placed on the problem of poor compliance in the treatment of schizophrenia, there has been little discussion on the concordance between patients and psychiatrists, an important contributing factor to patient‐centred care. Objective  To estimate the concordance between patients’ and psychiatrists’ (ordinal and cardinal) valuations of multiple goals for schizophrenia treatment and to illustrate the utility of the self‐explicated method in valuing a large number of treatment goals. Design  Twenty treatment goals were identified during focus groups and literature review and were presented to patients and psychiatrists during structured interviews. Respondents were asked to rank the multiple treatment goals and rate them on a 5‐point Likert scale. Three scores were calculated based on the ranking (1–20), rating (Likert scale) (1–5) and a self‐explicated method estimated as the product of rating and ranking score (1–100). Concordance was tested using Spearman’s rho for overall ordinal rankings and via anova and F‐test for the cardinal values assigned to a specific treatment goal. Participants  A total of 105 outpatients diagnosed with schizophrenia and 160 psychiatrists in Germany. Results  Patient and psychiatrist values were concordant when the ordinal properties of their valuations were assessed by rating (ρ = 0.63; P = 0.002), ranking (ρ = 0.51; P = 0.02) and self‐explicated methods (ρ = 0.54; P = 0.01). Significant discordances were found when comparing the cardinal value placed on any given treatment goal using all three approaches, but the self‐explicated method produced a more discerning statistic. Relative to patients, psychiatrists significantly (P < 0.05) overvalued reduced lack of emotion, improved sexual pleasure and improved communication while undervaluing reuptake of activities of daily living, improved satisfaction and recovered capacity

  6. Brief Report: Identical Male Twins Concordant for Asperger's Disorder

    ERIC Educational Resources Information Center

    Ishijima, Michiko; Kurita, Hiroshi

    2007-01-01

    The first case study of identical male twins concordant for DSM-IV Asperger's disorder (ASD) was presented. Their monozygocity was confirmed by short tandem repeat analyses with a probability of 99.999963%. Despite sharing the same DNA and environment, the twins are different in comorbidity (i.e., major depressive disorder in the elder and absence…

  7. The Concordance of Multilingual Legal Texts at the WTO

    ERIC Educational Resources Information Center

    Condon, Bradly J.

    2012-01-01

    Multilingualism is a sensitive and complex subject in a global organisation such as the World Trade Organization (WTO). In the WTO legal texts, there is a need for full concordance, not simply translation. This article begins with an overview of the issues raised by multilingual processes at the WTO in the negotiation, drafting, translation,…

  8. Concordance of somatic mutational profile in multiple primary melanomas.

    PubMed

    Adler, Nikki R; McLean, Catriona A; Wolfe, Rory; Kelly, John W; McArthur, Grant A; Haydon, Andrew; Tra, Thien; Cummings, Nicholas; Mar, Victoria J

    2018-03-30

    This study aimed to determine the frequency and concordance of BRAF and NRAS mutation in tumours arising in patients with multiple primary melanoma (MPM). Patients with MPM managed at one of three tertiary referral centres in Melbourne, Australia, from 2010 to 2015 were included. Incident and subsequent melanomas underwent mutation testing. Cohen's kappa (κ) coefficient assessed agreement between incident and subsequent primary melanomas for both BRAF and NRAS mutation status (mutant versus wild-type). Mutation testing of at least two primary tumours from 64 patients was conducted. There was poor agreement for both BRAF and NRAS mutation status between incident and subsequent melanomas (κ = 0.10, 95% CI -0.10 to 0.42; κ = 0.06, 95% CI -0.10 to 0.57, respectively). In view of the low concordance in BRAF mutation status between incident and subsequent melanomas, mutational analysis of metastatic tissue, rather than of a primary melanoma, in patients with MPM should be used to guide targeted therapy. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Concordance measure and discriminatory accuracy in transformation cure models.

    PubMed

    Zhang, Yilong; Shao, Yongzhao

    2018-01-01

    Many populations of early-stage cancer patients have non-negligible latent cure fractions that can be modeled using transformation cure models. However, there is a lack of statistical metrics to evaluate prognostic utility of biomarkers in this context due to the challenges associated with unknown cure status and heavy censorship. In this article, we develop general concordance measures as evaluation metrics for the discriminatory accuracy of transformation cure models including the so-called promotion time cure models and mixture cure models. We introduce explicit formulas for the consistent estimates of the concordance measures, and show that their asymptotically normal distributions do not depend on the unknown censoring distribution. The estimates work for both parametric and semiparametric transformation models as well as transformation cure models. Numerical feasibility of the estimates and their robustness to the censoring distributions are illustrated via simulation studies and demonstrated using a melanoma data set. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Predictors of health literacy and numeracy concordance among adolescent with special health care needs and their parents

    PubMed Central

    Chisolm, Deena J; Sarkar, Madhurima; Kelleher, Kelly J.; Sanders, Lee M.

    2015-01-01

    Background Parent and teen health literacies (HL) are employed as teens with chronic illnesses transition to health self-management and the adult health system. This study explores the relationships between parent and teen HL. Methods Teens ages 12-18 with chronic conditions and their parents, sampled from a pediatric Medicaid ACO, completed an interview assessing HL and self-reported competence with written and numeric health information. Rates of teen and parent HL, degree of concordance, and relationship between concordance and teen-reported competence with health materials were measured. Results Half (52%) of teens had adequate HL. 62% of teens reported competence with written health materials and 69% with numeric information. Correlation between parent and teen HL was modest but significant (phi=0.13; p=0.03). 47% of parent-teen dyads were concordant for adequate HL while 10% were concordant inadequate. Adequate teen HL was associated with parental adequate HL and parental education. Discordance was associated with self-reported competence with written material and numeric material. Conclusion Over half of parent-teen dyads had at least one member with less than adequate health literacy and parent-teen HL concordance were associated with teen perception of health literacy. These findings support the consideration of both independent and dyad HL levels in adolescent care. PMID:26513030

  11. Initializing concordance in frail elderly patients via a medicines organizer.

    PubMed

    Ryan-Woolley, Bernadette M; Rees, Judith A

    2005-05-01

    Concordance, which involves prescribing with rather than for patients, should result in less drug wastage (non-use), but is proving hard to put into practice. One possible way of easing elderly people and prescribers toward concordance is to use a medicines organizer (MO). To document medication wastage, using a pharmacy-prepared reusable MO, and explore, using a qualitative approach, use of this information on communication of individuals' drug regimens. Sixty-two sheltered housing residents, aged > or =60 years, participated in an exploratory controlled, matched study. The intervention group received medication in the MO, and the control group continued with standard packaging. Community pharmacists recorded details of wasted drugs returned during the 3-month study and, for the intervention group, 6, 9, and 12 months after the study. Medicines management data were collected from participants. Qualitative interviews were conducted with a sample of general practitioners (GPs) and community pharmacists to explore views on the role of the MO. Intervention group wastage was reduced from 18.1% (prestudy) to 1% at 12 months. No data on wastage were collected for the control group after the prestudy assessment. Sixty-one percent more prescription changes, including significant decreases in the number of prescribed drugs and dosages, were reported for the intervention group. GPs and pharmacists reported improvements in communication concerning medication-related dialog. This small exploratory study has shown that a pharmacy-prepared reusable MO provided visual, objective insights into medication wastage. This resulted in improved communication of drug needs and reduced wastage-the foundation for concordance.

  12. CADRE-SS, an in Silico Tool for Predicting Skin Sensitization Potential Based on Modeling of Molecular Interactions.

    PubMed

    Kostal, Jakub; Voutchkova-Kostal, Adelina

    2016-01-19

    Using computer models to accurately predict toxicity outcomes is considered to be a major challenge. However, state-of-the-art computational chemistry techniques can now be incorporated in predictive models, supported by advances in mechanistic toxicology and the exponential growth of computing resources witnessed over the past decade. The CADRE (Computer-Aided Discovery and REdesign) platform relies on quantum-mechanical modeling of molecular interactions that represent key biochemical triggers in toxicity pathways. Here, we present an external validation exercise for CADRE-SS, a variant developed to predict the skin sensitization potential of commercial chemicals. CADRE-SS is a hybrid model that evaluates skin permeability using Monte Carlo simulations, assigns reactive centers in a molecule and possible biotransformations via expert rules, and determines reactivity with skin proteins via quantum-mechanical modeling. The results were promising with an overall very good concordance of 93% between experimental and predicted values. Comparison to performance metrics yielded by other tools available for this endpoint suggests that CADRE-SS offers distinct advantages for first-round screenings of chemicals and could be used as an in silico alternative to animal tests where permissible by legislative programs.

  13. Do Skilled Elementary Teachers Hold Scientific Conceptions and Can They Accurately Predict the Type and Source of Students' Preconceptions of Electric Circuits?

    ERIC Educational Resources Information Center

    Lin, Jing-Wen

    2016-01-01

    Holding scientific conceptions and having the ability to accurately predict students' preconceptions are a prerequisite for science teachers to design appropriate constructivist-oriented learning experiences. This study explored the types and sources of students' preconceptions of electric circuits. First, 438 grade 3 (9 years old) students were…

  14. Validation of the Seating and Mobility Script Concordance Test

    ERIC Educational Resources Information Center

    Cohen, Laura J.; Fitzgerald, Shirley G.; Lane, Suzanne; Boninger, Michael L.; Minkel, Jean; McCue, Michael

    2009-01-01

    The purpose of this study was to develop the scoring system for the Seating and Mobility Script Concordance Test (SMSCT), obtain and appraise internal and external structure evidence, and assess the validity of the SMSCT. The SMSCT purpose is to provide a method for testing knowledge of seating and mobility prescription. A sample of 106 therapists…

  15. Concordance between maternal recall of birth complications and data from obstetrical records.

    PubMed

    Keenan, Kate; Hipwell, Alison; McAloon, Rose; Hoffmann, Amy; Mohanty, Arpita; Magee, Kelsey

    2017-02-01

    Prenatal complications are associated with poor outcomes in the offspring. Access to medical records is limited in the United States and investigators often rely on maternal report of prenatal complications. We tested concordance between maternal recall and birth records in a community-based sample of mothers participating in a longitudinal study in order to determine the accuracy of maternal recall of perinatal complications. Participants were 151 biological mothers, who were interviewed about gestational age at birth, birthweight, and the most commonly occurring birth complications: nuchal cord and meconium aspiration when the female child was on average 6years old, and for whom birth records were obtained. Concordance between reports was assessed using one-way random intra-class coefficients for continuous measures and kappa coefficients for dichotomous outcomes. Associations between maternal demographic and psychological factors and discrepancies also were tested. Concordance was excellent for continuously measured birthweight (ICC=0.85, p<0.001) and good for gestational age (ICC=0.68, p<0.001). Agreement was good for low birthweight (<2500g) (kappa=0.67, p<0.001), fair for preterm delivery (<37weeks gestation) (kappa=0.44, p<0.001), and poor for nuchal cord or meconium aspiration. Most discrepancies were characterized by presence according to birth record and absence according to maternal recall. Receipt of public assistance was associated with a decrease in discrepancy in report of nuchal cord. Concordance between maternal retrospective report and medical birth records varies across different types of perinatal events. There was little evidence that demographic or psychological factors increased the risk of discrepancies. Maternal recall based on continuous measures of perinatal factors may yield more valid data than dichotomous outcomes. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  16. Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties

    NASA Astrophysics Data System (ADS)

    Xie, Tian; Grossman, Jeffrey C.

    2018-04-01

    The use of machine learning methods for accelerating the design of crystalline materials usually requires manually constructed feature vectors or complex transformation of atom coordinates to input the crystal structure, which either constrains the model to certain crystal types or makes it difficult to provide chemical insights. Here, we develop a crystal graph convolutional neural networks framework to directly learn material properties from the connection of atoms in the crystal, providing a universal and interpretable representation of crystalline materials. Our method provides a highly accurate prediction of density functional theory calculated properties for eight different properties of crystals with various structure types and compositions after being trained with 1 04 data points. Further, our framework is interpretable because one can extract the contributions from local chemical environments to global properties. Using an example of perovskites, we show how this information can be utilized to discover empirical rules for materials design.

  17. Genetic and teratological considerations in the analysis of concordant and discordant abnormalities in twins.

    PubMed

    Gericke, G S

    1986-01-18

    Results from monozygotic (MZ) and dizygotic (DZ) twin research are often used in an attempt to gain a clearer understanding of the 'nature v. nurture' dilemma. Discordance between MZ twins has been considered to be environmental, and greater concordance in MZ compared with DZ pairs to be genetic. Current genetic and teratological theories considerably complicate the interpretation of concordance and discordance of abnormalities. The high rate of discordant intra-uterine death recently demonstrated in twins may profoundly influence the value of epidemiological studies usually performed in later life. Furthermore, indirect zygosity estimations based on sex ratios in DZ twins may be flawed because it is now recognized that increasing numbers of conditions are genetically heterogeneous. Emphasis is laid on problems of interpretation of discordance and concordance for developmental abnormalities in twins, and some possible mechanisms for their induction are discussed. Basic genetic concepts relevant to the expression of abnormalities in twins are outlined.

  18. Blood-based detection of RAS mutations to guide anti-EGFR therapy in colorectal cancer patients: concordance of results from circulating tumor DNA and tissue-based RAS testing.

    PubMed

    Schmiegel, Wolff; Scott, Rodney J; Dooley, Susan; Lewis, Wendy; Meldrum, Cliff J; Pockney, Peter; Draganic, Brian; Smith, Steve; Hewitt, Chelsee; Philimore, Hazel; Lucas, Amanda; Shi, Elva; Namdarian, Kateh; Chan, Timmy; Acosta, Danilo; Ping-Chang, Su; Tannapfel, Andrea; Reinacher-Schick, Anke; Uhl, Waldemar; Teschendorf, Christian; Wolters, Heiner; Stern, Josef; Viebahn, Richard; Friess, Helmut; Janssen, Klaus-Peter; Nitsche, Ulrich; Slotta-Huspenina, Julia; Pohl, Michael; Vangala, Deepak; Baraniskin, Alexander; Dockhorn-Dworniczak, Barbara; Hegewisch-Becker, Susanne; Ronga, Philippe; Edelstein, Daniel L; Jones, Frederick S; Hahn, Stephan; Fox, Stephen B

    2017-02-01

    An accurate blood-based RAS mutation assay to determine eligibility of metastatic colorectal cancer (mCRC) patients for anti-EGFR therapy would benefit clinical practice by better informing decisions to administer treatment independent of tissue availability. The objective of this study was to determine the level of concordance between plasma and tissue RAS mutation status in patients with mCRC to gauge whether blood-based RAS mutation testing is a viable alternative to standard-of-care RAS tumor testing. RAS testing was performed on plasma samples from newly diagnosed metastatic patients, or from recurrent mCRC patients using the highly sensitive digital PCR technology, BEAMing (beads, emulsions, amplification, and magnetics), and compared with DNA sequencing data of respective FFPE (formalin-fixed paraffin-embedded) tumor samples. Discordant tissue RAS results were re-examined by BEAMing, if possible. The prevalence of RAS mutations detected in plasma (51%) vs. tumor (53%) was similar, in accord with the known prevalence of RAS mutations observed in mCRC patient populations. The positive agreement between plasma and tumor RAS results was 90.4% (47/52), the negative agreement was 93.5% (43/46), and the overall agreement (concordance) was 91.8% (90/98). The high concordance of plasma and tissue results demonstrates that blood-based RAS mutation testing is a viable alternative to tissue-based RAS testing. © 2016 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

  19. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

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

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  20. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    DOE PAGES

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; ...

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  1. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory.

    PubMed

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; Drisdell, Walter S; Shirley, Eric L; Prendergast, David

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can be rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.

  2. Concordance of Gleason grading with three-dimensional ultrasound systematic biopsy and biopsy core pre-embedding.

    PubMed

    van der Aa, Anouk A M A; Mannaerts, Christophe K; van der Linden, Hans; Gayet, Maudy; Schrier, Bart Ph; Mischi, Massimo; Beerlage, Harrie P; Wijkstra, Hessel

    2018-02-01

    To determine the value of a three-dimensional (3D) greyscale transrectal ultrasound (TRUS)-guided prostate biopsy system and biopsy core pre-embedding method on concordance between Gleason scores of needle biopsies and radical prostatectomy (RP) specimens. Retrospective analysis of prostate biopsies and subsequent RP for PCa in the Jeroen Bosch Hospital, the Netherlands, from 2007 to 2016. Two cohorts were analysed: conventional 2D TRUS-guided biopsies and RP (2007-2013, n = 266) versus 3D TRUS-guided biopsies with pre-embedding (2013-2016, n = 129). The impact of 3D TRUS-guidance with pre-embedding on Gleason score (GS) concordance between biopsy and RP was evaluated using the κ-coefficient. Predictors of biopsy GS 6 upgrading were assessed using logistic regression models. Gleason concordance was comparable between the two cohorts with a κ = 0.44 for the 3D cohort, compared to κ = 0.42 for the 2D cohort. 3D TRUS-guidance with pre-embedding, did not significantly affect the risk of biopsy GS 6 upgrading in univariate and multivariate analysis. 3D TRUS-guidance with biopsy core pre-embedding did not improve Gleason concordance. Improved detection techniques are needed for recognition of low-grade disease upgrading.

  3. An empirical approach to improving tidal predictions using recent real-time tide gauge data

    NASA Astrophysics Data System (ADS)

    Hibbert, Angela; Royston, Samantha; Horsburgh, Kevin J.; Leach, Harry

    2014-05-01

    Classical harmonic methods of tidal prediction are often problematic in estuarine environments due to the distortion of tidal fluctuations in shallow water, which results in a disparity between predicted and observed sea levels. This is of particular concern in the Bristol Channel, where the error associated with tidal predictions is potentially greater due to an unusually large tidal range of around 12m. As such predictions are fundamental to the short-term forecasting of High Water (HW) extremes, it is vital that alternative solutions are found. In a pilot study, using a year-long observational sea level record from the Port of Avonmouth in the Bristol Channel, the UK National Tidal and Sea Level Facility (NTSLF) tested the potential for reducing tidal prediction errors, using three alternatives to the Harmonic Method of tidal prediction. The three methods evaluated were (1) the use of Artificial Neural Network (ANN) models, (2) the Species Concordance technique and (3) a simple empirical procedure for correcting Harmonic Method High Water predictions based upon a few recent observations (referred to as the Empirical Correction Method). This latter method was then successfully applied to sea level records from an additional 42 of the 45 tide gauges that comprise the UK Tide Gauge Network. Consequently, it is to be incorporated into the operational systems of the UK Coastal Monitoring and Forecasting Partnership in order to improve short-term sea level predictions for the UK and in particular, the accurate estimation of HW extremes.

  4. Accurate prediction of acute fish toxicity of fragrance chemicals with the RTgill-W1 cell assay.

    PubMed

    Natsch, Andreas; Laue, Heike; Haupt, Tina; von Niederhäusern, Valentin; Sanders, Gordon

    2018-03-01

    Testing for acute fish toxicity is an integral part of the environmental safety assessment of chemicals. A true replacement of primary fish tissue was recently proposed using cell viability in a fish gill cell line (RTgill-W1) as a means of predicting acute toxicity, showing good predictivity on 35 chemicals. To promote regulatory acceptance, the predictivity and applicability domain of novel tests need to be carefully evaluated on chemicals with existing high-quality in vivo data. We applied the RTgill-W1 cell assay to 38 fragrance chemicals with a wide range of both physicochemical properties and median lethal concentration (LC50) values and representing a diverse range of chemistries. A strong correlation (R 2  = 0.90-0.94) between the logarithmic in vivo LC50 values, based on fish mortality, and the logarithmic in vitro median effect concentration (EC50) values based on cell viability was observed. A leave-one-out analysis illustrates a median under-/overprediction from in vitro EC50 values to in vivo LC50 values by a factor of 1.5. This assay offers a simple, accurate, and reliable alternative to in vivo acute fish toxicity testing for chemicals, presumably acting mainly by a narcotic mode of action. Furthermore, the present study provides validation of the predictivity of the RTgill-W1 assay on a completely independent set of chemicals that had not been previously tested and indicates that fragrance chemicals are clearly within the applicability domain. Environ Toxicol Chem 2018;37:931-941. © 2017 SETAC. © 2017 SETAC.

  5. Lexington and Concord, Massachusetts

    NASA Technical Reports Server (NTRS)

    2007-01-01

    On the night of April 18/19, 1775, Paul Revere rode from Boston to Lexington, Mass., to warn John Hancock and Samuel Adams that the British were coming. On April 19, there was a skirmish on the Battle Green, with shots being fired both from the Battle Green and the nearby Buckman Tavern. After the rout, the British marched on toward Concord. The battle in Lexington allowed the Concord militia time to organize at the Old North Bridge, where they were able to turn back the British and prevent them from capturing and destroying the militia's arms stores.

    This image from the Advanced Spaceborne Thermal Emission and Reflection Radiometer instrument on NASA's Terra satellite, acquired in October 2006, depicts this area of great importance in U.S. history. These two small Massachusetts towns are now dwarfed by Hanscom Air Force Base between them.

    With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra spacecraft. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

    The broad spectral coverage and high spectral resolution of ASTER provides scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    The U.S. science

  6. A cross-race effect in metamemory: Predictions of face recognition are more accurate for members of our own race

    PubMed Central

    Hourihan, Kathleen L.; Benjamin, Aaron S.; Liu, Xiping

    2012-01-01

    The Cross-Race Effect (CRE) in face recognition is the well-replicated finding that people are better at recognizing faces from their own race, relative to other races. The CRE reveals systematic limitations on eyewitness identification accuracy and suggests that some caution is warranted in evaluating cross-race identification. The CRE is a problem because jurors value eyewitness identification highly in verdict decisions. In the present paper, we explore how accurate people are in predicting their ability to recognize own-race and other-race faces. Caucasian and Asian participants viewed photographs of Caucasian and Asian faces, and made immediate judgments of learning during study. An old/new recognition test replicated the CRE: both groups displayed superior discriminability of own-race faces, relative to other-race faces. Importantly, relative metamnemonic accuracy was also greater for own-race faces, indicating that the accuracy of predictions about face recognition is influenced by race. This result indicates another source of concern when eliciting or evaluating eyewitness identification: people are less accurate in judging whether they will or will not recognize a face when that face is of a different race than they are. This new result suggests that a witness’s claim of being likely to recognize a suspect from a lineup should be interpreted with caution when the suspect is of a different race than the witness. PMID:23162788

  7. Accurate RNA 5-methylcytosine site prediction based on heuristic physical-chemical properties reduction and classifier ensemble.

    PubMed

    Zhang, Ming; Xu, Yan; Li, Lei; Liu, Zi; Yang, Xibei; Yu, Dong-Jun

    2018-06-01

    RNA 5-methylcytosine (m 5 C) is an important post-transcriptional modification that plays an indispensable role in biological processes. The accurate identification of m 5 C sites from primary RNA sequences is especially useful for deeply understanding the mechanisms and functions of m 5 C. Due to the difficulty and expensive costs of identifying m 5 C sites with wet-lab techniques, developing fast and accurate machine-learning-based prediction methods is urgently needed. In this study, we proposed a new m 5 C site predictor, called M5C-HPCR, by introducing a novel heuristic nucleotide physicochemical property reduction (HPCR) algorithm and classifier ensemble. HPCR extracts multiple reducts of physical-chemical properties for encoding discriminative features, while the classifier ensemble is applied to integrate multiple base predictors, each of which is trained based on a separate reduct of the physical-chemical properties obtained from HPCR. Rigorous jackknife tests on two benchmark datasets demonstrate that M5C-HPCR outperforms state-of-the-art m 5 C site predictors, with the highest values of MCC (0.859) and AUC (0.962). We also implemented the webserver of M5C-HPCR, which is freely available at http://cslab.just.edu.cn:8080/M5C-HPCR/. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Clinicopathological concordance and discordance in three monozygotic twin pairs with familial Alzheimer's disease

    PubMed Central

    Brickell, Kiri L; Leverenz, James B; Steinbart, Ellen J; Rumbaugh, Malia; Schellenberg, Gerard D; Nochlin, David; Lampe, Thomas H; Holm, Ida E; Van Deerlin, Vivianna; Yuan, Wuxing; Bird, Thomas D

    2007-01-01

    Aim Neuropathological examination of both individuals in a monozygotic (MZ) twin pair with Alzheimer's disease (AD) is rare, especially in the molecular genetic era. We had the opportunity to assess the concordance and discordance of clinical presentation and neuropathology in three MZ twin pairs with AD. Methods The MZ twins were identified and characterised by the University of Washington Alzheimer's Disease Research Center. We reviewed the available clinical and neuropathological records for all six cases looking specifically for concordance and discordance of clinical phenotype, neuritic amyloid plaques (NP), neurofibrillary tangles (NFT) and Lewy related pathology (LRP). Results Discordance in age of onset for developing AD in the MZ twins varied from 4 to 18 years. Clinical presentations also differed between twins. One twin presented with a dementia with Lewy Body clinical syndrome while the other presented with typical clinical AD. Neuropathology within the MZ twin pairs was concordant for NP and NFT, regardless of duration of disease, and was discordant for LRP. This difference was most marked in the late onset AD twin pair. One pair was found to have a mutation in presenilin‐1 (PS1) (A79V) with remarkably late onset in a family member. Conclusions MZ twins with AD can vary considerably in age of onset, presentation and disease duration. The concordance of NP and NFT pathological change and the discordance of LRP support the concept that, in AD, the former are primarily under genetic control whereas the latter (LRP) is more influenced by disease duration and environmental factors. The A79V mutation in PS1 can be associated with very late onset of dementia. PMID:17615170

  9. The Concord Pavilion: A City Succeeds at Promoting the Performing Arts.

    ERIC Educational Resources Information Center

    Toffoli, John, Jr.

    1983-01-01

    The author attributes the success of the Concord Pavilion (California) to two things, marketing and experience. Experience has taught administrators to make better, more selective programing choices, and marketing has helped them to sell those programs and events. (JMK)

  10. Fertility intentions among HIV-infected, sero-concordant Kenyan couples in Nyanza Province, Kenya

    PubMed Central

    Dworkin, Shari; Harrington, Elizabeth; Kwena, Zachary; Onono, Maricianah; Bukusi, Elizabeth; Cohen, Craig R.; Grossma, Daniel; Newmann, Sara J.

    2013-01-01

    Research in sub-Saharan Africa has shown significant diversity in how HIV influences infected couples’ fertility intentions. Supporting HIV-infected, sero-concordant couples in sub-Saharan Africa to make informed choices about their fertility options has not received sufficient attention. In-depth interviews were conducted among 23 HIV-positive, sero-concordant married couples in Kenya, to better understand how HIV impacted fertility intentions. HIV compelled many to reconsider fertility plans, sometimes promoting childbearing intentions in some individuals but often reducing fertility plans among most, largely due to fears of early death, health concerns, stigma, perinatal HIV transmission and financial difficulties (particularly in men). Preferences for sons and large families influenced some couples’ intentions to continue childbearing, although none had discussed their intentions with health care providers. Additional support and services for HIV-infected, sero-concordant couples are needed. Family planning counselling should be tailored to the unique concerns of HIV-infected couples, addressing perinatal transmission but also individual, couple-level, and socio-cultural fertility expectations. Community-level programmes are needed to reduce stigma and make HIV-infected couples more comfortable in discussing fertility intentions with health care providers. PMID:23885924

  11. High-resolution microendoscope images of middle ear cholesteatoma and surrounding tissue: evaluation of interobserver concordance.

    PubMed

    Bradley, James; Jiang, Nancy; Levy, Lauren; Richards-Kortum, Rebecca; Sikora, Andrew; Smouha, Eric

    2014-04-01

    Investigate how accurately otolaryngologists could differentiate between images obtained with high-resolution microendoscopy (HRME) of ex vivo cholesteatoma specimens and surrounding middle ear epithelium. HRME images of surgically resected cholesteatoma and middle ear epithelium were obtained and otolaryngologists classified these images. Tertiary medical center. Resected cholesteatoma and middle ear epithelium were stained with a contrast agent, proflavine, and HRME images were captured. Specimens were sent for standard histopathology and compared with HRME images. Quality-controlled images were used to assemble a training set. After viewing training images, otolaryngologists without prior cholesteatoma HRME experience reviewed and classified test images. Ten cholesteatoma and 9 middle ear specimens were collected, of which 17 representative cholesteatoma and 19 middle ear epithelium images were extracted for a testing set. Qualitative analysis for concordance between HRME images and histological images yielded a strong correlation between modalities. The mean accuracy of all reviewers in correctly identifying images was 95% (95% confidence interval [CI], 92%-98%). The sensitivity to correctly detect cholesteatoma images was 98% (95% CI, 93%-100%), and the specificity was 92% (95% CI, 87%-97%). The Fleiss kappa interrater reliability score was 0.83, (95% CI, 0.77-0.89). Medical professionals can quickly be trained to accurately distinguish between HRME images of cholesteatoma and normal middle ear epithelium, both of which have distinct imaging characteristics. Real-time HRME optical imaging can potentially improve the results of otologic surgery by allowing for extirpation of cholesteatomas while eliminating residual disease.

  12. Emotion dysregulation and dyadic conflict in depressed and typical adolescents: Evaluating concordance across psychophysiological and observational measures

    PubMed Central

    Crowell, Sheila E.; Baucom, Brian R.; Yaptangco, Mona; Bride, Daniel; Hsiao, Ray; McCauley, Elizabeth; Beauchaine, Theodore P.

    2014-01-01

    Many depressed adolescents experience difficulty regulating their emotions. These emotion regulation difficulties appear to emerge in part from socialization processes within families and then generalize to other contexts. However, emotion dysregulation is typically assessed within the individual, rather than in the social relationships that shape and maintain dysregulation. In this study, we evaluated concordance of physiological and observational measures of emotion dysregulation during interpersonal conflict, using a multilevel actor-partner interdependence model (APIM). Participants were 75 mother-daughter dyads, including 50 depressed adolescents with or without a history of self-injury, and 25 typically developing controls. Behavior dysregulation was operationalized as observed aversiveness during a conflict discussion, and physiological dysregulation was indexed by respiratory sinus arrhythmia (RSA). Results revealed different patterns of concordance for control versus depressed participants. Controls evidenced a concordant partner (between-person) effect, and showed increased physiological regulation during minutes when their partner was more aversive. In contrast, clinical dyad members displayed a concordant actor (within-person) effect, becoming simultaneously physiologically and behaviorally dysregulated. Results inform current understanding of emotion dysregulation across multiple levels of analysis. PMID:24607894

  13. [Are non-clinical studies predictive of adverse events in humans?].

    PubMed

    Claude, N

    2007-09-01

    The predictibility of adverse events induced by drugs in non-clinical safety studies performed on in vitro and/or in vivo models is a key point for the safety of humans exposed to pharmaceuticals. The strength and the weakness of animal studies to predict human toxicity were assessed by an international study on the concordance of the toxicity of 150 pharmaceuticals observed in humans with that observed in experimental animals. The results showed a good correlation (70% of the adverse events in humans were detected in animal studies) and an early time to first appearance of concordant animal toxicity: 94% were first observed in studies of 1 month or less in duration. The highest incidence of overall concordance was seen in hematological and cardiovascular adverse effects and the least was seen in cutaneous and ophthalmological adverse effects. These studies, scientifically and regulatory standardized, need, in some cases to be adapted to specific problems linked to sensitive populations (young, old or with a pathology which could be worsened by the drug), or specific pharmaceuticals (produced by biotechnology). Some severe adverse events are not detected in conventional animal models (immuno-allergy, idiosyncrasy). Taken together, these elements support the value of toxicology studies to predict many human toxic events associated with pharmaceuticals. Nevertheless, a part of human toxicity is not detected by these experimental approaches, and new tools developed through progress in biology and bio-informatics should reduce this uncertainly margin.

  14. Accuracy of gap analysis habitat models in predicting physical features for wildlife-habitat associations in the southwest U.S.

    USGS Publications Warehouse

    Boykin, K.G.; Thompson, B.C.; Propeck-Gray, S.

    2010-01-01

    Despite widespread and long-standing efforts to model wildlife-habitat associations using remotely sensed and other spatially explicit data, there are relatively few evaluations of the performance of variables included in predictive models relative to actual features on the landscape. As part of the National Gap Analysis Program, we specifically examined physical site features at randomly selected sample locations in the Southwestern U.S. to assess degree of concordance with predicted features used in modeling vertebrate habitat distribution. Our analysis considered hypotheses about relative accuracy with respect to 30 vertebrate species selected to represent the spectrum of habitat generalist to specialist and categorization of site by relative degree of conservation emphasis accorded to the site. Overall comparison of 19 variables observed at 382 sample sites indicated ???60% concordance for 12 variables. Directly measured or observed variables (slope, soil composition, rock outcrop) generally displayed high concordance, while variables that required judgments regarding descriptive categories (aspect, ecological system, landform) were less concordant. There were no differences detected in concordance among taxa groups, degree of specialization or generalization of selected taxa, or land conservation categorization of sample sites with respect to all sites. We found no support for the hypothesis that accuracy of habitat models is inversely related to degree of taxa specialization when model features for a habitat specialist could be more difficult to represent spatially. Likewise, we did not find support for the hypothesis that physical features will be predicted with higher accuracy on lands with greater dedication to biodiversity conservation than on other lands because of relative differences regarding available information. Accuracy generally was similar (>60%) to that observed for land cover mapping at the ecological system level. These patterns demonstrate

  15. Core self-evaluations and job and life satisfaction: the role of self-concordance and goal attainment.

    PubMed

    Judge, Timothy A; Bono, Joyce E; Erez, Amir; Locke, Edwin A

    2005-03-01

    The present study tested a model explaining how the core self-evaluations (i.e., positive self-regard) concept is linked to job and life satisfaction. The self-concordance model, which focuses on motives underlying goal pursuit, was used as an explanatory framework. Data were collected from 2 samples: (a) 183 university students (longitudinal measures of goal attainment and life satisfaction were used) and (b) 251 employees (longitudinal measures of goal attainment and job satisfaction were utilized). In both studies, the core self-evaluations concept was positively related to goal self-concordance, meaning that individuals with positive self-regard were more likely to pursue goals for intrinsic and identified (value-congruent) reasons. Furthermore, in both studies, goal self-concordance was related to satisfaction (job satisfaction in Study 1 and life satisfaction in Study 2).

  16. The NAFLD Index: A Simple and Accurate Screening Tool for the Prediction of Non-Alcoholic Fatty Liver Disease.

    PubMed

    Ichino, Naohiro; Osakabe, Keisuke; Sugimoto, Keiko; Suzuki, Koji; Yamada, Hiroya; Takai, Hiroji; Sugiyama, Hiroko; Yukitake, Jun; Inoue, Takashi; Ohashi, Koji; Hata, Tadayoshi; Hamajima, Nobuyuki; Nishikawa, Toru; Hashimoto, Senju; Kawabe, Naoto; Yoshioka, Kentaro

    2015-01-01

    Non-alcoholic fatty liver disease (NAFLD) is a common debilitating condition in many industrialized countries that increases the risk of cardiovascular disease. The aim of this study was to derive a simple and accurate screening tool for the prediction of NAFLD in the Japanese population. A total of 945 participants, 279 men and 666 women living in Hokkaido, Japan, were enrolled among residents who attended a health check-up program from 2010 to 2014. Participants with an alcohol consumption > 20 g/day and/or a chronic liver disease, such as chronic hepatitis B, chronic hepatitis C or autoimmune hepatitis, were excluded from this study. Clinical and laboratory data were examined to identify predictive markers of NAFLD. A new predictive index for NAFLD, the NAFLD index, was constructed for men and for women. The NAFLD index for men = -15.5693+0.3264 [BMI] +0.0134 [triglycerides (mg/dl)], and for women = -31.4686+0.3683 [BMI] +2.5699 [albumin (g/dl)] +4.6740[ALT/AST] -0.0379 [HDL cholesterol (mg/dl)]. The AUROC of the NAFLD index for men and for women was 0.87(95% CI 0.88-1.60) and 0.90 (95% CI 0.66-1.02), respectively. The cut-off point of -5.28 for men predicted NAFLD with an accuracy of 82.8%. For women, the cut-off point of -7.65 predicted NAFLD with an accuracy of 87.7%. A new index for the non-invasive prediction of NAFLD, the NAFLD index, was constructed using available clinical and laboratory data. This index is a simple screening tool to predict the presence of NAFLD.

  17. Australian validation of the Cancer of the Prostate Risk Assessment Post-Surgical score to predict biochemical recurrence after radical prostatectomy.

    PubMed

    Beckmann, Kerri; O'Callaghan, Michael; Vincent, Andrew; Roder, David; Millar, Jeremy; Evans, Sue; McNeil, John; Moretti, Kim

    2018-03-01

    The Cancer of the Prostate Risk Assessment Post-Surgical (CAPRA-S) score is a simple post-operative risk assessment tool predicting disease recurrence after radical prostatectomy, which is easily calculated using available clinical data. To be widely useful, risk tools require multiple external validations. We aimed to validate the CAPRA-S score in an Australian multi-institutional population, including private and public settings and reflecting community practice. The study population were all men on the South Australian Prostate Cancer Clinical Outcomes Collaborative Database with localized prostate cancer diagnosed during 1998-2013, who underwent radical prostatectomy without adjuvant therapy (n = 1664). Predictive performance was assessed via Kaplan-Meier and Cox proportional regression analyses, Harrell's Concordance index, calibration plots and decision curve analysis. Biochemical recurrence occurred in 342 (21%) cases. Five-year recurrence-free probabilities for CAPRA-S scores indicating low (0-2), intermediate (3-5) and high risk were 95, 79 and 46%, respectively. The hazard ratio for CAPRA-S score increments was 1.56 (95% confidence interval 1.49-1.64). The Concordance index for 5-year recurrence-free survival was 0.77. The calibration plot showed good correlation between predicted and observed recurrence-free survival across scores. Limitations include the retrospective nature and small numbers with higher CAPRA-S scores. The CAPRA-S score is an accurate predictor of recurrence after radical prostatectomy in our cohort, supporting its utility in the Australian setting. This simple tool can assist in post-surgical selection of patients who would benefit from adjuvant therapy while avoiding morbidity among those less likely to benefit. © 2017 Royal Australasian College of Surgeons.

  18. A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information.

    PubMed

    Yi, Hai-Cheng; You, Zhu-Hong; Huang, De-Shuang; Li, Xiao; Jiang, Tong-Hai; Li, Li-Ping

    2018-06-01

    The interactions between non-coding RNAs (ncRNAs) and proteins play an important role in many biological processes, and their biological functions are primarily achieved by binding with a variety of proteins. High-throughput biological techniques are used to identify protein molecules bound with specific ncRNA, but they are usually expensive and time consuming. Deep learning provides a powerful solution to computationally predict RNA-protein interactions. In this work, we propose the RPI-SAN model by using the deep-learning stacked auto-encoder network to mine the hidden high-level features from RNA and protein sequences and feed them into a random forest (RF) model to predict ncRNA binding proteins. Stacked assembling is further used to improve the accuracy of the proposed method. Four benchmark datasets, including RPI2241, RPI488, RPI1807, and NPInter v2.0, were employed for the unbiased evaluation of five established prediction tools: RPI-Pred, IPMiner, RPISeq-RF, lncPro, and RPI-SAN. The experimental results show that our RPI-SAN model achieves much better performance than other methods, with accuracies of 90.77%, 89.7%, 96.1%, and 99.33%, respectively. It is anticipated that RPI-SAN can be used as an effective computational tool for future biomedical researches and can accurately predict the potential ncRNA-protein interacted pairs, which provides reliable guidance for biological research. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

    PubMed

    Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

    2017-11-06

    Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

  20. Concordance between fine-needle aspiration and core biopsies for osseous lesions by lesion imaging appearance and CT attenuation.

    PubMed

    Li, John; Weissberg, Zoe; Bevilacqua, Thomas A; Yu, Gordon; Weber, Kristy; Sebro, Ronnie

    2018-04-01

    To compare the concordance between fine-needle aspiration and core biopsies for osseous lesions by lesion imaging appearance and CT attenuation. Retrospective review of 215 FNAs of osseous lesions performed in conjunction with core biopsy at our institution over a 6-year period (2011-2016). FNAs were interpreted independently of core biopsies. We assessed if FNA in conjunction with core biopsy increased diagnostic accuracy compared to core biopsy alone. We also calculated the concordance between FNA and core biopsy by lesion appearance, lesion CT attenuation, lesion histology, lesion location and FNA needle gauge size. Core biopsy alone provided the diagnosis in 207/215 cases (96.3%), however, the FNA provided the diagnosis in the remaining 8/215 cases (3.7%) where the core biopsy was non-diagnostic. There were 154 (71.6%) lytic lesions, 21 (9.8%) blastic lesions, 25 (11.6%) mixed lytic and blastic lesions and 15 (7.0%) lesions that were neither lytic nor blastic. The concordance between FNA and core biopsy for lytic osseous lesions (136/154 cases, 88.3%) was statistically significantly higher than that for blastic osseous lesions (13/21 cases, 61.9%) [P = 4.2 × 10 -3 ; 95% CI (0.02, 0.50)]. The concordance between FNA and core biopsy was higher for low-attenuation- (110/126) than high-attenuation (58/77) lesions (P = 0.028). The concordance between FNA and core biopsy was also higher for metastases (102/119 cases, 85.7%) than non-metastases (78/96, 81.3%) [P = 0.487; 95% CI (- 0.15, 0.065)]. There was no difference in the rate of concordance between FNA and core biopsy by lesion location or FNA needle gauge size (P > 0.05). FNA with core biopsy increases diagnostic rate compared to core biopsy alone or FNA alone. The concordance between FNA and core biopsy is higher for lytic lesions than for blastic lesions; and higher for low-attenuation lesions than for high-attenuation lesions.

  1. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

    PubMed

    Yu, Haoyu S; Deng, Yuqing; Wu, Yujie; Sindhikara, Dan; Rask, Amy R; Kimura, Takayuki; Abel, Robert; Wang, Lingle

    2017-12-12

    Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.

  2. Assessing sex assignment concordance with genotype and phenotype.

    PubMed

    Suresh, Deepa; Crawford, Jessica; Axelrad, Marni E; Gunn, Sheila K; McCullough, Laurence; Smith, O' Brian; Sutton, Vernon R; Roth, David; Karaviti, Lefkothea P; Dietrich, Jennifer E

    2013-03-14

    To catalogue patients with DSD and to assess the concordance of genotype and phenotype with sex assignment at birth compared to sex assignment before and following assessment by a Gender Medicine Team (GMT) at one institution, as an initial step in formulating standardized guidelines for management of these conditions. After obtaining IRB approval, a retrospective chart review was conducted patients seen in the Gender Medicine Clinic (GMC) between 2006-2009 at Texas Children's Hospital (TCH), Houston, Texas. McNemar's test and Kappa agreement provided associations of various factors with sex assignment at birth prior to GMT assessment and after GMT assessment. Forty-seven patients seen in the GMC with confirmed DSD. Forty-seven patients met the inclusion criteria. The mean age of the patients at the time of GMT evaluation was 9.1+/-6.1 years; 61.7% had male karyotype, and 38.3% had female karyotype; 51.1% had a male external phenotype, 42.6% had a female external phenotype, and 6.4% had phenotypic ambiguity. Sex assignment was concordant with genotype and phenotype in 63.8% and 86.4%, respectively of cases at the time of birth and in 76.6% and 97.7%, respectively, of cases after assessment by GMT. Long-term outcomes are needed to establish standardized practice guidelines for decision-making.

  3. Concordance correlation for model performance assessment: An example with reference evapotranspiration

    USDA-ARS?s Scientific Manuscript database

    Procedures for assessing model performance in agronomy are often arbitrary and not always helpful. An omnibus analysis statistic, concordance correlation, is widely known and used in many other sciences. An illustrative example is presented here. The analysis assumes the exact relationship “observat...

  4. Limited Sampling Strategy for Accurate Prediction of Pharmacokinetics of Saroglitazar: A 3-point Linear Regression Model Development and Successful Prediction of Human Exposure.

    PubMed

    Joshi, Shuchi N; Srinivas, Nuggehally R; Parmar, Deven V

    2018-03-01

    Our aim was to develop and validate the extrapolative performance of a regression model using a limited sampling strategy for accurate estimation of the area under the plasma concentration versus time curve for saroglitazar. Healthy subject pharmacokinetic data from a well-powered food-effect study (fasted vs fed treatments; n = 50) was used in this work. The first 25 subjects' serial plasma concentration data up to 72 hours and corresponding AUC 0-t (ie, 72 hours) from the fasting group comprised a training dataset to develop the limited sampling model. The internal datasets for prediction included the remaining 25 subjects from the fasting group and all 50 subjects from the fed condition of the same study. The external datasets included pharmacokinetic data for saroglitazar from previous single-dose clinical studies. Limited sampling models were composed of 1-, 2-, and 3-concentration-time points' correlation with AUC 0-t of saroglitazar. Only models with regression coefficients (R 2 ) >0.90 were screened for further evaluation. The best R 2 model was validated for its utility based on mean prediction error, mean absolute prediction error, and root mean square error. Both correlations between predicted and observed AUC 0-t of saroglitazar and verification of precision and bias using Bland-Altman plot were carried out. None of the evaluated 1- and 2-concentration-time points models achieved R 2 > 0.90. Among the various 3-concentration-time points models, only 4 equations passed the predefined criterion of R 2 > 0.90. Limited sampling models with time points 0.5, 2, and 8 hours (R 2 = 0.9323) and 0.75, 2, and 8 hours (R 2 = 0.9375) were validated. Mean prediction error, mean absolute prediction error, and root mean square error were <30% (predefined criterion) and correlation (r) was at least 0.7950 for the consolidated internal and external datasets of 102 healthy subjects for the AUC 0-t prediction of saroglitazar. The same models, when applied to the AUC 0-t

  5. Towards more accurate and reliable predictions for nuclear applications

    NASA Astrophysics Data System (ADS)

    Goriely, Stephane; Hilaire, Stephane; Dubray, Noel; Lemaître, Jean-François

    2017-09-01

    The need for nuclear data far from the valley of stability, for applications such as nuclear astrophysics or future nuclear facilities, challenges the robustness as well as the predictive power of present nuclear models. Most of the nuclear data evaluation and prediction are still performed on the basis of phenomenological nuclear models. For the last decades, important progress has been achieved in fundamental nuclear physics, making it now feasible to use more reliable, but also more complex microscopic or semi-microscopic models in the evaluation and prediction of nuclear data for practical applications. Nowadays mean-field models can be tuned at the same level of accuracy as the phenomenological models, renormalized on experimental data if needed, and therefore can replace the phenomenological inputs in the evaluation of nuclear data. The latest achievements to determine nuclear masses within the non-relativistic HFB approach, including the related uncertainties in the model predictions, are discussed. Similarly, recent efforts to determine fission observables within the mean-field approach are described and compared with more traditional existing models.

  6. Emergency Department Management of Patients With Febrile Neutropenia: Guideline Concordant or Overly Aggressive?

    PubMed

    Baugh, Christopher W; Wang, Thomas J; Caterino, Jeffrey M; Baker, Olesya N; Brooks, Gabriel A; Reust, Audrey C; Pallin, Daniel J

    2017-01-01

    The Infectious Diseases Society of America and the American Society of Clinical Oncology recommend risk stratification of patients with febrile neutropenia (FN) and discharge with oral antibiotics for low-risk patients. We studied guideline concordance and clinical outcomes of FN management in our emergency department (ED). Our urban, tertiary care teaching hospital provides all emergency and inpatient services to a large comprehensive cancer center. We performed a structured chart review of all FN patients seen in our ED from January 2010 to December 2014. Using electronic medical records, we identified all visits by patients with fever and an absolute neutrophil count of <1000 cells/mm 3 and then included only patients without a clear source of infection. Following national guidelines, we classified patients as low or high risk and assessed guideline concordance in disposition and parenteral versus oral antibiotic therapy by risk category as our main outcome measure. Of 173 qualifying visits, we classified 44 (25%) as low risk and 129 (75%) as high risk. Management was guideline concordant in 121 (70%, 95% confidence interval [CI] = 63% to 77%). Management was guideline discordant in 43 (98%, 95% CI = 88% to 100%) of low-risk patients versus 9 (7%, 95% CI = 3% to 13%) of high-risk patients (relative risk [RR] = 14, 95% CI = 7.5 to 26). Of 52 guideline-discordant cases, 36 (83%, 95% CI = 72% to 93%) involved low-risk cases with treatment that was more aggressive than recommended. Guideline concordance was low among low-risk patients, with management tending to be more aggressive than recommended. Unless data emerge that undermine the guidelines, we believe that many of these hospitalizations and parenteral antibiotic regimens can be avoided, decreasing the risks associated with hospitalization, while improving antibiotic stewardship and patient comfort. © 2016 by the Society for Academic Emergency Medicine.

  7. Complementary role of the Memorial Sloan Kettering Cancer Center nomogram to the American Joint Committee on Cancer system for the prediction of relapse of major salivary gland carcinoma after surgery.

    PubMed

    Chou, Wen-Chi; Chang, Kai-Ping; Lu, Chang-Hsien; Chen, Miao-Fen; Cheng, Yu-Fan; Yeh, Kun-Yun; Wang, Cheng-Hsu; Lin, Yung-Chang; Yeh, Ta-Sen

    2017-05-01

    The purpose of this study was to test the Memorial Sloan Kettering Cancer Center (MSKCC) nomogram in predicting recurrence risk of major salivary gland carcinoma in an Asian cohort. We retrospectively enrolled 149 patients who had undergone intended curative resections for major salivary gland carcinoma between 2007 and 2012. The performance of the MSKCC nomogram and the American Joint Committee on Cancer (AJCC) seventh staging system in predicting recurrence risk was compared. The MSKCC nomogram and the AJCC staging system both accurately predicted the 5-year recurrence probabilities, with the concordance index (c-index = 0.82; 95% confidence interval [CI], 0.75-0.89 vs c-index, 0.77; 95% CI, 0.68-0.87; p = .45) in patients with major salivary gland carcinomas after curative surgeries. Comparing to the actual observed events, the calibration plot indicated that the MSKCC nomogram accurately estimated the recurrence in low-risk groups but tended to overestimate in high-risk groups. When using the MSKCC nomogram to predict the 5-year recurrence-free probability in each AJCC stage, the prediction was very good for patients with AJCC stages I and II disease (c-index = 0.92 and 0.90, respectively) and modest for those of AJCC stages III and IVa (c-index = 0.51 and 0.62, respectively). The MSKCC nomogram and the AJCC staging system each had its value in predicting recurrence of major salivary gland cancers. When using the MSKCC nomogram to predict the 5-year recurrence-free probability in each AJCC stage, the MSKCC nomogram was more accurate in predicting recurrence risks in those patients with AJCC stage I and II diseases than those with late-stage diseases. © 2017 Wiley Periodicals, Inc. Head Neck 39: 860-867, 2017. © 2017 Wiley Periodicals, Inc.

  8. The Kaiser Permanente Clinician Cultural and Linguistic Assessment Initiative: Research and Development in Patient–Provider Language Concordance

    PubMed Central

    MSN, Gayle Tang; Lanza, Oscar; Rodriguez, Fátima Marinely; Chang, Annie

    2011-01-01

    Patient–clinician language concordance is a critical component of the language access equation and is considered the gold standard for communication. As a result of lack of validated testing standards, measures, and tools, Kaiser Permanente developed the Clinician Cultural and Linguistic Assessment Initiative to ensure verifiable linguistic proficiency in clinical encounters and has established a standard level whereby the clinician is deemed to have a qualifying level of proficiency in communicating directly with patients independent of an interpreter. Our benchmarking efforts in language concordance have been rooted with the key aim to identify talented bilingual and bicultural clinician workforce and to establish the systems foundation to coordinate appropriate language services. We share accomplishments, lessons learned, and promising practices to inform future efforts in language concordance. PMID:21228282

  9. Accurate electrical prediction of memory array through SEM-based edge-contour extraction using SPICE simulation

    NASA Astrophysics Data System (ADS)

    Shauly, Eitan; Rotstein, Israel; Peltinov, Ram; Latinski, Sergei; Adan, Ofer; Levi, Shimon; Menadeva, Ovadya

    2009-03-01

    The continues transistors scaling efforts, for smaller devices, similar (or larger) drive current/um and faster devices, increase the challenge to predict and to control the transistor off-state current. Typically, electrical simulators like SPICE, are using the design intent (as-drawn GDS data). At more sophisticated cases, the simulators are fed with the pattern after lithography and etch process simulations. As the importance of electrical simulation accuracy is increasing and leakage is becoming more dominant, there is a need to feed these simulators, with more accurate information extracted from physical on-silicon transistors. Our methodology to predict changes in device performances due to systematic lithography and etch effects was used in this paper. In general, the methodology consists on using the OPCCmaxTM for systematic Edge-Contour-Extraction (ECE) from transistors, taking along the manufacturing and includes any image distortions like line-end shortening, corner rounding and line-edge roughness. These measurements are used for SPICE modeling. Possible application of this new metrology is to provide a-head of time, physical and electrical statistical data improving time to market. In this work, we applied our methodology to analyze a small and large array's of 2.14um2 6T-SRAM, manufactured using Tower Standard Logic for General Purposes Platform. 4 out of the 6 transistors used "U-Shape AA", known to have higher variability. The predicted electrical performances of the transistors drive current and leakage current, in terms of nominal values and variability are presented. We also used the methodology to analyze an entire SRAM Block array. Study of an isolation leakage and variability are presented.

  10. Patient-Provider Concordance with Behavioral Change Goals Drives Measures of Motivational Interviewing Consistency

    PubMed Central

    Laws, M. Barton; Rose, Gary S.; Beach, Mary Catherine; Lee, Yoojin; Rogers, William S.; Velasco, Alyssa Bianca; Wilson, Ira B.

    2015-01-01

    Objective Motivational Interviewing (MI) consistent talk by a counselor is thought to produce “change talk” in clients. However, it is possible that client resistance to behavior change can produce MI inconsistent counselor behavior. Methods We applied a coding scheme which identifies all of the behavioral counseling about a given issue during a visit (“episodes”), assesses patient concordance with the behavioral goal, and labels providers’ counseling style as facilitative or directive, to a corpus of routine outpatient visits by people with HIV. Using a different data set of comparable encounters, we applied the concepts of episode and concordance, and coded using the Motivational Interviewing Treatment Integrity system. Results Patient concordance/discordance was not observed to change during any episode. Provider directiveness was strongly associated with patient discordance in the first study, and MI inconsistency was strongly associated with discordance in the second. Conclusion Observations that MI-consistent behavior by medical providers is associated with patient change talk or outcomes should be evaluated cautiously, as patient resistance may provoke MI-inconsistency. Practice Implications Counseling episodes in routine medical visits are typically too brief for client talk to evolve toward change. Providers with limited training may have particular difficulty maintaining MI consistency with resistant clients. PMID:25791372

  11. Patient-provider concordance with behavioral change goals drives measures of motivational interviewing consistency.

    PubMed

    Laws, Michael Barton; Rose, Gary S; Beach, Mary Catherine; Lee, Yoojin; Rogers, William S; Velasco, Alyssa Bianca; Wilson, Ira B

    2015-06-01

    Motivational Interviewing (MI) consistent talk by a counselor is thought to produce "change talk" in clients. However, it is possible that client resistance to behavior change can produce MI inconsistent counselor behavior. We applied a coding scheme which identifies all of the behavioral counseling about a given issue during a visit ("episodes"), assesses patient concordance with the behavioral goal, and labels providers' counseling style as facilitative or directive, to a corpus of routine outpatient visits by people with HIV. Using a different data set of comparable encounters, we applied the concepts of episode and concordance, and coded using the Motivational Interviewing Treatment Integrity system. Patient concordance/discordance was not observed to change during any episode. Provider directiveness was strongly associated with patient discordance in the first study, and MI inconsistency was strongly associated with discordance in the second. Observations that MI-consistent behavior by medical providers is associated with patient change talk or outcomes should be evaluated cautiously, as patient resistance may provoke MI-inconsistency. Counseling episodes in routine medical visits are typically too brief for client talk to evolve toward change. Providers with limited training may have particular difficulty maintaining MI consistency with resistant clients. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Age Differences in Goal Concordance, Time Use, and Well-Being

    ERIC Educational Resources Information Center

    Chen, Yiwei; Lee, Yue-Ting; Pethtel, Olivia L.; Gutowitz, Michael S.; Kirk, Robert M.

    2012-01-01

    The primary purpose of the present study was to investigate age differences in goal concordance, time use, and Well-Being. Past research has found that despite age-related decline in life circumstances (e.g., health), the Well-Being of older adults is as high as young adults. The present study used a novel approach to explore the Paradox of…

  13. Cerebral asymmetry in twins: predictions of the right shift theory.

    PubMed

    Annett, Marian

    2003-01-01

    A study of the heritability of lobar brain volumes in twins has introduced a new approach to questions about the genetics of cerebral asymmetry. In addition to the classic comparison between monozygotic (MZ) and dizygotic (DZ) twins, a contrast was made between pairs of two right-handers (RR pairs) and pairs including one or more non-right-hander (non-RR pairs), in the light of the right shift (RS) theory of handedness. This paper explains the predictions of the RS model for pair concordance for genotype, cerebral asymmetry and handedness in healthy MZ and DZ twins. It shows how predictions for cerebral asymmetry vary between RR and non-RR pairs over a range of incidences of left-handedness. Although MZ twins are always concordant for genotype and DZ twins may be discordant, differences for handedness and cerebral asymmetry are expected to be small, consistent with the scarcity of significant effects in the literature. Marked differences between RR and non-RR pairs are predicted at all levels of incidence, the differences slightly larger in MZ than DZ pairs.

  14. Emotion dysregulation and dyadic conflict in depressed and typical adolescents: evaluating concordance across psychophysiological and observational measures.

    PubMed

    Crowell, Sheila E; Baucom, Brian R; Yaptangco, Mona; Bride, Daniel; Hsiao, Ray; McCauley, Elizabeth; Beauchaine, Theodore P

    2014-04-01

    Many depressed adolescents experience difficulty in regulating their emotions. These emotion regulation difficulties appear to emerge in part from socialization processes within families and then generalize to other contexts. However, emotion dysregulation is typically assessed within the individual, rather than in the social relationships that shape and maintain dysregulation. In this study, we evaluated concordance of physiological and observational measures of emotion dysregulation during interpersonal conflict, using a multilevel actor-partner interdependence model (APIM). Participants were 75 mother-daughter dyads, including 50 depressed adolescents with or without a history of self-injury, and 25 typically developing controls. Behavior dysregulation was operationalized as observed aversiveness during a conflict discussion, and physiological dysregulation was indexed by respiratory sinus arrhythmia (RSA). Results revealed different patterns of concordance for control versus depressed participants. Controls evidenced a concordant partner (between-person) effect, and showed increased physiological regulation during minutes when their partner was more aversive. In contrast, clinical dyad members displayed a concordant actor (within-person) effect, becoming simultaneously physiologically and behaviorally dysregulated. Results inform current understanding of emotion dysregulation across multiple levels of analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Estimating energy expenditure in vascular surgery patients: Are predictive equations accurate enough?

    PubMed

    Suen, J; Thomas, J M; Delaney, C L; Spark, J I; Miller, M D

    2016-12-01

    Malnutrition is prevalent in vascular surgical patients who commonly seek tertiary care at advanced stages of disease. Adjunct nutrition support is therefore pertinent to optimise patient outcomes. To negate consequences related to excessive or suboptimal dietary energy intake, it is essential to accurately determine energy expenditure and subsequent requirements. This study aims to compare resting energy expenditure (REE) measured by indirect calorimetry, a commonly used comparator, to REE estimated by predictive equations (Schofield, Harris-Benedict equations and Miller equation) to determine the most suitable equation for vascular surgery patients. Data were collected from four studies that measured REE in 77 vascular surgery patients. Bland-Altman analyses were conducted to explore agreement. Presence of fixed or proportional bias was assessed by linear regression analyses. In comparison to measured REE, on average REE was overestimated when Schofield (+857 kJ/day), Harris-Benedict (+801 kJ/day) and Miller (+71 kJ/day) equations were used. Wide limits of agreement led to an over or underestimation from 1552 to 1755 kJ. Proportional bias was absent in Schofield (R 2  = 0.005, p = 0.54) and Harris-Benedict equations (R 2  = 0.045, p = 0.06) but was present in the Miller equation (R 2  = 0.210, p < 0.01) even after logarithmic transformation (R 2  = 0.213, p < 0.01). Whilst the Miller equation tended to overestimate resting energy expenditure and was affected by proportional bias, the limits of agreement and mean bias were smaller compared to Schofield and Harris-Benedict equations. This suggested that it is the preferred predictive equation for vascular surgery patients. Future research to refine the Miller equation to improve its overall accuracy will better inform the provision of nutritional support for vascular surgery patients and subsequently improve outcomes. Alternatively, an equation might be developed specifically for use with

  16. Prediction of Bispectral Index during Target-controlled Infusion of Propofol and Remifentanil: A Deep Learning Approach.

    PubMed

    Lee, Hyung-Chul; Ryu, Ho-Geol; Chung, Eun-Jin; Jung, Chul-Woo

    2018-03-01

    The discrepancy between predicted effect-site concentration and measured bispectral index is problematic during intravenous anesthesia with target-controlled infusion of propofol and remifentanil. We hypothesized that bispectral index during total intravenous anesthesia would be more accurately predicted by a deep learning approach. Long short-term memory and the feed-forward neural network were sequenced to simulate the pharmacokinetic and pharmacodynamic parts of an empirical model, respectively, to predict intraoperative bispectral index during combined use of propofol and remifentanil. Inputs of long short-term memory were infusion histories of propofol and remifentanil, which were retrieved from target-controlled infusion pumps for 1,800 s at 10-s intervals. Inputs of the feed-forward network were the outputs of long short-term memory and demographic data such as age, sex, weight, and height. The final output of the feed-forward network was the bispectral index. The performance of bispectral index prediction was compared between the deep learning model and previously reported response surface model. The model hyperparameters comprised 8 memory cells in the long short-term memory layer and 16 nodes in the hidden layer of the feed-forward network. The model training and testing were performed with separate data sets of 131 and 100 cases. The concordance correlation coefficient (95% CI) were 0.561 (0.560 to 0.562) in the deep learning model, which was significantly larger than that in the response surface model (0.265 [0.263 to 0.266], P < 0.001). The deep learning model-predicted bispectral index during target-controlled infusion of propofol and remifentanil more accurately compared to the traditional model. The deep learning approach in anesthetic pharmacology seems promising because of its excellent performance and extensibility.

  17. Attitudes toward concordance in psychiatry: a comparative, cross-sectional study of psychiatric patients and mental health professionals

    PubMed Central

    2012-01-01

    Background Concordance and Shared Decision-Making (SDM) are considered measures of the quality of care that improves communication, promotes patient participation, creates a positive relationship with the healthcare professional, and results in greater adherence with the treatment plan. Methods This study compares the attitudes of 225 mental health professionals (125 psychiatrists and 100 psychiatry registrars) and 449 psychiatric outpatients towards SDM and concordance in medicine taking by using the "Leeds Attitude toward Concordance Scale" (LATCon). Results The internal consistency of the scale was good in all three samples (Cronbach's α: patients = 0.82, psychiatrists = 0.76, and registrars = 0.82). Patients scored significantly lower (1.96 ± 0.48) than professionals (P < .001 in both cases), while no statistically significant differences between psychiatrists (2.32 ± 0.32) and registrars (2.23 ± 0.35) were registered; the three groups showed a positive attitude towards concordance in most indicators. Patients are clearly in favor of being informed and that their views and preferences be taken into account during the decision-making process, although they widely consider that the final decision must be the doctor's responsibility. Among mental health professionals, the broader experience provides a greater conviction of the importance of the patient's decision about treatment. Conclusions We observed a positive attitude towards concordance in the field of psychotropic drugs prescription both in professionals and among patients, but further studies are needed to address the extent to which this apparently accepted model is reflected in the daily practice of mental health professionals. PMID:22646974

  18. Evaluation of concordance among three cardiac output measurement techniques in adult patients during cardiovascular surgery postoperative care.

    PubMed

    Muñoz, L; Velandia, A; Reyes, L E; Arevalo-Rodríguez, I; Mejía, C; Asprilla, D; Uribe, D V; Arevalo, J J

    2017-12-01

    The standard method for cardiac output measuring is thermodilution although it is an invasive technique. Transesophageal Echocardiography (TEE) offers a dynamic and functional alternative to thermodilution. Analyze concordance between two TEE methods and thermodilution for cardiac output assessment. Observational concordance study in cardiovascular surgery patients that required pulmonary artery catheter. TEE cardiac output measurement at both mitral annulus (MA) and left ventricle outflow tract (LVOT) were performed. Results were compared with thermodilution. Correlation was evaluated by Lin's concordance correlation coefficient and Bland-Altman analysis. Statistical analysis was undertaken in STATA 13.0. Twenty-five patients were enrolled. Fifty two percent of patients were male, median age and ejection fraction was 63 years and 35% respectively. Median thermodilution, LVOT and MA -measured cardiac output was 3.25 L/min, 3.46 L/min and 8.4 L/min respectively. Different values between thermodilution and MA measurements were found (Lin concordance=0.071; Confidence Interval 95%=-0.009 to 0.151; Spearman's correlation=0.22) as values between thermodilution and LVOT (Lin concordance=0.232; Confidence Interval 95%=-0.12 a 0.537; Spearman's correlation 0.28). Bland-Altman analysis showed greater difference between MA measurements and thermodilution (DM=-0.408; Bland-Altman Limits=-0.809 to -0.007), than the other echocardiographic findings (DM=0.007; Bland-Altman Limits=-0.441 to 0.428). Results from cardiac output measurement by doppler and 2D-TEE on both MA and LVOT do not correlate with those obtained by thermodilution. Copyright © 2017 Elsevier España, S.L.U. y SEMICYUC. All rights reserved.

  19. Concordance With Prevention Guidelines and Subsequent Cancer, Cardiovascular Disease, and Mortality: A Longitudinal Study of Older Adults.

    PubMed

    Greenlee, Heather; Strizich, Garrett; Lovasi, Gina S; Kaplan, Robert C; Biggs, Mary L; Li, Christopher I; Richardson, John; Burke, Gregory L; Fitzpatrick, Annette L; Fretts, Amanda M; Psaty, Bruce M; Fried, Linda P

    2017-11-15

    Reports on the associations between multiple clinical and behavioral health indicators and major health outcomes among older adults are scarce. We prospectively examined concordance with guidelines from the American Cancer Society and American Heart Association for disease prevention in relation to cancer, cardiovascular disease (CVD), and mortality among Cardiovascular Health Study enrollees aged 65-98 years who, at baseline assessment in 1989-1996 (n = 3,491), were free of CVD and cancer. Total and cause-specific mortality, as well as incidence of cancer and CVD, were lower with higher guideline concordance. Independent of body mass index, blood pressure, total cholesterol, and fasting plasma glucose, better health behaviors (diet, physical activity, and alcohol consumption) were associated with lower mortality (2-sided P < 0.0001). Among individuals with ideal levels for 3-4 of these 4 cardiometabolic biomarkers, those with poor concordance with health behavior recommendations had higher mortality compared with those who had the highest concordance with these behavioral recommendations (adjusted mortality hazard ratio = 1.82, 95% confidence interval: 1.25, 2.67). Older adults who are concordant with recommendations for cancer and CVD prevention have reduced rates of chronic disease and mortality. Interventions to achieve and maintain healthy lifestyle behaviors may offer benefits both in the presence and absence of adverse traditional clinical risk factors. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows

    NASA Astrophysics Data System (ADS)

    Bijleveld, H. A.; Veldman, A. E. P.

    2014-12-01

    A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.

  1. [Concordance among invasive diagnostic procedures for Helicobacter pylori infection in adults].

    PubMed

    Sánchez-Cuén, Jaime Alberto; Canizalez-Román, Vicente Adrián; León-Sicairos, Nidia Maribel; Irineo-Cabrales, Ana Bertha; Bernal-Magaña, Gregorio

    2015-01-01

    Compare the strength of concordance between culture, histology, rapid urease test for diagnosis of Helicobacter pylori infection and histopathological findings relationship and frequency of positivity among such diagnostic procedures. Diagnostic test study. The study population were subjects with endoscopy and take samples of gastric antral. Rapid urease test (one sample), histology (two samples) and culture (two samples), and histopathological findings of gastric mucosa were performed. Statistical design with Student's t, Fisher exact test, Kappa coefficient. We reviewed 108 subjects, 28 (25.9%) men, 80 (74.1%) women, mean age was 49.1 years (SD 15.1). The Kappa coefficient was 0.729 and 0.377 between culture with histology and rapid urease test, respectively; likewise the Kappa coefficient was 0.565 between histology and rapid urease test. The strength of concordance was higher between histology with culture and rapid urease test; the most recommended being histology in clinical practice for the detection of Helicobacter pylori infection.

  2. Integrating metabolic performance, thermal tolerance, and plasticity enables for more accurate predictions on species vulnerability to acute and chronic effects of global warming.

    PubMed

    Magozzi, Sarah; Calosi, Piero

    2015-01-01

    Predicting species vulnerability to global warming requires a comprehensive, mechanistic understanding of sublethal and lethal thermal tolerances. To date, however, most studies investigating species physiological responses to increasing temperature have focused on the underlying physiological traits of either acute or chronic tolerance in isolation. Here we propose an integrative, synthetic approach including the investigation of multiple physiological traits (metabolic performance and thermal tolerance), and their plasticity, to provide more accurate and balanced predictions on species and assemblage vulnerability to both acute and chronic effects of global warming. We applied this approach to more accurately elucidate relative species vulnerability to warming within an assemblage of six caridean prawns occurring in the same geographic, hence macroclimatic, region, but living in different thermal habitats. Prawns were exposed to four incubation temperatures (10, 15, 20 and 25 °C) for 7 days, their metabolic rates and upper thermal limits were measured, and plasticity was calculated according to the concept of Reaction Norms, as well as Q10 for metabolism. Compared to species occupying narrower/more stable thermal niches, species inhabiting broader/more variable thermal environments (including the invasive Palaemon macrodactylus) are likely to be less vulnerable to extreme acute thermal events as a result of their higher upper thermal limits. Nevertheless, they may be at greater risk from chronic exposure to warming due to the greater metabolic costs they incur. Indeed, a trade-off between acute and chronic tolerance was apparent in the assemblage investigated. However, the invasive species P. macrodactylus represents an exception to this pattern, showing elevated thermal limits and plasticity of these limits, as well as a high metabolic control. In general, integrating multiple proxies for species physiological acute and chronic responses to increasing

  3. Intimate Partner Aggression Reporting Concordance and Correlates of Agreement among Men with Alcohol Use Disorders and Their Female Partners

    ERIC Educational Resources Information Center

    Panuzio, Jillian; O'Farrell, Timothy J.; Marshall, Amy D.; Murphy, Christopher M.; Murphy, Marie; Taft, Casey T.

    2006-01-01

    This study examined relationship aggression reporting concordance among 303 men with alcohol use disorders and their female partners enrolled in couples-based alcohol abuse treatment. Agreement for physical and psychological aggression was generally consistent with, or higher than, concordance rates reported among other populations. Men's…

  4. Concordant integrative gene set enrichment analysis of multiple large-scale two-sample expression data sets.

    PubMed

    Lai, Yinglei; Zhang, Fanni; Nayak, Tapan K; Modarres, Reza; Lee, Norman H; McCaffrey, Timothy A

    2014-01-01

    Gene set enrichment analysis (GSEA) is an important approach to the analysis of coordinate expression changes at a pathway level. Although many statistical and computational methods have been proposed for GSEA, the issue of a concordant integrative GSEA of multiple expression data sets has not been well addressed. Among different related data sets collected for the same or similar study purposes, it is important to identify pathways or gene sets with concordant enrichment. We categorize the underlying true states of differential expression into three representative categories: no change, positive change and negative change. Due to data noise, what we observe from experiments may not indicate the underlying truth. Although these categories are not observed in practice, they can be considered in a mixture model framework. Then, we define the mathematical concept of concordant gene set enrichment and calculate its related probability based on a three-component multivariate normal mixture model. The related false discovery rate can be calculated and used to rank different gene sets. We used three published lung cancer microarray gene expression data sets to illustrate our proposed method. One analysis based on the first two data sets was conducted to compare our result with a previous published result based on a GSEA conducted separately for each individual data set. This comparison illustrates the advantage of our proposed concordant integrative gene set enrichment analysis. Then, with a relatively new and larger pathway collection, we used our method to conduct an integrative analysis of the first two data sets and also all three data sets. Both results showed that many gene sets could be identified with low false discovery rates. A consistency between both results was also observed. A further exploration based on the KEGG cancer pathway collection showed that a majority of these pathways could be identified by our proposed method. This study illustrates that we can

  5. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  6. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins

    PubMed Central

    Yang, Jing; He, Bao-Ji; Jang, Richard; Zhang, Yang; Shen, Hong-Bin

    2015-01-01

    Abstract Motivation: Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g. >3 bonds, is too low to effectively assist structure assembly simulations. Results: We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins. Availability and implementation: http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/ Contact: zhng@umich.edu or hbshen@sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26254435

  7. Development of a New Model for Accurate Prediction of Cloud Water Deposition on Vegetation

    NASA Astrophysics Data System (ADS)

    Katata, G.; Nagai, H.; Wrzesinsky, T.; Klemm, O.; Eugster, W.; Burkard, R.

    2006-12-01

    Scarcity of water resources in arid and semi-arid areas is of great concern in the light of population growth and food shortages. Several experiments focusing on cloud (fog) water deposition on the land surface suggest that cloud water plays an important role in water resource in such regions. A one-dimensional vegetation model including the process of cloud water deposition on vegetation has been developed to better predict cloud water deposition on the vegetation. New schemes to calculate capture efficiency of leaf, cloud droplet size distribution, and gravitational flux of cloud water were incorporated in the model. Model calculations were compared with the data acquired at the Norway spruce forest at the Waldstein site, Germany. High performance of the model was confirmed by comparisons of calculated net radiation, sensible and latent heat, and cloud water fluxes over the forest with measurements. The present model provided a better prediction of measured turbulent and gravitational fluxes of cloud water over the canopy than the Lovett model, which is a commonly used cloud water deposition model. Detailed calculations of evapotranspiration and of turbulent exchange of heat and water vapor within the canopy and the modifications are necessary for accurate prediction of cloud water deposition. Numerical experiments to examine the dependence of cloud water deposition on the vegetation species (coniferous and broad-leaved trees, flat and cylindrical grasses) and structures (Leaf Area Index (LAI) and canopy height) are performed using the presented model. The results indicate that the differences of leaf shape and size have a large impact on cloud water deposition. Cloud water deposition also varies with the growth of vegetation and seasonal change of LAI. We found that the coniferous trees whose height and LAI are 24 m and 2.0 m2m-2, respectively, produce the largest amount of cloud water deposition in all combinations of vegetation species and structures in the

  8. The covariant entropy conjecture and concordance cosmological models

    NASA Astrophysics Data System (ADS)

    He, Song; Zhang, Hongbao

    2008-10-01

    Recently a covariant entropy conjecture has been proposed for dynamical horizons. We apply this conjecture to concordance cosmological models, namely, those cosmological models filled with perfect fluids, in the presence of a positive cosmological constant. As a result, we find that this conjecture has a severe constraint power. Not only does this conjecture rule out those cosmological models disfavored by the anthropic principle, but also it imposes an upper bound 10-60 on the cosmological constant for our own universe, which thus provides an alternative macroscopic perspective for understanding the long-standing cosmological constant problem.

  9. Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging.

    PubMed

    Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A

    2015-02-05

    As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1). Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Calibration of the Concorde radiation detection instrument and measurements at SST altitude.

    DOT National Transportation Integrated Search

    1971-06-01

    Performance tests were carried out on a solar cosmic radiation detection instrument developed for the Concorde SST. The instrument calibration curve (log dose-rate vs instrument reading) was reasonably linear from 0.004 to 1 rem/hr for both gamma rad...

  11. A Descriptive Enquiry into Subject-Verb Concord in English Existential Constructions

    ERIC Educational Resources Information Center

    Tsuchida, Takehiro

    2011-01-01

    Subject-verb concord in English existential constructions is often viewed as problematic from both prescriptive and descriptive approaches to grammar and causes considerable confusion among teachers and learners of English as a second language (ESL). This paper aims to disentangle debates over the curious usage of the "there" + plural noun phrase…

  12. Predicting umbilical artery pH during labour: Development and validation of a nomogram using fetal heart rate patterns.

    PubMed

    Ramanah, Rajeev; Omar, Sikiyah; Guillien, Alicia; Pugin, Aurore; Martin, Alain; Riethmuller, Didier; Mottet, Nicolas

    2018-06-01

    Nomograms are statistical models that combine variables to obtain the most accurate and reliable prediction for a particular risk. Fetal heart rate (FHR) interpretation alone has been found to be poorly predictive for fetal acidosis while other clinical risk factors exist. The aim of this study was to create and validate a nomogram based on FHR patterns and relevant clinical parameters to provide a non-invasive individualized prediction of umbilical artery pH during labour. A retrospective observational study was conducted on 4071 patients in labour presenting singleton pregnancies at >34 gestational weeks and delivering vaginally. Clinical characteristics, FHR patterns and umbilical cord gas of 1913 patients were used to construct a nomogram predicting an umbilical artery (Ua) pH <7.18 (10th centile of the study population) after an univariate and multivariate stepwise logistic regression analysis. External validation was obtained from an independent cohort of 2158 patients. Area under the receiver operating characteristics (ROC) curve, sensitivity, specificity, positive and negative predictive values of the nomogram were determined. Upon multivariate analysis, parity (p < 0.01), induction of labour (p = 0.01), a prior uterine scar (p = 0.02), maternal fever (p = 0.02) and the type of FHR (p < 0.01) were significantly associated with an Ua pH <7.18 (p < 0.05). Apgar score at 1, 5 and 10 min were significantly lower in the group with an Ua pH <7.18 (p < 0.01). The nomogram constructed had a Concordance Index of 0.75 (area under the curve) with a sensitivity of 57%, a specificity of 91%, a negative predictive value of 5% and a positive predictive value of 99%. Calibration found no difference between the predicted probabilities and the observed rate of Ua pH <7.18 (p = 0.63). The validation set had a Concordance Index of 0.72 and calibration with a p < 0.77. We successfully developed and validated a nomogram to predict Ua pH by

  13. Effects of patient-provider race concordance and smoking status on lung cancer risk perception accuracy among African-Americans.

    PubMed

    Persky, Susan; Kaphingst, Kimberly A; Allen, Vincent C; Senay, Ibrahim

    2013-06-01

    Communication of lung cancer risk information between providers and African-American patients occurs in a context marked by race-based health disparities. A controlled experiment assessed whether perceived physician race influenced African-American patients' (n = 127) risk perception accuracy following the provision of objective lung cancer risk information. Participants interacted with a virtual reality-based, simulated physician who provided personalized cancer risk information. Participants who interacted with a racially discordant virtual doctor were less accurate in their risk perceptions at post-test than those who interacted with a concordant virtual doctor, F(1,94) = 4.02, p = .048. This effect was amplified among current smokers. Effects were not mediated by trust in the provider, engagement with the health care system, or attention during the encounter. The current study demonstrates that African-American patients' perceptions of a doctor's race are sufficient to independently impact their processing of lung cancer risk information.

  14. Effects of Patient-Provider Race Concordance and Smoking Status on Lung Cancer Risk Perception Accuracy among African Americans

    PubMed Central

    Persky, Susan; Kaphingst, Kimberly A.; Allen, Vincent C.; Senay, Ibrahim

    2013-01-01

    Background Communication of lung cancer risk information between providers and African-American patients occurs in a context marked by race-based health disparities. Purpose A controlled experiment assessed whether perceived physician race influenced African-American patients’ (n=127) risk perception accuracy following the provision of objective lung cancer risk information. Methods Participants interacted with a virtual reality-based, simulated physician who provided personalized cancer risk information. Results Participants who interacted with a racially discordant virtual doctor were less accurate in their risk perceptions at post-test than those who interacted with a concordant virtual doctor, F(1,94)=4.02, p=.048. This effect was amplified among current smokers. Effects were not mediated by trust in the provider, engagement with the health care system, or attention during the encounter. Conclusions The current study demonstrates that African-American patients’ perceptions of a doctor’s race are sufficient to independently impact their processing of lung cancer risk information. PMID:23389688

  15. Accurate Predictions of Mean Geomagnetic Dipole Excursion and Reversal Frequencies, Mean Paleomagnetic Field Intensity, and the Radius of Earth's Core Using McLeod's Rule

    NASA Technical Reports Server (NTRS)

    Voorhies, Coerte V.; Conrad, Joy

    1996-01-01

    The geomagnetic spatial power spectrum R(sub n)(r) is the mean square magnetic induction represented by degree n spherical harmonic coefficients of the internal scalar potential averaged over the geocentric sphere of radius r. McLeod's Rule for the magnetic field generated by Earth's core geodynamo says that the expected core surface power spectrum (R(sub nc)(c)) is inversely proportional to (2n + 1) for 1 less than n less than or equal to N(sub E). McLeod's Rule is verified by locating Earth's core with main field models of Magsat data; the estimated core radius of 3485 kn is close to the seismologic value for c of 3480 km. McLeod's Rule and similar forms are then calibrated with the model values of R(sub n) for 3 less than or = n less than or = 12. Extrapolation to the degree 1 dipole predicts the expectation value of Earth's dipole moment to be about 5.89 x 10(exp 22) Am(exp 2)rms (74.5% of the 1980 value) and the expected geomagnetic intensity to be about 35.6 (mu)T rms at Earth's surface. Archeo- and paleomagnetic field intensity data show these and related predictions to be reasonably accurate. The probability distribution chi(exp 2) with 2n+1 degrees of freedom is assigned to (2n + 1)R(sub nc)/(R(sub nc). Extending this to the dipole implies that an exceptionally weak absolute dipole moment (less than or = 20% of the 1980 value) will exist during 2.5% of geologic time. The mean duration for such major geomagnetic dipole power excursions, one quarter of which feature durable axial dipole reversal, is estimated from the modern dipole power time-scale and the statistical model of excursions. The resulting mean excursion duration of 2767 years forces us to predict an average of 9.04 excursions per million years, 2.26 axial dipole reversals per million years, and a mean reversal duration of 5533 years. Paleomagnetic data show these predictions to be quite accurate. McLeod's Rule led to accurate predictions of Earth's core radius, mean paleomagnetic field

  16. Guidelines-concordant empiric antimicrobial therapy and mortality in patients with severe community-acquired pneumonia requiring mechanical ventilation.

    PubMed

    Sakamoto, Yukiyo; Yamauchi, Yasuhiro; Yasunaga, Hideo; Takeshima, Hideyuki; Hasegawa, Wakae; Jo, Taisuke; Matsui, Hiroki; Fushimi, Kiyohide; Nagase, Takahide

    2017-01-01

    Community-acquired pneumonia (CAP) has high morbidity and mortality among adults. Several clinical guidelines recommend prompt administration of combined antimicrobial therapy. However, the association between guidelines concordance and mortality in patients with severe pneumonia remains unclear. The present study aimed to examine the impact of guidelines-concordant empiric antimicrobial therapy on 7-day mortality in patients with extremely severe pneumonia who required mechanical ventilation at admission, using a nationwide inpatient database in Japan. Data of CAP patients aged over 20 years who required mechanical ventilation at admission between April 2012 and March 2014 were retrospectively analyzed. Multivariable logistic regression analysis was performed to examine the association between guidelines-concordant empiric antimicrobial therapy and all-cause 7-day mortality, with adjustment for patient backgrounds and pneumonia severity. There were a total of 3719 eligible patients, 836 (22.5%) of whom received guidelines-concordant combination therapy. Overall, 7-day mortality was 29.5%. Higher 7-day mortality was associated with advanced age, confusion, lower systolic blood pressure, malignant tumor or immunocompromised state, and C-reactive protein ≥20mg/dl or infiltration occupying two-thirds of one lung on chest radiography. After adjustment for these variables, guidelines-concordant combined antimicrobial therapy was associated with significantly lower 7-day mortality (odds ratio: 0.78; 95% confidence interval: 0.65-0.95; P=0.013). Adherence to initial empiric treatment as recommended by the guidelines was associated with better short-term prognosis in patients with extremely severe pneumonia who required mechanical ventilation on hospital admission. Copyright © 2016 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

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

    PubMed

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

    2013-01-01

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

  18. Caregiver-Teacher Concordance of Challenging Behaviors in Children with Autism Spectrum Disorder Served in Community Mental Health Settings

    PubMed Central

    Chlebowski, Colby; Brookman-Frazee, Lauren

    2018-01-01

    Children with autism spectrum disorder (ASD) exhibit high rates of challenging behaviors that impair functioning and represent the primary presenting problem in mental health (MH) services. Obtaining symptom reports from multiple informants is critical for treatment planning. This study evaluated caregiver-teacher concordance of ratings of the intensity of challenging behaviors in children with ASD receiving MH services, and identified child clinical factors associated with concordance. This sample included 141 children (M = 9.07 years), their caregivers, and teachers. Caregiver-teacher concordance of challenging behaviors was low and impacted by the degree and type of child psychiatric comorbidity. Findings support need for increased attention to the range of psychiatric problems children with ASD present to tailor treatment recommendations and service delivery. PMID:28343342

  19. Concordance of Motion Sensor and Clinician-Rated Fall Risk Scores in Older Adults.

    PubMed

    Elledge, Julie

    2017-12-01

    As the older adult population in the United States continues to grow, developing reliable, valid, and practical methods for identifying fall risk is a high priority. Falls are prevalent in older adults and contribute significantly to morbidity and mortality rates and rising health costs. Identifying at-risk older adults and intervening in a timely manner can reduce falls. Conventional fall risk assessment tools require a health professional trained in the use of each tool for administration and interpretation. Motion sensor technology, which uses three-dimensional cameras to measure patient movements, is promising for assessing older adults' fall risk because it could eliminate or reduce the need for provider oversight. The purpose of this study was to assess the concordance of fall risk scores as measured by a motion sensor device, the OmniVR Virtual Rehabilitation System, with clinician-rated fall risk scores in older adult outpatients undergoing physical rehabilitation. Three standardized fall risk assessments were administered by the OmniVR and by a clinician. Validity of the OmniVR was assessed by measuring the concordance between the two assessment methods. Stability of the OmniVR fall risk ratings was assessed by measuring test-retest reliability. The OmniVR scores showed high concordance with the clinician-rated scores and high stability over time, demonstrating comparability with provider measurements.

  20. Multisite concordance of apparent diffusion coefficient measurements across the NCI Quantitative Imaging Network.

    PubMed

    Newitt, David C; Malyarenko, Dariya; Chenevert, Thomas L; Quarles, C Chad; Bell, Laura; Fedorov, Andriy; Fennessy, Fiona; Jacobs, Michael A; Solaiyappan, Meiyappan; Hectors, Stefanie; Taouli, Bachir; Muzi, Mark; Kinahan, Paul E; Schmainda, Kathleen M; Prah, Melissa A; Taber, Erin N; Kroenke, Christopher; Huang, Wei; Arlinghaus, Lori R; Yankeelov, Thomas E; Cao, Yue; Aryal, Madhava; Yen, Yi-Fen; Kalpathy-Cramer, Jayashree; Shukla-Dave, Amita; Fung, Maggie; Liang, Jiachao; Boss, Michael; Hylton, Nola

    2018-01-01

    Diffusion weighted MRI has become ubiquitous in many areas of medicine, including cancer diagnosis and treatment response monitoring. Reproducibility of diffusion metrics is essential for their acceptance as quantitative biomarkers in these areas. We examined the variability in the apparent diffusion coefficient (ADC) obtained from both postprocessing software implementations utilized by the NCI Quantitative Imaging Network and online scan time-generated ADC maps. Phantom and in vivo breast studies were evaluated for two ([Formula: see text]) and four ([Formula: see text]) [Formula: see text]-value diffusion metrics. Concordance of the majority of implementations was excellent for both phantom ADC measures and in vivo [Formula: see text], with relative biases [Formula: see text] ([Formula: see text]) and [Formula: see text] (phantom [Formula: see text]) but with higher deviations in ADC at the lowest phantom ADC values. In vivo [Formula: see text] concordance was good, with typical biases of [Formula: see text] to 3% but higher for online maps. Multiple b -value ADC implementations were separated into two groups determined by the fitting algorithm. Intergroup mean ADC differences ranged from negligible for phantom data to 2.8% for [Formula: see text] in vivo data. Some higher deviations were found for individual implementations and online parametric maps. Despite generally good concordance, implementation biases in ADC measures are sometimes significant and may be large enough to be of concern in multisite studies.

  1. Robust and accurate decoding of motoneuron behavior and prediction of the resulting force output.

    PubMed

    Thompson, Christopher K; Negro, Francesco; Johnson, Michael D; Holmes, Matthew R; McPherson, Laura Miller; Powers, Randall K; Farina, Dario; Heckman, Charles J

    2018-05-03

    The spinal alpha motoneuron is the only cell in the human CNS whose discharge can be routinely recorded in humans. We have reengineered motor unit collection and decomposition approaches, originally developed in humans, to measure the neural drive to muscle and estimate muscle force generation in the decerebrate cat model. Experimental, computational, and predictive approaches are used to demonstrate the validity of this approach across a wide range of modes to activate the motor pool. The utility of this approach is shown through the ability to track individual motor units across trials, allowing for better predictions of muscle force than the electromyography signal, and providing insights in to the stereotypical discharge characteristics in response to synaptic activation of the motor pool. This approach now allows for a direct link between the intracellular data of single motoneurons, the discharge properties of motoneuron populations, and muscle force generation in the same preparation. The discharge of a spinal alpha motoneuron and the resulting contraction of its muscle fibers represents the functional quantum of the motor system. Recent advances in the recording and decomposition of the electromyographic signal allows for the identification of several tens of concurrently active motor units. These detailed population data provide the potential to achieve deep insights into the synaptic organization of motor commands. Yet most of our understanding of the synaptic input to motoneurons is derived from intracellular recordings in animal preparations. Thus, it is necessary to extend the new electrode and decomposition methods to recording of motor unit populations in these same preparations. To achieve this goal, we use high-density electrode arrays and decomposition techniques, analogous to those developed for humans, to record and decompose the activity of tens of concurrently active motor units in a hindlimb muscle in the decerebrate cat. Our results showed

  2. Mean Expected Error in Prediction of Total Body Water: A True Accuracy Comparison between Bioimpedance Spectroscopy and Single Frequency Regression Equations

    PubMed Central

    Abtahi, Shirin; Abtahi, Farhad; Ellegård, Lars; Johannsson, Gudmundur; Bosaeus, Ingvar

    2015-01-01

    For several decades electrical bioimpedance (EBI) has been used to assess body fluid distribution and body composition. Despite the development of several different approaches for assessing total body water (TBW), it remains uncertain whether bioimpedance spectroscopic (BIS) approaches are more accurate than single frequency regression equations. The main objective of this study was to answer this question by calculating the expected accuracy of a single measurement for different EBI methods. The results of this study showed that all methods produced similarly high correlation and concordance coefficients, indicating good accuracy as a method. Even the limits of agreement produced from the Bland-Altman analysis indicated that the performance of single frequency, Sun's prediction equations, at population level was close to the performance of both BIS methods; however, when comparing the Mean Absolute Percentage Error value between the single frequency prediction equations and the BIS methods, a significant difference was obtained, indicating slightly better accuracy for the BIS methods. Despite the higher accuracy of BIS methods over 50 kHz prediction equations at both population and individual level, the magnitude of the improvement was small. Such slight improvement in accuracy of BIS methods is suggested insufficient to warrant their clinical use where the most accurate predictions of TBW are required, for example, when assessing over-fluidic status on dialysis. To reach expected errors below 4-5%, novel and individualized approaches must be developed to improve the accuracy of bioimpedance-based methods for the advent of innovative personalized health monitoring applications. PMID:26137489

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

    PubMed

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

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  4. Child and Caregiver Concordance of Potentially Traumatic Events Experienced by Orphaned and Abandoned Children

    PubMed Central

    Guru Rajan, Divya; Shirey, Kristen; Ostermann, Jan; Whetten, Rachel; O’Donnell, Karen; Whetten, Kathryn

    2013-01-01

    Exposure to trauma is associated with significant emotional and behavioral difficulties among children (Perepletchikova & Kaufman, 2010). Overall, reports of trauma and violence experienced by children are discrepant from those of their caregivers (Lewis et al., 2012). Even less is known about the extent of concordance between orphans and their caregivers. This study examines the correlates of concordance in reported traumatic experiences between 1,269 orphaned and abandoned children (OAC) and their caregivers. The OAC lived in family-settings in 5 low and middle income countries and were part of a longitudinal study, “Positive Outcomes for Orphans” (POFO) that enrolled children aged 6 to 12 at baseline. By examining concordance with respect to specific types of trauma reported, this study expands the understanding of who reports which types of traumas experienced by orphaned and abandoned children, thereby improving the potential to provide targeted interventions for children who have experienced such events. In this study, children and caregivers were asked separately if the child had experienced different types of potentially traumatic events. Children were significantly more likely to report physical abuse, sexual abuse and family violence than were caregivers. Caregivers were significantly more likely than children to report natural disasters and accidents. High levels of concordance were found in the reporting of wars, riots, killings, and deaths in the family. The impacts of trauma on behavior and mental health are profound, and highly effective interventions targeting sequelae of childhood trauma are currently being developed for use in low resource areas. Findings from this study demonstrate that it is feasible to conduct screening for potentially traumatic events utilizing child self-report in resource limited settings and that child self-report is crucial in evaluating trauma, particularly family violence and physical or sexual assault. PMID:25379051

  5. Accurate prediction of collapse temperature using optical coherence tomography-based freeze-drying microscopy.

    PubMed

    Greco, Kristyn; Mujat, Mircea; Galbally-Kinney, Kristin L; Hammer, Daniel X; Ferguson, R Daniel; Iftimia, Nicusor; Mulhall, Phillip; Sharma, Puneet; Kessler, William J; Pikal, Michael J

    2013-06-01

    The objective of this study was to assess the feasibility of developing and applying a laboratory tool that can provide three-dimensional product structural information during freeze-drying and which can accurately characterize the collapse temperature (Tc ) of pharmaceutical formulations designed for freeze-drying. A single-vial freeze dryer coupled with optical coherence tomography freeze-drying microscopy (OCT-FDM) was developed to investigate the structure and Tc of formulations in pharmaceutically relevant products containers (i.e., freeze-drying in vials). OCT-FDM was used to measure the Tc and eutectic melt of three formulations in freeze-drying vials. The Tc as measured by OCT-FDM was found to be predictive of freeze-drying with a batch of vials in a conventional laboratory freeze dryer. The freeze-drying cycles developed using OCT-FDM data, as compared with traditional light transmission freeze-drying microscopy (LT-FDM), resulted in a significant reduction in primary drying time, which could result in a substantial reduction of manufacturing costs while maintaining product quality. OCT-FDM provides quantitative data to justify freeze-drying at temperatures higher than the Tc measured by LT-FDM and provides a reliable upper limit to setting a product temperature in primary drying. Copyright © 2013 Wiley Periodicals, Inc.

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

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

  7. Concordant association validates MGMT methylation and protein expression as favorable prognostic factors in glioma patients on alkylating chemotherapy (Temozolomide).

    PubMed

    Pandith, Arshad A; Qasim, Iqbal; Zahoor, Wani; Shah, Parveen; Bhat, Abdul R; Sanadhya, Dheera; Shah, Zafar A; Naikoo, Niyaz A

    2018-04-30

    O 6 -methylguanine-DNA methyltransferase (MGMT) promoter methylation and its subsequent loss of protein expression has been identified to have a variable impact on clinical outcome of glioma patients indicated for chemotherapy with alkylating agents (Temozolomide). This study investigated methylation status of MGMT gene along with in situ protein expression in malignant glioma patients of different histological types to evaluate the associated clinical outcome vis-a-vis use of alkylating drugs and radiotherapy. Sixty three cases of glioma were evaluated for MGMT promoter methylation by methylation-specific PCR (MS-PCR) and protein expression by immunostaining (IHC). Methylation status of MGMT and loss of protein expression showed a very high concordant association with better survival and progression free survival (PFS) (p < 0.0001). Multivariate Cox regression analysis showed both MGMT methylation and loss of protein as significant independent prognostic factors in glioma patients with respect to lower Hazard Ratio (HR) for better OS and PFS) [p < 0.05]. Interestingly concordant MGMT methylation and lack of protein showed better response in TMZ therapy treated patient subgroups with HR of 2.02 and 0.76 (p < 0.05). We found the merits of prognostication of MGMT parameters, methylation as well as loss of its protein as predictive factors for favorable outcome in terms of better survival for TMZ therapy.

  8. Concorde noise-induced building vibrations, John F. Kennedy International Airport

    NASA Technical Reports Server (NTRS)

    Mayes, W. H.; Deloach, R.; Stephens, D. G.; Cawthorn, J. M.; Holmes, H. K.; Lewis, R. B.; Holliday, B. G.; Miller, W. T.; Ward, D. W.

    1978-01-01

    The outdoor/indoor noise levels and associated vibration levels resulting from aircraft and nonaircraft events were recorded at eight homesites and a school. In addition, limited subjective tests were conducted to examine the human detection/annoyance thresholds for building vibration and rattle caused by aircraft noise. Presented herein are the majority of the window and wall vibration data recorded during Concorde and subsonic aircraft overflights.

  9. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina

    PubMed Central

    Maturana, Matias I.; Apollo, Nicholas V.; Hadjinicolaou, Alex E.; Garrett, David J.; Cloherty, Shaun L.; Kameneva, Tatiana; Grayden, David B.; Ibbotson, Michael R.; Meffin, Hamish

    2016-01-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron’s electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy. PMID:27035143

  10. Correlates of unmet need for contraception in Bangladesh: does couples' concordance in household decision making matter?

    PubMed

    Uddin, Jalal; Pulok, Mohammad Habibullah; Sabah, Md Nasim-Us

    2016-07-01

    A large body of literature has highlighted that women's household decision-making power is associated with better reproductive health outcomes, while most of the studies tend to measure such power from only women's point of view. Using both husband's and wife's matched responses to decision-making questions, this study examined the association between couples' concordant and discordant decision makings, and wife's unmet need for contraception in Bangladesh. This study used couple's data set (n=3336) from Bangladesh Demographic and Health Survey of 2007. Multivariate logistic regression was used to examine the likelihood of unmet need for contraception among married women of reproductive age. Study results suggested that couples who support the equalitarian power structure seemed to be more powerful in meeting the unmet demand for contraception. Logistic regression analysis revealed that compared to couple's concordant joint decision making, concordance in husband-only or other's involvement in decision making was associated with higher odds of unmet need for contraception. Wives exposed to family planning information discussed family planning more often with husbands, and those from richest households were less likely to have unmet need for contraception. Couple's concordant joint decision making, reflecting the concept of equalitarian power structure, appeared to be a significant analytic category. Policy makers in the field of family planning may promote community-based outreach programs and communication campaigns for family planning focusing on egalitarian gender roles in the household. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Differences in Parent-Provider Concordance Regarding Prognosis and Goals of Care Among Children With Advanced Cancer

    PubMed Central

    Rosenberg, Abby R.; Orellana, Liliana; Kang, Tammy I.; Geyer, J. Russell; Feudtner, Chris; Dussel, Veronica; Wolfe, Joanne

    2014-01-01

    Purpose Concordance between parents of children with advanced cancer and health care providers has not been described. We aimed to describe parent-provider concordance regarding prognosis and goals of care, including differences by cancer type. Patients and Methods A total of 104 pediatric patients with recurrent or refractory cancer were enrolled at three large children's hospitals. On enrollment, their parents and providers were invited to complete a survey assessing perceived prognosis and goals of care. Patients' survival status was retrospectively abstracted from medical records. Concordance was assessed via discrepancies in perceived prognosis, κ statistics, and McNemar's test. Distribution of categorical variables and survival rates across cancer type were compared with Fisher's exact and log-rank tests, respectively. Results Data were available from 77 dyads (74% of enrolled). Parent-provider agreement regarding prognosis and goals of care was poor (κ, 0.12 to 0.30). Parents were more likely to report cure was likely (P < .001). The frequency of perceived likelihood of cure and the goal of cure varied by cancer type for both parents and providers (P < .001 to .004). Relatively optimistic responses were more common among parents and providers of patients with hematologic malignancies, although there were no differences in survival. Conclusion Parent-provider concordance regarding prognosis and goals in advanced pediatric cancer is generally poor. Perceptions of prognosis and goals of care vary by cancer type. Understanding these differences may inform parent-provider communication and decision making. PMID:25024073

  12. Moderate efficiency of clinicians' predictions decreased for blurred clinical conditions and benefits from the use of BRASS index. A longitudinal study on geriatric patients' outcomes.

    PubMed

    Signorini, Giulia; Dagani, Jessica; Bulgari, Viola; Ferrari, Clarissa; de Girolamo, Giovanni

    2016-01-01

    Accurate prognosis is an essential aspect of good clinical practice and efficient health services, particularly for chronic and disabling diseases, as in geriatric populations. This study aims to examine the accuracy of clinical prognostic predictions and to devise prediction models combining clinical variables and clinicians' prognosis for a geriatric patient sample. In a sample of 329 consecutive older patients admitted to 10 geriatric units, we evaluated the accuracy of clinicians' prognosis regarding three outcomes at discharge: global functioning, length of stay (LoS) in hospital, and destination at discharge (DD). A comprehensive set of sociodemographic, clinical, and treatment-related information were also collected. Moderate predictive performance was found for all three outcomes: area under receiver operating characteristic curve of 0.79 and 0.78 for functioning and LoS, respectively, and moderate concordance, Cohen's K = 0.45, between predicted and observed DD. Predictive models found the Blaylock Risk Assessment Screening Score together with clinicians' judgment relevant to improve predictions for all outcomes (absolute improvement in adjusted and pseudo-R(2) up to 19%). Although the clinicians' estimates were important factors in predicting global functioning, LoS, and DD, more research is needed regarding both methodological aspects and clinical measurements, to improve prognostic clinical indices. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Race/Ethnicity and Health Care Communication: Does Patient-Provider Concordance Matter?

    PubMed

    Sweeney, Casey F; Zinner, Darren; Rust, George; Fryer, George E

    2016-11-01

    Although many minority patients would prefer a provider of their own race/ethnicity, the influence of this relationship on patient-provider communication remains unknown. This analysis examined the effect of patient-provider race/ethnicity concordance on patient-reported provider communication quality using data from the Medical Expenditure Panel Survey years 2002-2012. Ordinary least squares regressions were executed on communication rating, measured by the Consumer Assessment of Health Providers and Systems. Only 13.8% of black, non-Hispanic patients reported their usual source of care provider matched their race/ethnicity, compared with 94.4% of white, non-Hispanic patients and 43.8% of Hispanic patients. Differences in communication ratings were driven by patient race, rather than provider race. Although black, non-Hispanic patients rate their communication significantly higher than their counterparts overall, there was no significant influence of patient-provider racial concordance on ratings of communication when controlling for other sociodemographic variables. Minorities may seek the services of minority providers, but they are not more satisfied with patient-provider communication experience than when in race-discordant provider arrangements.

  14. The impact of concordant communication in outpatient care planning - nurses' perspective.

    PubMed

    Olsson, Maivor; Larsson, Lena G; Flensner, Gullvi; Bäck-Pettersson, Siv

    2012-09-01

    To elucidate registered nurses' experiences of coordinated care planning in outpatient care. Coordinated care planning has been studied from the perspectives of both patients and nurses in inpatient care, but it is deficient in outpatient care. Qualitative content analysis of interviews with 10 registered nurses participating in two focus groups. An overall theme was identified: creating concordant communication in relation to patient and health-care providers. The result is based on four categories and nine subcategories. Nurses need extraordinary communication skills to reach concordance in outpatient care planning. In addition to involving and supporting the patients and next of kin in the decision-making process, the outcome of the nursing process must be understood by colleagues and members of other professions and health-care providers (non-nursing). An effective outpatient care-planning process requires that care managers understand the impact of communicating, transferring information and reaching consensus with other health-care providers, actively supporting employees in the outpatient care-planning process and contributing to the development of common goals and policy documents across organisational boundaries. © 2012 Blackwell Publishing Ltd.

  15. Combining Mean and Standard Deviation of Hounsfield Unit Measurements from Preoperative CT Allows More Accurate Prediction of Urinary Stone Composition Than Mean Hounsfield Units Alone.

    PubMed

    Tailly, Thomas; Larish, Yaniv; Nadeau, Brandon; Violette, Philippe; Glickman, Leonard; Olvera-Posada, Daniel; Alenezi, Husain; Amann, Justin; Denstedt, John; Razvi, Hassan

    2016-04-01

    The mineral composition of a urinary stone may influence its surgical and medical treatment. Previous attempts at identifying stone composition based on mean Hounsfield Units (HUm) have had varied success. We aimed to evaluate the additional use of standard deviation of HU (HUsd) to more accurately predict stone composition. We identified patients from two centers who had undergone urinary stone treatment between 2006 and 2013 and had mineral stone analysis and a computed tomography (CT) available. HUm and HUsd of the stones were compared with ANOVA. Receiver operative characteristic analysis with area under the curve (AUC), Youden index, and likelihood ratio calculations were performed. Data were available for 466 patients. The major components were calcium oxalate monohydrate (COM), uric acid, hydroxyapatite, struvite, brushite, cystine, and CO dihydrate (COD) in 41.4%, 19.3%, 12.4%, 7.5%, 5.8%, 5.4%, and 4.7% of patients, respectively. The HUm of UA and Br was significantly lower and higher than the HUm of any other stone type, respectively. HUm and HUsd were most accurate in predicting uric acid with an AUC of 0.969 and 0.851, respectively. The combined use of HUm and HUsd resulted in increased positive predictive value and higher likelihood ratios for identifying a stone's mineral composition for all stone types but COM. To the best of our knowledge, this is the first report of CT data aiding in the prediction of brushite stone composition. Both HUm and HUsd can help predict stone composition and their combined use results in higher likelihood ratios influencing probability.

  16. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints

    PubMed Central

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-01-01

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS–inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car. PMID:26927108

  17. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints.

    PubMed

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-02-24

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS-inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car.

  18. Concordance Between Patient and Family Reports of Family Functioning in Bipolar I Disorder and Major Depressive Disorder

    PubMed Central

    Weinstock, Lauren M.; Wenze, Susan J.; Munroe, Mary K.; Miller, Ivan W.

    2013-01-01

    Despite the extensive literature on family functioning and mood disorders, less is known about concordance between patient- and family-reported family functioning. To address this question, adults with bipolar I disorder (BD; n = 92), major depressive disorder (MDD; n = 121), and their family members (ns = 135 and 201, respectively) were recruited from hospital sources. All patients and their family members completed the Family Assessment Device (Epstein et al., 1983). Intraclass correlation coefficients revealed that, in contrast to the moderate degree of concordance in the MDD sample, degree of concordance between patient- and family-reported family functioning was significantly weaker in BD. Subsequent analysis revealed that this discordance was driven by the reports of the child and young adolescent family members of the patients with BD. Results highlight the importance of collateral reports in the assessment of family functioning, especially among families of patients with BD, in research and treatment. PMID:23588224

  19. From goal motivation to goal progress: the mediating role of coping in the Self-Concordance Model.

    PubMed

    Gaudreau, Patrick; Carraro, Natasha; Miranda, Dave

    2012-01-01

    The present studies examined the mediating role of self-regulatory mechanisms in the relationship between goal motivation and goal progress in the Self-Concordance Model. First, a systematic review, using meta-analytical path analysis, supported the mediating role of effort and action planning in the positive association between autonomous goal motivation and goal progress. Second, results from two additional empirical studies, using structural equation modeling, lent credence to the mediating role of coping in the relationship between goal motivation and goal progress of university students. Autonomous goal motivation was positively associated with task-oriented coping, which predicted greater goal progress during midterm exams (Study 1, N=702) and at the end of the semester in a different sample (Study 2, N=167). Controlled goal motivation was associated with greater disengagement-oriented coping (Study 1 and Study 2) and lesser use of task-oriented coping (Study 2), which reduced goal progress. These results held up after controlling for perceived stress (Study 2). Our findings highlight the importance of coping in the "inception-to-attainment" goal process because autonomous goal motivation indirectly rather than directly predicts goal progress of university students through their usage of task-oriented coping.

  20. Fatigue tests on big structure assemblies of concorde aircraft

    NASA Technical Reports Server (NTRS)

    Nguyen, V. P.; Perrais, J. P.

    1972-01-01

    Fatigue tests on structural assemblies of the Concorde supersonic transport aircraft are reported. Two main sections of the aircraft were subjected to pressure, mechanical load, and thermal static tests. The types of fatigue tests conducted and the results obtained are discussed. It was concluded that on a supersonic aircraft whose structural weight is a significant part of the weight analysis, many fatigue and static strength development tests should be made and fatigue and thermal tests of the structures are absolutely necessary.

  1. Water Withdrawals, Use, and Wastewater Return Flows in the Concord River Basin, Eastern Massachusetts, 1996-2000

    USGS Publications Warehouse

    Barlow, Lora K.; Hutchins, Linda M.; Desimone, Leslie A.

    2009-01-01

    Water withdrawals, use, and wastewater return flows for the Concord River Basin were estimated for the period 1996-2000. The study area in eastern Massachusetts is 400 square miles in area and includes the basins of two major tributaries, the Assabet and Sudbury Rivers, along with the Concord River, which starts at the confluence of the two tributaries. About 400,000 people lived in the basin during the study period, on the basis of an analysis of census data, land use, and population density. Public water systems served an estimated 87 percent of the people in the basin, and public wastewater systems served an estimated 65 percent of the basin population. The estimates of water withdrawals, use, wastewater return flows, and imports and exports for the Concord River Basin and 25 subbasins provide information that can be used in hydrologic analyses such as water budgets and can guide water-resources allocations for human and environmental needs. Withdrawals in the basin were estimated at 12,700 million gallons per year (Mgal/yr) during the study period, of which 10,100 Mgal/yr (about 80 percent) were withdrawn by public water-supply systems and 2,650 Mgal/yr were self-supplied by individual users. Water use in the basin and subbasins was estimated by using water withdrawals, average per capita use rates (about 72 gallons per day per person), land-use data, estimated population densities, and other information. Total water use in the basin, which included imports, was 19,200 Mgal/yr and was provided mostly (86.2 percent) by public supply. Domestic use (11,300 Mgal/yr) was the largest component, accounting for about 60 percent of total water use in the basin. Commercial use (3,770 Mgal/yr), industrial use (1,330 Mgal/yr), and agricultural use (including golf-course irrigation; 562 Mgal/yr) accounted for 19.6, 6.9, and 2.9 percent, respectively, of total use. Water that was unaccounted for in public-supply systems was estimated at 2,260 Mgal/yr, or 11.8 percent of

  2. An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data.

    PubMed

    Braaksma, Machtelt; Martens-Uzunova, Elena S; Punt, Peter J; Schaap, Peter J

    2010-10-19

    The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N-terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions.

  3. An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

    PubMed Central

    2010-01-01

    Background The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N-terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. Results A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. Conclusions We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions. PMID:20959013

  4. The Effects of Concordance-Based Electronic Glosses on L2 Vocabulary Learning

    ERIC Educational Resources Information Center

    Lee, Hansol; Warschauer, Mark; Lee, Jang Ho

    2017-01-01

    The present study investigates the effects of two different vocabulary learning conditions in digital reading environments equipped with electronic textual glossing. The first condition presents the concordance lines of a target lexical item, thereby making learners infer its meaning by reading the referenced sentences. The second condition…

  5. Script Concordance Testing in Continuing Professional Development: Local or International Reference Panels?

    ERIC Educational Resources Information Center

    Pleguezuelos, E. M.; Hornos, E.; Dory, V.; Gagnon, R.; Malagrino, P.; Brailovsky, C. A.; Charlin, B.

    2013-01-01

    Context: The PRACTICUM Institute has developed large-scale international programs of on-line continuing professional development (CPD) based on self-testing and feedback using the Practicum Script Concordance Test© (PSCT). Aims: To examine the psychometric consequences of pooling the responses of panelists from different countries (composite…

  6. Concordance Between Current Job and Usual Job in Occupational and Industry Groupings

    PubMed Central

    Luckhaupt, Sara E.; Cohen, Martha A.; Calvert, Geoffrey M.

    2015-01-01

    Objective To determine whether current job is a reasonable surrogate for usual job. Methods Data from the 2010 National Health Interview Survey were utilized to determine concordance between current and usual jobs for workers employed within the past year. Concordance was quantitated by kappa values for both simple and detailed industry and occupational groups. Good agreement is considered to be present when kappa values exceed 60. Results Overall kappa values ± standard errors were 74.5 ± 0.5 for simple industry, 72.4 ± 0.5 for detailed industry, 76.3 ± 0.4 for simple occupation, 73.7 ± 0.5 for detailed occupation, and 80.4 ± 0.6 for very broad occupational class. Sixty-five of 73 detailed industry groups and 78 of 81 detailed occupation groups evaluated had good agreement between current and usual jobs. Conclusions Current job can often serve as a reliable surrogate for usual job in epidemiologic studies. PMID:23969506

  7. Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

    PubMed

    Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; Nielsen, Morten

    2015-11-01

    A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4(+) T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1 .

  8. Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

    PubMed Central

    Ryan, Natalia; Chorley, Brian; Tice, Raymond R.; Judson, Richard; Corton, J. Christopher

    2016-01-01

    Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput formats. Computational methods are described here to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through chromatin immunoprecipitation coupled with DNA sequencing analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression datasets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including “very weak” agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals, the balanced accuracies were 95% and 98% for activation or suppression, respectively. These results demonstrate that the ERα gene expression biomarker can accurately identify ERα modulators in large collections of microarray data derived from MCF-7 cells. PMID:26865669

  9. [Concordance in the registry of dementia among the main sources of clinical information].

    PubMed

    Marta-Moreno, Javier; Obón-Azuara, Blanca; Gimeno-Felíu, Luis; Achkar-Tuglaman, Nesib Nicolás; Poblador-Plou, Beatriz; Calderón-Larrañaga, Amaia; Prados-Torres, Alexandra

    2016-01-01

    The objective of this work was to analyse the concordance in the registry of dementia among the main sources of clinical information, with the aim of determining their usefulness for epidemiological and clinical research. Descriptive study of patients assigned to the Aragon Health Service in 2010 (n=1,344,891). (i)the pharmacy billing database (n=9,392); (ii)Primary Care electronic health records (EHR) (n=9,471), and (iii)the hospital minimum basic data set (n=3,289). When studying the concordance of the databases, the group of patients with a specific treatment for dementia (i.e., acetylcholinesterase inhibitors and/or memantine) was taken as the reference. The diagnosis in Primary Care was missing for 47.3% of patients taking anti-dementia drugs. The same occurred with 38.3% of dementia patients admitted to hospital during the study year. Among patients with a diagnosis of dementia in the EHR, only half (52.3%) was under treatment for this condition. This percentage decreased to 34.4% in patients with the diagnosis registered in the hospital database. The weak concordance in the registry of the dementia diagnosis between the main health information systems makes their use and analysis more complex, and supports the need to include all available health data sources in order to gain a global picture of the epidemiological and clinical reality of this health condition. Copyright © 2015 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.

  10. Prediction of Waitlist Mortality in Adult Heart Transplant Candidates: The Candidate Risk Score.

    PubMed

    Jasseron, Carine; Legeai, Camille; Jacquelinet, Christian; Leprince, Pascal; Cantrelle, Christelle; Audry, Benoît; Porcher, Raphael; Bastien, Olivier; Dorent, Richard

    2017-09-01

    The cardiac allocation system in France is currently based on urgency and geography. Medical urgency is defined by therapies without considering objective patient mortality risk factors. This study aimed to develop a waitlist mortality risk score from commonly available candidate variables. The study included all patients, aged 16 years or older, registered on the national registry CRISTAL for first single-organ heart transplantation between January 2010 and December 2014. This population was randomly divided in a 2:1 ratio into derivation and validation cohorts. The association of variables at listing with 1-year waitlist death or delisting for worsening medical condition was assessed within the derivation cohort. The predictors were used to generate a candidate risk score (CRS). Validation of the CRS was performed in the validation cohort. Concordance probability estimation (CPE) was used to evaluate the discriminative capacity of the models. During the study period, 2333 patients were newly listed. The derivation (n =1 555) and the validation cohorts (n = 778) were similar. Short-term mechanical circulatory support, natriuretic peptide decile, glomerular filtration rate, and total bilirubin level were included in a simplified model and incorporated into the score. The Concordance probability estimation of the CRS was 0.73 in the derivation cohort and 0.71 in the validation cohort. The correlation between observed and expected 1-year waitlist mortality in the validation cohort was 0.87. The candidate risk score provides an accurate objective prediction of waitlist mortality. It is currently being used to develop a modified cardiac allocation system in France.

  11. Toxicity assessments of nonsteroidal anti-inflammatory drugs in isolated mitochondria, rat hepatocytes, and zebrafish show good concordance across chemical classes

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

    Nadanaciva, Sashi; Aleo, Michael D.; Strock, Christopher J.

    To reduce costly late-stage compound attrition, there has been an increased focus on assessing compounds in in vitro assays that predict attributes of human safety liabilities, before preclinical in vivo studies are done. Relevant questions when choosing a panel of assays for predicting toxicity are (a) whether there is general concordance in the data among the assays, and (b) whether, in a retrospective analysis, the rank order of toxicity of compounds in the assays correlates with the known safety profile of the drugs in humans. The aim of our study was to answer these questions using nonsteroidal anti-inflammatory drugs (NSAIDs)more » as a test set since NSAIDs are generally associated with gastrointestinal injury, hepatotoxicity, and/or cardiovascular risk, with mitochondrial impairment and endoplasmic reticulum stress being possible contributing factors. Eleven NSAIDs, flufenamic acid, tolfenamic acid, mefenamic acid, diclofenac, meloxicam, sudoxicam, piroxicam, diflunisal, acetylsalicylic acid, nimesulide, and sulindac (and its two metabolites, sulindac sulfide and sulindac sulfone), were tested for their effects on (a) the respiration of rat liver mitochondria, (b) a panel of mechanistic endpoints in rat hepatocytes, and (c) the viability and organ morphology of zebrafish. We show good concordance for distinguishing among/between NSAID chemical classes in the observations among the three approaches. Furthermore, the assays were complementary and able to correctly identify “toxic” and “non-toxic” drugs in accordance with their human safety profile, with emphasis on hepatic and gastrointestinal safety. We recommend implementing our multi-assay approach in the drug discovery process to reduce compound attrition. - Highlights: • NSAIDS cause liver and GI toxicity. • Mitochondrial uncoupling contributes to NSAID liver toxicity. • ER stress is a mechanism that contributes to liver toxicity. • Zebrafish and cell based assays are complimentary.« less

  12. Concordance and discordance between measured and perceived balance and the effect on gait speed and falls following stroke

    PubMed Central

    Liphart, Jodi; Gallichio, Joann; Tilson, Julie K; Pei, Qinglin; Wu, Samuel S; Duncan, Pamela W

    2016-01-01

    Objective To ascertain the existence of discordance between perceived and measured balance in persons with stroke and to examine the impact on walking speed and falls. Design A secondary analysis of a phase three, multicentered randomized controlled trial examining walking recovery following stroke. Subjects A total of 352 participants from the Locomotor Experience Applied Post-Stroke (LEAPS) trial. Methods Participants were categorized into four groups: two concordant and two discordant groups in relation to measured and perceived balance. Number and percentage of individuals with concordance and discordance were evaluated at two and 12 months. Walking speed and fall incidence between groups were examined. Main measures Perceived balance was measured by the Activity-specific Balance Confidence scale, measured balance was determined by the Berg Balance Scale and gait speed was measured by the 10-meter walk test. Results Discordance was present for 35.8% of participants at two months post-stroke with no statistically significant change in proportion at 12 months. Discordant participants with high perceived balance and low measured balance walked 0.09 m/s faster at two months than participants with concordant low perceived and measured balance (p < 0.05). Discordant participants with low perceived balance and high measured balance walked 0.15 m/s slower than those that were concordant with high perceived and measured balance (p ⩽ 0.0001) at 12 months. Concordant participants with high perceived and measured balance walked fastest and had fewer falls. Conclusions Discordance existed between perceived and measured balance in one-third of individuals at two and 12 months post-stroke. Perceived balance impacted gait speed but not fall incidence. PMID:25810426

  13. Motor Impairment in Sibling Pairs Concordant and Discordant for Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Hilton, Claudia List; Zhang, Yi; Whilte, Megan R.; Klohr, Cheryl L.; Constantino, John

    2012-01-01

    Aim: Although motor impairment is frequently observed in children with autism spectrum disorders (ASD), the manner in which these impairments aggregate in families affected by autism is unknown. We used a standardized measure of motor proficiency to objectively examine quantitative variation in motor proficiency in sibling pairs concordant and…

  14. English Collocation Learning through Corpus Data: On-Line Concordance and Statistical Information

    ERIC Educational Resources Information Center

    Ohtake, Hiroshi; Fujita, Nobuyuki; Kawamoto, Takeshi; Morren, Brian; Ugawa, Yoshihiro; Kaneko, Shuji

    2012-01-01

    We developed an English Collocations On Demand system offering on-line corpus and concordance information to help Japanese researchers acquire a better command of English collocation patterns. The Life Science Dictionary Corpus consists of approximately 90,000,000 words collected from life science related research papers published in academic…

  15. Concordance between patient and family reports of family functioning in bipolar I disorder and major depressive disorder.

    PubMed

    Weinstock, Lauren M; Wenze, Susan J; Munroe, Mary K; Miller, Ivan W

    2013-05-01

    Despite the extensive literature on family functioning and mood disorders, less is known about concordance between patient- and family-reported family functioning. To address this question, adults with bipolar I disorder (BD; n = 92) or major depressive disorder (MDD; n = 121) and their family members (n = 135 and 201, respectively) were recruited from hospital sources. All patients and their family members completed the Family Assessment Device (Epstein, Baldwin, Bishop. J Marital Fam Ther. 9:171-180, 1983). Intraclass correlation coefficients revealed that, in contrast to the moderate degree of concordance in the MDD sample, degree of concordance between patient- and family-reported family functioning was significantly weaker in BD. Subsequent analysis revealed that this discordance was driven by the reports of the child and young adolescent family members of the patients with BD. Results highlight the importance of collateral reports in the assessment of family functioning, especially among families of patients with BD, in research and treatment.

  16. Accurate thermoelastic tensor and acoustic velocities of NaCl

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

    Marcondes, Michel L., E-mail: michel@if.usp.br; Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455; Shukla, Gaurav, E-mail: shukla@physics.umn.edu

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor bymore » using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.« less

  17. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    PubMed

    Reynolds, Sheila M; Bilmes, Jeff A; Noble, William Stafford

    2010-07-08

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  18. Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens

    PubMed Central

    Reynolds, Sheila M.; Bilmes, Jeff A.; Noble, William Stafford

    2010-01-01

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence—301 base pairs, centered at the position to be scored—with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  19. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model

    PubMed Central

    DeLeon, Orlando; Hodis, Hagit; O’Malley, Yunxia; Johnson, Jacklyn; Salimi, Hamid; Zhai, Yinjie; Winter, Elizabeth; Remec, Claire; Eichelberger, Noah; Van Cleave, Brandon; Puliadi, Ramya; Harrington, Robert D.; Stapleton, Jack T.; Haim, Hillel

    2017-01-01

    The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties

  20. Concordance between VDU-users' ratings of comfort and perceived exertion with experts' observations of workplace layout and working postures.

    PubMed

    Lindegård, A; Karlberg, C; Wigaeus Tornqvist, E; Toomingas, A; Hagberg, M

    2005-05-01

    The aim of the present study was to evaluate the concordance (agreement) between VDU-users' ratings of comfort and ergonomists' observations of workplace layout, and the concordance between VDU-users' ratings of perceived exertion and ergonomists' observations of working postures during VDU-work. The study population consisted of 853 symptom free subjects. Data on perceived comfort in different dimensions and data regarding perceived exertion in different body locations were collected by means of a questionnaire. Data concerning workplace layout and working postures were collected with an observation protocol, by an ergonomist. Concordance between ratings of comfort and observations of workplace layout was reasonably good for the chair and the keyboard (0.60, 0.58) and good regarding the screen and the input device (0.72, 0.61). Concordance between ratings of perceived exertion and observations of working postures indicated good agreement (0.63-0.77) for all measured body locations (neck, shoulder, wrist and trunk). In conclusion ratings of comfort and perceived exertion could be used as cost-efficient and user-friendly methods for practitioners to identify high exposure to poor workplace layout and poor working postures.

  1. How doctors' communication style and race concordance influence African-Caribbean patients when disclosing depression.

    PubMed

    Adams, A; Realpe, A; Vail, L; Buckingham, C D; Erby, L H; Roter, D

    2015-10-01

    To determine the impact of doctors' communication style and doctor-patient race concordance on UK African-Caribbeans' comfort in disclosing depression. 160 African-Caribbean and 160 white British subjects, stratified by gender and history of depression, participated in simulated depression consultations with video-recorded doctors. Doctors were stratified by black or white race, gender and a high (HPC) or low patient-centred (LPC) communication style, giving a full 2×2×2 factorial design. Afterwards, participants rated aspects of doctors' communication style, their comfort in disclosing depression and treatment preferences Race concordance had no impact on African-Caribbeans' comfort in disclosing depression. However a HPC versus LPC communication style made them significantly more positive about their interactions with doctors (p=0.000), their overall comfort (p=0.003), their comfort in disclosing their emotional state (p=0.001), and about considering talking therapy (p=0.01); but less positive about considering antidepressant medication (p=0.01). Doctors' communication style was shown to be more important than patient race or race concordance in influencing African Caribbeans' depression consultation experiences. Changing doctors' communication style may help reduce disparities in depression care. Practitioners should cultivate a HPC style to make African-Caribbeans more comfortable when disclosing depression, so that it is less likely to be missed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  2. Brief Report: On the Concordance Percentages for Autistic Spectrum Disorder of Twins

    ERIC Educational Resources Information Center

    Bohm, Henry V.; Stewart, Melbourne G.

    2009-01-01

    In the development of genetic theories of Autistic Spectrum Disorder (ASD) various characteristics of monozygotic (MZ) and dizygotic (DZ) twins are often considered. This paper sets forth a possible refinement in the interpretation of the MZ twin concordance percentages for ASD underlying such genetic theories, and, drawing the consequences from…

  3. Transjugular Intrahepatic Portosystemic Shunt Dysfunction: Concordance of Clinical Findings, Doppler Ultrasound Examination, and Shunt Venography.

    PubMed

    Owen, Joshua M; Gaba, Ron Charles

    2016-01-01

    The objective of this study was to evaluate the concordance between clinical symptoms, Doppler ultrasound (US), and shunt venography for the detection of stent-graft transjugular intrahepatic portosystemic shunt (TIPS) dysfunction. Forty-one patients (M:F 30:11, median age 55 years) who underwent contemporaneous clinical exam, Doppler US, and TIPS venography between 2003 and 2014 were retrospectively studied. Clinical symptoms (recurrent ascites or variceal bleeding) were dichotomously classified as present/absent, and US and TIPS venograms were categorized in a binary fashion as normal/abnormal. US abnormalities included high/low (>190 or <90 cm/s) TIPS velocity, significant velocity rise/fall (>50 cm/s), absent flow, and return of antegrade intra-hepatic portal flow. Venographic abnormalities included shunt stenosis/occlusion and/or pressure gradient elevation. Clinical and imaging concordance rates were calculated. Fifty-two corresponding US examinations and venograms were assessed. The median time between studies was 3 days. Forty of 52 (77%) patients were symptomatic, 33/52 (64%) US examinations were abnormal, and 20/52 (38%) TIPS venograms were abnormal. Concordance between clinical symptoms and TIPS venography was 48% (25/52), while the agreement between US and shunt venography was 65% (34/52). Clinical symptoms and the US concurred in 60% (31/52) of the patients. The sensitivity of clinical symptoms and US for the detection of venographically abnormal shunts was 80% (16/20) and 85% (17/20), respectively. Both clinical symptoms and the US had low specificity (25%, 8/32 and 50%, 16/32) for venographically abnormal shunts. Clinical findings and the US had low concordance rates with TIPS venography, with acceptable sensitivity but poor specificity. These findings suggest the need for improved noninvasive imaging methods for stent-graft TIPS surveillance.

  4. Transjugular Intrahepatic Portosystemic Shunt Dysfunction: Concordance of Clinical Findings, Doppler Ultrasound Examination, and Shunt Venography

    PubMed Central

    Owen, Joshua M; Gaba, Ron Charles

    2016-01-01

    Objectives: The objective of this study was to evaluate the concordance between clinical symptoms, Doppler ultrasound (US), and shunt venography for the detection of stent-graft transjugular intrahepatic portosystemic shunt (TIPS) dysfunction. Materials and Methods: Forty-one patients (M:F 30:11, median age 55 years) who underwent contemporaneous clinical exam, Doppler US, and TIPS venography between 2003 and 2014 were retrospectively studied. Clinical symptoms (recurrent ascites or variceal bleeding) were dichotomously classified as present/absent, and US and TIPS venograms were categorized in a binary fashion as normal/abnormal. US abnormalities included high/low (>190 or <90 cm/s) TIPS velocity, significant velocity rise/fall (>50 cm/s), absent flow, and return of antegrade intra-hepatic portal flow. Venographic abnormalities included shunt stenosis/occlusion and/or pressure gradient elevation. Clinical and imaging concordance rates were calculated. Results: Fifty-two corresponding US examinations and venograms were assessed. The median time between studies was 3 days. Forty of 52 (77%) patients were symptomatic, 33/52 (64%) US examinations were abnormal, and 20/52 (38%) TIPS venograms were abnormal. Concordance between clinical symptoms and TIPS venography was 48% (25/52), while the agreement between US and shunt venography was 65% (34/52). Clinical symptoms and the US concurred in 60% (31/52) of the patients. The sensitivity of clinical symptoms and US for the detection of venographically abnormal shunts was 80% (16/20) and 85% (17/20), respectively. Both clinical symptoms and the US had low specificity (25%, 8/32 and 50%, 16/32) for venographically abnormal shunts. Conclusion: Clinical findings and the US had low concordance rates with TIPS venography, with acceptable sensitivity but poor specificity. These findings suggest the need for improved noninvasive imaging methods for stent-graft TIPS surveillance. PMID:27563495

  5. Effects of a health information system data quality intervention on concordance in Mozambique: time-series analyses from 2009-2012.

    PubMed

    Wagenaar, Bradley H; Gimbel, Sarah; Hoek, Roxanne; Pfeiffer, James; Michel, Cathy; Manuel, João Luis; Cuembelo, Fatima; Quembo, Titos; Afonso, Pires; Porthé, Victoria; Gloyd, Stephen; Sherr, Kenneth

    2015-01-01

    We assessed the effects of a three-year national-level, ministry-led health information system (HIS) data quality intervention and identified associated health facility factors. Monthly summary HIS data concordance between a gold standard data quality audit and routine HIS data was assessed in 26 health facilities in Sofala Province, Mozambique across four indicators (outpatient consults, institutional births, first antenatal care visits, and third dose of diphtheria, pertussis, and tetanus vaccination) and five levels of health system data aggregation (daily facility paper registers, monthly paper facility reports, monthly paper district reports, monthly electronic district reports, and monthly electronic provincial reports) through retrospective yearly audits conducted July-August 2010-2013. We used mixed-effects linear models to quantify changes in data quality over time and associated health system determinants. Median concordance increased from 56.3% during the baseline period (2009-2010) to 87.5% during 2012-2013. Concordance improved by 1.0% (confidence interval [CI]: 0.60, 1.5) per month during the intervention period of 2010-2011 and 1.6% (CI: 0.89, 2.2) per month from 2011-2012. No significant improvements were observed from 2009-2010 (during baseline period) or 2012-2013. Facilities with more technical staff (aβ: 0.71; CI: 0.14, 1.3), more first antenatal care visits (aβ: 3.3; CI: 0.43, 6.2), and fewer clinic beds (aβ: -0.94; CI: -1.7, -0.20) showed more improvements. Compared to facilities with no stock-outs, facilities with five essential drugs stocked out had 51.7% (CI: -64.8 -38.6) lower data concordance. A data quality intervention was associated with significant improvements in health information system data concordance across public-sector health facilities in rural and urban Mozambique. Concordance was higher at those facilities with more human resources for health and was associated with fewer clinic-level stock-outs of essential medicines

  6. Concordance with prescribing information dosage recommendations for dipeptidyl-peptidase-4 inhibitors among type 2 diabetes mellitus patients with moderate to severe chronic kidney disease.

    PubMed

    Huang, Huan; Shetty, Sharash; Bauer, Elise; Lang, Kathleen

    2018-06-01

    To estimate the proportion of patients with moderate to severe chronic kidney disease (CKD) whose initial dipeptidyl-peptidase-4 inhibitor (DPP4-i) dosage was concordant with prescribing information (label) recommendations in the United States. Adult patients with type 2 diabetes mellitus (T2DM) who initiated a DPP4-i (linagliptin, sitagliptin, saxagliptin) between 1 January 2011 and 30 June 2014 were identified using electronic medical records and administrative claims, with index date being the date of first observed DPP4-i treatment. Patients were required to have chronic kidney disease (CKD) stage 3b, 4 or 5 (estimated Glomerular Filtration Rate [eGFR] value <45 ml/min/1.73 m 2 ) during the 12 month pre-index period. Patients were classified as concordant or not concordant based on whether the first prescribed dose was consistent with label recommendations. Demographics, clinical characteristics, resource use and costs during pre-index were evaluated by DPP4-i concordance status. Of the 492 patients (323 sitagliptin, 57 saxagliptin, 112 linagliptin), 36.2% were prescribed doses that were not concordant with label recommendations (44.9% for sitagliptin, 57.9% for saxagliptin and 0% for linagliptin [which does not require dosage adjustment]). Concordant patients were slightly older (mean age 71 years vs. 68, p = .01) but had similar gender distribution (55% vs. 60% female, p = .31) compared to those who were not concordant. They had lower general health status (Charlson Comorbidity Score 2.6 vs. 2.2, p = .03), and had similar pre-index all-cause total costs ($25,245 vs. $21,972, p = .68) and lower pre-index T2DM-related costs ($1618 vs. $1922, p = .05). More than a third of DPP4-i patients with CKD stage 3b or higher were prescribed doses not concordant with DPP4-i label dosage recommendations.

  7. Risk prediction models of breast cancer: a systematic review of model performances.

    PubMed

    Anothaisintawee, Thunyarat; Teerawattananon, Yot; Wiratkapun, Chollathip; Kasamesup, Vijj; Thakkinstian, Ammarin

    2012-05-01

    The number of risk prediction models has been increasingly developed, for estimating about breast cancer in individual women. However, those model performances are questionable. We therefore have conducted a study with the aim to systematically review previous risk prediction models. The results from this review help to identify the most reliable model and indicate the strengths and weaknesses of each model for guiding future model development. We searched MEDLINE (PubMed) from 1949 and EMBASE (Ovid) from 1974 until October 2010. Observational studies which constructed models using regression methods were selected. Information about model development and performance were extracted. Twenty-five out of 453 studies were eligible. Of these, 18 developed prediction models and 7 validated existing prediction models. Up to 13 variables were included in the models and sample sizes for each study ranged from 550 to 2,404,636. Internal validation was performed in four models, while five models had external validation. Gail and Rosner and Colditz models were the significant models which were subsequently modified by other scholars. Calibration performance of most models was fair to good (expected/observe ratio: 0.87-1.12), but discriminatory accuracy was poor to fair both in internal validation (concordance statistics: 0.53-0.66) and in external validation (concordance statistics: 0.56-0.63). Most models yielded relatively poor discrimination in both internal and external validation. This poor discriminatory accuracy of existing models might be because of a lack of knowledge about risk factors, heterogeneous subtypes of breast cancer, and different distributions of risk factors across populations. In addition the concordance statistic itself is insensitive to measure the improvement of discrimination. Therefore, the new method such as net reclassification index should be considered to evaluate the improvement of the performance of a new develop model.

  8. Lack of concordance amongst measurements of individual anaerobic threshold and maximal lactate steady state on a cycle ergometer.

    PubMed

    Arratibel-Imaz, Iñaki; Calleja-González, Julio; Emparanza, Jose Ignacio; Terrados, Nicolas; Mjaanes, Jeffrey M; Ostojic, Sergej M

    2016-01-01

    The calculation of exertion intensity, in which a change is produced in the metabolic processes which provide the energy to maintain physical work, has been defined as the anaerobic threshold (AT). The direct calculation of maximal lactate steady state (MLSS) would require exertion intensities over a long period of time and with sufficient rest periods which would prove significantly difficult for daily practice. Many protocols have been used for the indirect calculation of MLSS. The aim of this study is to determine if the results of measurements with 12 different AT calculation methods and calculation software [Keul, Simon, Stegmann, Bunc, Dickhuth (TKM and WLa), Dmax, Freiburg, Geiger-Hille, Log-Log, Lactate Minimum] can be used interchangeably, including the method of the fixed threshold of Mader/OBLA's 4 mmol/l and then to compare them with the direct measurement of MLSS. There were two parts to this research. Phase 1: results from 162 exertion tests chosen at random from the 1560 tests. Phase 2: sixteen athletes (n = 16) carried out different tests on five consecutive days. There was very high concordance among all the methods [intraclass correlation coefficient (ICC) > 0.90], except Log-Log in relation to the Stegamnn, Dmax, Dickhuth-WLa and Geiger-Hille. The Dickhuth-TKM showed a high tendency towards concordance, with Dmax (2.2 W) and Dickhuth-WLa (0.1 W). The Dickhuth-TKM method presented a high tendency to concordance with Dickhuth-WLa (0.5 W), Freiburg (7.4 W), MLSS (2.0 W), Bunc (8.9 W), Dmax (0.1 W). The calculation of MLSS power showed a high tendency to concordance, with Dickhuth-TKM (2 W), Dmax (2.1 W), Dickhuth-WLa (1.5 W). The fixed threshold of 4 mmol/l or OBLA produces slightly different and higher results than those obtained with all the methods analyzed, including MLSS, meaning an overestimation of power in the individual anaerobic threshold. The Dickhuth-TKM, Dmax and Dickhuth-WLa methods defined a high concordance on a cycle ergometer

  9. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models

    NASA Astrophysics Data System (ADS)

    Blackman, Jonathan; Field, Scott E.; Galley, Chad R.; Szilágyi, Béla; Scheel, Mark A.; Tiglio, Manuel; Hemberger, Daniel A.

    2015-09-01

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic -2Yℓm waveform modes resolved by the NR code up to ℓ=8 . We compare our surrogate model to effective one body waveforms from 50 M⊙ to 300 M⊙ for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  10. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models.

    PubMed

    Blackman, Jonathan; Field, Scott E; Galley, Chad R; Szilágyi, Béla; Scheel, Mark A; Tiglio, Manuel; Hemberger, Daniel A

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  11. Exploring the Circulation Dynamics of Mississippi Sound and Bight Using the CONCORDE Synthesis Model

    NASA Astrophysics Data System (ADS)

    Pan, C.; Dinniman, M. S.; Fitzpatrick, P. J.; Lau, Y.; Cambazoglu, M. K.; Parra, S. M.; Hofmann, E. E.; Dzwonkowski, B.; Warner, S. J.; O'Brien, S. J.; Dykstra, S. L.; Wiggert, J. D.

    2017-12-01

    As part of the modeling effort of the GOMRI (Gulf of Mexico Research Initiative)-funded CONCORDE consortium, a high resolution ( 400 m) regional ocean model is implemented for the Mississippi (MS) Sound and Bight. The model is based on the Coupled Ocean Atmosphere Wave Sediment Transport Modeling System (COAWST), with initial and lateral boundary conditions drawn from data assimilative 3-day forecasts of the 1km-resolution Gulf of Mexico Navy Coastal Ocean Model (GOM-NCOM). The model initiates on 01/01/2014 and runs for 3 years. The model results are validated with available remote sensing data and with CONCORDE's moored and ship-based in-situ observations. Results from a three-year simulation (2014-2016) show that ocean circulation and water properties of the MS Sound and Bight are sensitive to meteorological forcing. A low resolution surface forcing, drawn from the North America Regional Reanalysis (NARR), and a high resolution forcing, called CONCORDE Meteorological Analysis (CMA) ) that resolves the diurnal sea breeze, are used to drive the model to examine the sensitivity of the circulation to surface forcing. The model responses to the low resolution NARR forcing and to the high resolution CMA are compared in detail for the CONCORDE Fall and Spring field campaigns when contemporaneous in situ data are available, with a focus on how simulated exchanges between MS Sound and MS Bight are impacted. In most cases, the model shows higher simulation skill when it is driven by CMA. Freshwater plumes of the MS River, MS Sound and Mobile Bay influence the shelf waters of the MS Bight in terms of material budget and dynamics. Drifters and dye experiments near Mobile Bay demonstrate that material exchanges between Mobile Bay and the Sound, and between the Sound and Bight, are sensitive to the wind strength and direction. A model - data comparison targeting the Mobile Bay plume suggests that under both northerly and southerly wind conditions the model is capable of

  12. A NEW CLINICAL PREDICTION CRITERION ACCURATELY DETERMINES A SUBSET OF PATIENTS WITH BILATERAL PRIMARY ALDOSTERONISM BEFORE ADRENAL VENOUS SAMPLING.

    PubMed

    Kocjan, Tomaz; Janez, Andrej; Stankovic, Milenko; Vidmar, Gaj; Jensterle, Mojca

    2016-05-01

    Adrenal venous sampling (AVS) is the only available method to distinguish bilateral from unilateral primary aldosteronism (PA). AVS has several drawbacks, so it is reasonable to avoid this procedure when the results would not affect clinical management. Our objective was to identify a clinical criterion that can reliably predict nonlateralized AVS as a surrogate for bilateral PA that is not treated surgically. A retrospective diagnostic cross-sectional study conducted at Slovenian national endocrine referral center included 69 consecutive patients (mean age 56 ± 8 years, 21 females) with PA who underwent AVS. PA was confirmed with the saline infusion test (SIT). AVS was performed sequentially during continuous adrenocorticotrophic hormone (ACTH) infusion. The main outcome measures were variables associated with nonlateralized AVS to derive a clinical prediction rule. Sixty-seven (97%) patients had a successful AVS and were included in the statistical analysis. A total of 39 (58%) patients had nonlateralized AVS. The combined criterion of serum potassium ≥3.5 mmol/L, post-SIT aldosterone <18 ng/dL, and either no or bilateral tumor found on computed tomography (CT) imaging had perfect estimated specificity (and thus 100% positive predictive value) for bilateral PA, saving an estimated 16% of the patients (11/67) from unnecessary AVS. The best overall classification accuracy (50/67 = 75%) was achieved using the post-SIT aldosterone level <18 ng/dL alone, which yielded 74% sensitivity and 75% specificity for predicting nonlateralized AVS. Our clinical prediction criterion appears to accurately determine a subset of patients with bilateral PA who could avoid unnecessary AVS and immediately commence with medical treatment.

  13. A short note on jackknifing the concordance correlation coefficient.

    PubMed

    Feng, Dai; Baumgartner, Richard; Svetnik, Vladimir

    2014-02-10

    Lin's concordance correlation coefficient (CCC) is a very popular scaled index of agreement used in applied statistics. To obtain a confidence interval (CI) for the estimate of CCC, jackknifing was proposed and shown to perform well in simulation as well as in applications. However, a theoretical proof of the validity of the jackknife CI for the CCC has not been presented yet. In this note, we establish a sufficient condition for using the jackknife method to construct the CI for the CCC. Copyright © 2013 John Wiley & Sons, Ltd.

  14. Social Network Concordance in Food Choice Among Spouses, Friends, and Siblings

    PubMed Central

    Jacques, Paul F.; Christakis, Nicholas A.

    2011-01-01

    Objectives. We investigated whether eating behaviors were concordant among diverse sets of social ties. Methods. We analyzed the socioeconomic and demographic distribution of eating among 3418 members of the Framingham Heart Study observed from 1991 to 2001. We used a data-classification procedure to simplify choices into 7 nonoverlapping patterns that we matched with information on social network ties. We used correlation analysis to examine eating associations among 4 types of peers (spouses, friends, brothers, and sisters). Longitudinal multiple logistic regression was used to evaluate evidence for peer influences on eating. Results. Of all peer types, spouses showed the strongest concordances in eating patterns over time after adjustment for social contextual factors. Across all peers, the eating pattern most likely to be shared by socially connected individuals was “alcohol and snacks.” Models estimating one's current eating pattern on the basis of a peer's prior eating provided supportive evidence of a social influence process. Conclusions. Certain eating patterns appeared to be socially transmissible across different kinds of relationships. These findings represent an important step in specifying the relevant social environment in the study of health behaviors to include eating. PMID:21940920

  15. Concordance of gross surgical and final fixed margins in vulvar intraepithelial neoplasia 3 and vulvar cancer.

    PubMed

    DeSimone, Christopher P; Crisp, Meredith P; Ueland, Frederick R; DePriest, Paul D; van Nagell, John R; Lele, Subodh M; Modesitt, Susan C

    2006-08-01

    To prospectively evaluate the concordance of initial surgical vulvar margins and final fixed margins and to determine the amount of microscopic pathology of grossly negative margins in women with vulvar intraepithelial neoplasia (VIN) 3 or vulvar carcinoma. Women with VIN 3 or vulvar carcinoma undergoing surgical excision were identified. Prior to excision, acetic acid was used to highlight the lesions, and 2 sutures were placed, 1 at the edge of gross disease and another 1 cm distal from the first. After specimen removal and fixation, the distance between sutures and microscopic involvement of VIN was determined. Twenty-seven women were enrolled; however, only 19 had final fixed specimens that could be accurately measured. The median fixed distance of the vulvar margin was 0.85 cm (mean, 0.83; SD, 0.19) as compared to the gross, 1-cm margin (p = 0.001). Three subjects (16%) had microscopic involvement by VIN 3 in the grossly negative epithelium between the 2 sutures, but none had a positive peripheral margin. The gross surgical margin after vulvar resection is reduced by 15% when measured in its final fixed state, and a grossly negative 1-cm margin will seldom harbor significant disease.

  16. The influence of ethnic concordance and discordance on verbal reports and nonverbal behaviours of pain.

    PubMed

    Hsieh, Annie Y; Tripp, Dean A; Ji, Li-Jun

    2011-09-01

    This study's aim was to examine the influence of ethnic concordance on Chinese participants' pain report and nonverbal pain expression in a laboratory setting. Participants (n=102) were exposed to a cold pressor task under 1 of 2 conditions: Chinese milieu (n=52; participants exposed to Chinese experimenters and language), or European Canadian milieu (n=50; participants exposed to Euro-Canadian experimenters and English language). A reference group with 86 Euro-Canadian participants, exposed to the Euro-Canadian milieu only, was included for comparison. The Chinese groups did not differ on pain intensity during the pain task. However, Chinese participants in the Chinese milieu reported significantly higher affective pain and displayed more nonverbal behaviour of pain than the Chinese participants in the Euro-Canadian milieu. In addition, compared to the Euro-Canadian group, both Chinese groups reported higher pain intensity during the pain task and greater affective pain after immersion. The results demonstrated that an ethnically concordant milieu is associated with increased nonverbal pain displays and affective pain report. These findings suggest that research on ethnic disparities in pain treatment should examine ethnic concordance between observer and individual in pain. Copyright © 2011 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  17. Achieving 95% cross-methodological concordance in HER2 testing: causes and implications of discordant cases.

    PubMed

    Grimm, Erin E; Schmidt, Rodney A; Swanson, Paul E; Dintzis, Suzanne M; Allison, Kimberly H

    2010-08-01

    We were interested in determining our concordance between fluorescence in situ hybridization (FISH) and a previously validated immunohistochemical HER2 assay to identify possible reasons for discordance and to determine if all reasons for discordance were addressed by the American Society of Clinical Oncology/College of American Pathologists guidelines. We reviewed 697 cases (2004-2007) in which HER2 immunohistochemical and FISH testing were concurrently done. Overall concordance between nonequivocal immunohistochemical and FISH results was 96%. Of the 19 discordant cases, 13 (68%) were interpreted as positive immunohistochemically but negative by FISH. The primary reason for this discordance was immunohistochemical interpretation. Weak stain intensity, granular staining, and interpretation in areas of crush artifact were identified as the most common issues. Of the 6 cases interpreted as immunohistochemically negative and FISH-positive, 2 were from patients known to be receiving trastuzumab at the time of biopsy, 1 was very close to the FISH equivocal category, and 4 cases had fewer than 1.5 CEP17 signals per cell (1 patient in this group was also receiving trastuzumab). Focusing on issues with HER2 immunohistochemical interpretation can improve concordance rates for immunohistochemically positive cases, but biologic reasons may explain some discordant immunohistochemically negative cases.

  18. Hydrodynamics of concordant and discordant fixed bed open-channel confluences

    NASA Astrophysics Data System (ADS)

    Birjukova Canelas, Olga; Lage Ferreira, Rui Miguel; Heleno Cardoso, António

    2017-04-01

    The detailed characterization of the flow field in river confluences constitutes a relevant step towards the understanding of the hydro-morpho-dynamics of these key zones of the fluvial system. With a few exceptions, existing works on this topic covered concordant bed scenarios, meaning that both confluent channels had the same elevation. This laboratory study aims to contribute to a detailed three-dimensional characterization of the flow field at a fixed bed confluence, as well as to shed light on how bed elevation discordance modifies the flow patterns of the converging flows. While the junction angle and the discharge ratio were kept fixed, two scenarios were studied on the basis of detailed water level and 3D ADV measurements at the denser mesh ever. The internal flow structure of the concordant bed scenario mostly complied with the classical conceptual models. A relevant difference concerns the size of the stagnation zone, much smaller close to the bed of the discordant bed confluence. A more significant difference is a horizontal flow structure, not previously identified in the literature, characterized by strong streamwise mean vorticity and strong secondary motion. It is observed for the discordant bed case, occurring along the inner wall of the main channel and downstream the junction corner. This structure is spatially well-correlated to a pronounced imbalance of cross-stream and vertical normal Reynolds stresses. This highlights the role of Reynolds stress anisotropy (RSA) that is generated in the shear layers than accompany the entrance of the tributary flow. Since this structure is not present in the concordant case, where RSA is also evident, it is argued that convective effects should also play a role in its formation, presumably due to deflection of the flow in the main channel by the tributary. The newly identified secondary motion should, thus, be a combination of Prandtĺs second kind and Prandtĺs first kind of secondary flow. The relative

  19. A predictive index of axillary nodal involvement in operable breast cancer.

    PubMed Central

    De Laurentiis, M.; Gallo, C.; De Placido, S.; Perrone, F.; Pettinato, G.; Petrella, G.; Carlomagno, C.; Panico, L.; Delrio, P.; Bianco, A. R.

    1996-01-01

    We investigated the association between pathological characteristics of primary breast cancer and degree of axillary nodal involvement and obtained a predictive index of the latter from the former. In 2076 cases, 17 histological features, including primary tumour and local invasion variables, were recorded. The whole sample was randomly split in a training (75% of cases) and a test sample. Simple and multiple correspondence analysis were used to select the variables to enter in a multinomial logit model to build an index predictive of the degree of nodal involvement. The response variable was axillary nodal status coded in four classes (N0, N1-3, N4-9, N > or = 10). The predictive index was then evaluated by testing goodness-of-fit and classification accuracy. Covariates significantly associated with nodal status were tumour size (P < 0.0001), tumour type (P < 0.0001), type of border (P = 0.048), multicentricity (P = 0.003), invasion of lymphatic and blood vessels (P < 0.0001) and nipple invasion (P = 0.006). Goodness-of-fit was validated by high concordance between observed and expected number of cases in each decile of predicted probability in both training and test samples. Classification accuracy analysis showed that true node-positive cases were well recognised (84.5%), but there was no clear distinction among the classes of node-positive cases. However, 10 year survival analysis showed a superimposible prognostic behaviour between predicted and observed nodal classes. Moreover, misclassified node-negative patients (i.e. those who are predicted positive) showed an outcome closer to patients with 1-3 metastatic nodes than to node-negative ones. In conclusion, the index cannot completely substitute for axillary node information, but it is a predictor of prognosis as accurate as nodal involvement and identifies a subgroup of node-negative patients with unfavourable prognosis. PMID:8630286

  20. The predictive validity of quality of evidence grades for the stability of effect estimates was low: a meta-epidemiological study.

    PubMed

    Gartlehner, Gerald; Dobrescu, Andreea; Evans, Tammeka Swinson; Bann, Carla; Robinson, Karen A; Reston, James; Thaler, Kylie; Skelly, Andrea; Glechner, Anna; Peterson, Kimberly; Kien, Christina; Lohr, Kathleen N

    2016-02-01

    To determine the predictive validity of the U.S. Evidence-based Practice Center (EPC) approach to GRADE (Grading of Recommendations Assessment, Development and Evaluation). Based on Cochrane reports with outcomes graded as high quality of evidence (QOE), we prepared 160 documents which represented different levels of QOE. Professional systematic reviewers dually graded the QOE. For each document, we determined whether estimates were concordant with high QOE estimates of the Cochrane reports. We compared the observed proportion of concordant estimates with the expected proportion from an international survey. To determine the predictive validity, we used the Hosmer-Lemeshow test to assess calibration and the C (concordance) index to assess discrimination. The predictive validity of the EPC approach to GRADE was limited. Estimates graded as high QOE were less likely, estimates graded as low or insufficient QOE more likely to remain stable than expected. The EPC approach to GRADE could not reliably predict the likelihood that individual bodies of evidence remain stable as new evidence becomes available. C-indices ranged between 0.56 (95% CI, 0.47 to 0.66) and 0.58 (95% CI, 0.50 to 0.67) indicating a low discriminatory ability. The limited predictive validity of the EPC approach to GRADE seems to reflect a mismatch between expected and observed changes in treatment effects as bodies of evidence advance from insufficient to high QOE. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Concordance of In-Home "Smart" Scale Measurement with Body Weight Measured In-Person.

    PubMed

    Ross, Kathryn M; Wing, Rena R

    2016-06-01

    Newer "smart" scales that transmit participants' body weights directly to data collection centers offer the opportunity to simplify weight assessment in weight management research; however, little data exist on the concordance of these data compared to weights measured at in-person assessments. We compared the weights of 58 participants (mean±SD BMI = 31.6±4.8, age = 52.1±9.7 years, 86.2% White, 65.5% Female) measured by study staff at an in-person assessment visit to weights measured on the same day at home using BodyTrace "smart" scales. These measures occurred after 3 months of an internet-based weight management intervention. Weight (mean±SD) measured at the 3-month in-person assessment visit was 81.5±14.7kg compared to 80.4±14.5kg measured on the same day using in-home body weight scales; mean bias =1.1±0.8kg, 95% limits of agreement = -0.5 to 2.6. Two outliers in the data suggest that there may be greater variability between measurements for participants weighing above 110 kg. Results suggest good concordance between the measurements and support the use of the BodyTrace smart scale in weight management research. Future trials using BodyTrace scales for outcome assessment should clearly define protocols for measurement and associated instructions to participants (e.g., instruct individuals to weigh at the same time of day, similarly clothed). Finally, measure concordance should be investigated in a group of individuals weighing more than 110kg.

  2. Familial concordance for age at natural menopause: results from the Breakthrough Generations Study.

    PubMed

    Morris, Danielle H; Jones, Michael E; Schoemaker, Minouk J; Ashworth, Alan; Swerdlow, Anthony J

    2011-09-01

    Existing estimates of the heritability of menopause age have a wide range. Furthermore, few studies have analyzed to what extent familial similarities might reflect shared environment, rather than shared genes. We therefore analyzed familial concordance for age at natural menopause and the effects of shared genetic and environmental factors on this concordance. Participants were 2,060 individuals comprising first-degree relatives, aged 31 to 90 years, and participating in the UK Breakthrough Generations Study. Menopause data were collected using a self-administered questionnaire and analyzed using logistic regression and variance-components models. Women were at an increased risk of early menopause (≤45 y) if their mother (odds ratio, 6.2; P < 0.001) or non-twin sister (odds ratio, 5.5; P < 0.001) had had an early menopause. Likewise, women had an increased risk of late menopause (≥54 y) if their relative had had a late menopause (mother: odds ratio, 6.1; P < 0.01; non-twin sister: odds ratio, 2.3; P < 0.001). Estimated heritability was 41.6% (P < 0.01), with an additional 13.6% (P = 0.02) of the variation in menopause age attributed to environmental factors shared by sisters. We confirm that early menopause aggregates within families and show, for the first time, that there is also strong familial concordance for late menopause. Both genes and shared environment were the source of variation in menopause age. Past heritability estimates have not accounted for shared environment, and thus, the effect of genetic variants on menopause age may previously have been overestimated.

  3. Accurate prediction of complex free surface flow around a high speed craft using a single-phase level set method

    NASA Astrophysics Data System (ADS)

    Broglia, Riccardo; Durante, Danilo

    2017-11-01

    This paper focuses on the analysis of a challenging free surface flow problem involving a surface vessel moving at high speeds, or planing. The investigation is performed using a general purpose high Reynolds free surface solver developed at CNR-INSEAN. The methodology is based on a second order finite volume discretization of the unsteady Reynolds-averaged Navier-Stokes equations (Di Mascio et al. in A second order Godunov—type scheme for naval hydrodynamics, Kluwer Academic/Plenum Publishers, Dordrecht, pp 253-261, 2001; Proceedings of 16th international offshore and polar engineering conference, San Francisco, CA, USA, 2006; J Mar Sci Technol 14:19-29, 2009); air/water interface dynamics is accurately modeled by a non standard level set approach (Di Mascio et al. in Comput Fluids 36(5):868-886, 2007a), known as the single-phase level set method. In this algorithm the governing equations are solved only in the water phase, whereas the numerical domain in the air phase is used for a suitable extension of the fluid dynamic variables. The level set function is used to track the free surface evolution; dynamic boundary conditions are enforced directly on the interface. This approach allows to accurately predict the evolution of the free surface even in the presence of violent breaking waves phenomena, maintaining the interface sharp, without any need to smear out the fluid properties across the two phases. This paper is aimed at the prediction of the complex free-surface flow field generated by a deep-V planing boat at medium and high Froude numbers (from 0.6 up to 1.2). In the present work, the planing hull is treated as a two-degree-of-freedom rigid object. Flow field is characterized by the presence of thin water sheets, several energetic breaking waves and plungings. The computational results include convergence of the trim angle, sinkage and resistance under grid refinement; high-quality experimental data are used for the purposes of validation, allowing to

  4. Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Li, Li-Ping; Huang, De-Shuang; Yan, Gui-Ying; Nie, Ru; Huang, Yu-An

    2017-04-04

    Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era. In this article, we report a novel computational model combining our newly developed discriminative vector machine classifier (DVM) and an improved Weber local descriptor (IWLD) for the prediction of PPIs. Two components, differential excitation and orientation, are exploited to build evolutionary features for each protein sequence. The main characteristics of the proposed method lies in introducing an effective feature descriptor IWLD which can capture highly discriminative evolutionary information from position-specific scoring matrixes (PSSM) of protein data, and employing the powerful and robust DVM classifier. When applying the proposed method to Yeast and H. pylori data sets, we obtained excellent prediction accuracies as high as 96.52% and 91.80%, respectively, which are significantly better than the previous methods. Extensive experiments were then performed for predicting cross-species PPIs and the predictive results were also pretty promising. To further validate the performance of the proposed method, we compared it with the state-of-the-art support vector machine (SVM) classifier on Human data set. The experimental results obtained indicate that our method is highly effective for PPIs prediction and can be taken as a supplementary tool for future proteomics research.

  5. Establishment of an in silico phototoxicity prediction method by combining descriptors related to photo-absorption and photo-reaction.

    PubMed

    Haranosono, Yu; Kurata, Masaaki; Sakaki, Hideyuki

    2014-08-01

    One of the mechanisms of phototoxicity is photo-reaction, such as reactive oxygen species (ROS) generation following photo-absorption. We focused on ROS generation and photo-absorption as key-steps, because these key-steps are able to be described by photochemical properties, and these properties are dependent on chemical structure. Photo-reactivity of a compound is described by HOMO-LUMO Gap (HLG), generally. Herein, we showed that HLG can be used as a descriptor of the generation of reactive oxygen species. Moreover, the maximum-conjugated π electron number (PENMC), which we found as a descriptor of photo-absorption, could also predict in vitro phototoxicity. Each descriptor could predict in vitro phototoxicity with 70.0% concordance, but there was un-predicted area found (gray zone). Interestingly, some compounds in each gray zone were not common, indicating that the combination of two descriptors could improve prediction potential. We reset the cut-off lines to define positive zone, negative zone and gray zone for each descriptor. Thereby we overlapped HLG and PENMC in a graph, and divided the total area to nine zones with cut-off lines of each descriptor. The rules to prediction were decided to achieve the best concordance, and the concordances were improved up to 82.8% for self-validation, 81.6% for cross-validation. We found common properties among false positive or negative compounds, photo-reactive structure and photo-allergenic, respectively. In addition, our method could be adapted to compounds rich in structural diversity using only chemical structure without any statistical analysis and complicated calculation.

  6. Public health surveillance of cancer survival in the United States and worldwide: The contribution of the CONCORD programme.

    PubMed

    Allemani, Claudia; Coleman, Michel P

    2017-12-15

    CONCORD is a programme for the global surveillance of cancer survival. In 2015, the second cycle of the program (CONCORD-2) established long-term surveillance of cancer survival worldwide, for the first time, in the largest cancer survival study published to date. CONCORD-2 provided cancer survival trends for 25,676,887 patients diagnosed during the 15-year period between 1995 and 2009 with 1 of 10 common cancers that collectively represented 63% of the global cancer burden in 2009. Herein, the authors summarize the past, describe the present, and outline the future of the CONCORD programme. They discuss the difference between population-based studies and clinical trials, and review the importance of international comparisons of population-based cancer survival. This study will focus on the United States. The authors explain why population-based survival estimates are crucial for driving effective cancer control strategies to reduce the wide and persistent disparities in cancer survival between white and black patients, which are likely to be attributable to differences in access to early diagnosis and optimal treatment. Cancer 2017;123:4977-81. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  7. Availability of Care Concordant With Patient-centered Medical Home Principles Among Those With Chronic Conditions: Measuring Care Outcomes.

    PubMed

    Pourat, Nadereh; Charles, Shana A; Snyder, Sophie

    2016-03-01

    Care delivery redesign in the form of patient-centered medical home (PCMH) is considered as a potential solution to improve patient outcomes and reduce costs, particularly for patients with chronic conditions. But studies of prevalence or impact at the population level are rare. We aimed to assess whether desired outcomes indicating better care delivery and patient-centeredness were associated with receipt of care according to 3 important PCMH principles. We analyzed data from a representative population survey in California in 2009, focusing on a population with chronic condition who had a usual source of care. We used bivariate, logistic, and negative-binomial regressions. The indicators of PCMH concordant care included continuity of care (personal doctor), care coordination, and care management (individual treatment plan). Outcomes included flu shots, count of outpatient visits, any emergency department visit, timely provider communication, and confidence in self-care. We found that patients whose care was concordant with all 3 PCMH principles were more likely to receive flu shots, more outpatient care, and timely response from providers. Concordance with 2 principles led to some desired outcomes. Concordance with only 1 principle was not associated with desired outcomes. Patients who received care that met 3 key aspects of PCMH: coordination, continuity, and management, had better quality of care and more efficient use of the health care system.

  8. Inter and intra-observer concordance for the diagnosis of portal hypertension gastropathy.

    PubMed

    Casas, Meritxell; Vergara, Mercedes; Brullet, Enric; Junquera, Félix; Martínez-Bauer, Eva; Miquel, Mireia; Sánchez-Delgado, Jordi; Dalmau, Blai; Campo, Rafael; Calvet, Xavier

    2018-03-01

    At present there is no fully accepted endoscopic classification for the assessment of the severity of portal hypertensive gastropathy (PHG). Few studies have evaluated inter and intra-observer concordance or the degree of concordance between different endoscopic classifications. To evaluate inter and intra-observer agreement for the presence of portal hypertensive gastropathy and enteropathy using different endoscopic classifications. Patients with liver cirrhosis were included into the study. Enteroscopy was performed under sedation. The location of lesions and their severity was recorded. Images were videotaped and subsequently evaluated independently by three different endoscopists, one of whom was the initial endoscopist. The agreement between observations was assessed using the kappa index. Seventy-four patients (mean age 63.2 years, 53 males and 21 females) were included. The agreement between the three endoscopists regarding the presence or absence of PHG using the Tanoue and McCormack classifications was very low (kappa scores = 0.16 and 0.27, respectively). The current classifications of portal hypertensive gastropathy have a very low degree of intra and inter-observer agreement for the diagnosis and assessment of gastropathy severity.

  9. Developing a burn injury severity score (BISS): adding age and total body surface area burned to the injury severity score (ISS) improves mortality concordance.

    PubMed

    Cassidy, J Tristan; Phillips, Michael; Fatovich, Daniel; Duke, Janine; Edgar, Dale; Wood, Fiona

    2014-08-01

    There is limited research validating the injury severity score (ISS) in burns. We examined the concordance of ISS with burn mortality. We hypothesized that combining age and total body surface area (TBSA) burned to the ISS gives a more accurate mortality risk estimate. Data from the Royal Perth Hospital Trauma Registry and the Royal Perth Hospital Burns Minimum Data Set were linked. Area under the receiver operating characteristic curve (AUC) measured concordance of ISS with mortality. Using logistic regression models with death as the dependent variable we developed a burn-specific injury severity score (BISS). There were 1344 burns with 24 (1.8%) deaths, median TBSA 5% (IQR 2-10), and median age 36 years (IQR 23-50). The results show ISS is a good predictor of death for burns when ISS≤15 (OR 1.29, p=0.02), but not for ISS>15 (ISS 16-24: OR 1.09, p=0.81; ISS 25-49: OR 0.81, p=0.19). Comparing the AUCs adjusted for age, gender and cause, ISS of 84% (95% CI 82-85%) and BISS of 95% (95% CI 92-98%), demonstrated superior performance of BISS as a mortality predictor for burns. ISS is a poor predictor of death in severe burns. The BISS combines ISS with age and TBSA and performs significantly better than the ISS. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

  10. Concordance of vitamin D peripheral levels in infertile couples' partners.

    PubMed

    Paffoni, Alessio; Ferrari, Stefania; Mangiarini, Alice; Noli, Stefania; Bulfoni, Alessandro; Vigano, Paola; Parazzini, Fabio; Somigliana, Edgardo

    2017-08-01

    A large number of evidence supports the role of vitamin D insufficiency in both women and men infertility. However, no studies have evaluated the rate of concordance of vitamin D status between the partners. This finding might open new scenarios in the interpretation of the available data linking vitamin D insufficiency and infertility. In the present cross-sectional study, 103 consecutive infertile couples were recruited between April and May 2014. Both partners concomitantly provided a serum sample for the assessment of 25-hydroxy-vitamin D [25-(OH)-D]. Vitamin D insufficiency was defined as serum 25-(OH)-D <20 ng/ml. One hundred-fifty subjects (73 women and 77 males) were 25-(OH)-D insufficient, corresponding to a rate of 73%. Overall, concordance was observed in 73 couples (71%), thus higher than the expected 61% (0.732 + 0.272) based on chance (p = 0.007). The Pearson coefficient of correlation R2 between the partners of the couples was 0.52 (p < 0.001). No statistically significant differences emerged when evaluating the rate of 25-(OH)-D insufficiency according to the causes of infertility. Serum 25-(OH)-D correlates within the partners of infertile couples. Further evidence is warranted to determine the clinical relevance and possible clinical applications of this finding.

  11. Using radiance predicted by the P3 approximation in a spherical geometry to predict tissue optical properties

    NASA Astrophysics Data System (ADS)

    Dickey, Dwayne J.; Moore, Ronald B.; Tulip, John

    2001-01-01

    For photodynamic therapy of solid tumors, such as prostatic carcinoma, to be achieved, an accurate model to predict tissue parameters and light dose must be found. Presently, most analytical light dosimetry models are fluence based and are not clinically viable for tissue characterization. Other methods of predicting optical properties, such as Monet Carlo, are accurate but far too time consuming for clinical application. However, radiance predicted by the P3-Approximation, an anaylitical solution to the transport equation, may be a viable and accurate alternative. The P3-Approximation accurately predicts optical parameters in intralipid/methylene blue based phantoms in a spherical geometry. The optical parameters furnished by the radiance, when introduced into fluence predicted by both P3- Approximation and Grosjean Theory, correlate well with experimental data. The P3-Approximation also predicts the optical properties of prostate tissue, agreeing with documented optical parameters. The P3-Approximation could be the clinical tool necessary to facilitate PDT of solid tumors because of the limited number of invasive measurements required and the speed in which accurate calculations can be performed.

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

    NASA Astrophysics Data System (ADS)

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

    2018-04-01

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

  13. A structural MRI study in monozygotic twins concordant or discordant for attention/hyperactivity problems: Evidence for genetic and environmental heterogeneity in the developing brain

    PubMed Central

    van ’t Ent, D.; Lehn, H.; Derks, E.M.; Hudziak, J.J.; Van Strien, N.M.; Veltman, D.J.; De Geus, E.J.C.; Todd, R.D.; Boomsma, D.I.

    2007-01-01

    Several structural brain abnormalities have been reported in patients with Attention Deficit Hyperactivity Disorder (ADHD). However, the aetiology of these brain changes is still unclear. To investigate genetic and environmental influences on ADHD related neurobiological changes we performed Voxel Based Morphometry on MRI scans from monozygotic (MZ) twins selected from a large longitudinal population database to be highly concordant or highly discordant for ratings on the Child Behavior Checklist Attention Problem scale (CBCL-AP). Children scoring low on the CBCL-AP are at low risk for ADHD, whereas children scoring high on this scale are at high risk for ADHD. Brain differences between concordant high risk twin pairs and concordant low risk twin pairs likely reflect the genetic risk for ADHD; brain differences between the low risk and high risk twins from discordant MZ twin pairs reflect the environmental risk for ADHD. A major difference between comparisons of high and low risk twins from concordant pairs and high/low twins from discordant pairs was found for the prefrontal lobes. The concordant high risk pairs showed volume loss in orbitofrontal subdivisions. High risk members from the discordant twin pairs exhibited volume reduction in the right inferior dorsolateral prefontal cortex. In addition, the posterior corpus callosum was compromised in concordant high risk pairs, only. Our findings indicate that inattention and hyperactivity symptoms are associated with anatomical abnormalities of a distributed action-attentional network. Different brain areas of this network appear to be affected in inattention/hyperactivity caused by genetic (i.e., high concordant MZ pairs) versus environmental (i.e., high-low discordant MZ pairs) risk factors. These results provide clues that further our understanding of brain alterations in ADHD. PMID:17346990

  14. Combining first-principles and data modeling for the accurate prediction of the refractive index of organic polymers

    NASA Astrophysics Data System (ADS)

    Afzal, Mohammad Atif Faiz; Cheng, Chong; Hachmann, Johannes

    2018-06-01

    Organic materials with a high index of refraction (RI) are attracting considerable interest due to their potential application in optic and optoelectronic devices. However, most of these applications require an RI value of 1.7 or larger, while typical carbon-based polymers only exhibit values in the range of 1.3-1.5. This paper introduces an efficient computational protocol for the accurate prediction of RI values in polymers to facilitate in silico studies that can guide the discovery and design of next-generation high-RI materials. Our protocol is based on the Lorentz-Lorenz equation and is parametrized by the polarizability and number density values of a given candidate compound. In the proposed scheme, we compute the former using first-principles electronic structure theory and the latter using an approximation based on van der Waals volumes. The critical parameter in the number density approximation is the packing fraction of the bulk polymer, for which we have devised a machine learning model. We demonstrate the performance of the proposed RI protocol by testing its predictions against the experimentally known RI values of 112 optical polymers. Our approach to combine first-principles and data modeling emerges as both a successful and a highly economical path to determining the RI values for a wide range of organic polymers.

  15. Concordance between administrative health data and medical records for diabetes status in coronary heart disease patients: a retrospective linked data study

    PubMed Central

    2013-01-01

    Background Administrative data are a valuable source of estimates of diabetes prevalence for groups such as coronary heart disease (CHD) patients. The primary aim of this study was to measure concordance between medical records and linked administrative health data for recording diabetes in CHD patients, and to assess temporal differences in concordance. Secondary aims were to determine the optimal lookback period for identifying diabetes in this patient group, whether concordance differed for Indigenous people, and to identify predictors of false positives and negatives in administrative data. Methods A population representative sample of 3943 CHD patients hospitalized in Western Australia in 1998 and 2002–04 were selected, and designated according to the International Classification of Diseases (ICD) version in use at the time (ICD-9 and ICD-10 respectively). Crude prevalence and concordance were compared for the two samples. Concordance measures were estimated from administrative data comparing diabetes status recorded on the selected CHD admission (‘index admission’) and on any hospitalization in the previous 1, 2, 5, 10 or 15 years, against hospital medical records. Potential modifiers of agreement were determined using chi-square tests and multivariable logistic regression models. Results Identification of diabetes on the index CHD admission was underestimated more in the ICD-10 than ICD-9 sample (sensitivity 81.5% versus 91.1%, underestimation 15.1% versus 4.4% respectively). Sensitivity increased to 89.6% in the ICD-10 period using at least 10 years of hospitalization history. Sensitivity was higher and specificity lower in Indigenous patients, and followed a similar pattern of improving concordance with increasing lookback period. Characteristics associated with false negatives for diabetes on the index CHD hospital admission were elective admission, in-hospital death, principal diagnosis, and in the ICD-10 period only, fewer recorded comorbidities

  16. Concordance between administrative health data and medical records for diabetes status in coronary heart disease patients: a retrospective linked data study.

    PubMed

    Nedkoff, Lee; Knuiman, Matthew; Hung, Joseph; Sanfilippo, Frank M; Katzenellenbogen, Judith M; Briffa, Tom G

    2013-10-01

    Administrative data are a valuable source of estimates of diabetes prevalence for groups such as coronary heart disease (CHD) patients. The primary aim of this study was to measure concordance between medical records and linked administrative health data for recording diabetes in CHD patients, and to assess temporal differences in concordance. Secondary aims were to determine the optimal lookback period for identifying diabetes in this patient group, whether concordance differed for Indigenous people, and to identify predictors of false positives and negatives in administrative data. A population representative sample of 3943 CHD patients hospitalized in Western Australia in 1998 and 2002-04 were selected, and designated according to the International Classification of Diseases (ICD) version in use at the time (ICD-9 and ICD-10 respectively). Crude prevalence and concordance were compared for the two samples. Concordance measures were estimated from administrative data comparing diabetes status recorded on the selected CHD admission ('index admission') and on any hospitalization in the previous 1, 2, 5, 10 or 15 years, against hospital medical records. Potential modifiers of agreement were determined using chi-square tests and multivariable logistic regression models. Identification of diabetes on the index CHD admission was underestimated more in the ICD-10 than ICD-9 sample (sensitivity 81.5% versus 91.1%, underestimation 15.1% versus 4.4% respectively). Sensitivity increased to 89.6% in the ICD-10 period using at least 10 years of hospitalization history. Sensitivity was higher and specificity lower in Indigenous patients, and followed a similar pattern of improving concordance with increasing lookback period. Characteristics associated with false negatives for diabetes on the index CHD hospital admission were elective admission, in-hospital death, principal diagnosis, and in the ICD-10 period only, fewer recorded comorbidities. The accuracy of identifying

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

    PubMed

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

    2014-01-01

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

  18. Environmental assessment proposed license renewal of Nuclear Metals, Inc. Concord, Massachusetts

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

    Miller, R.L.; Easterly, C.E.; Lombardi, C.E.

    1997-02-01

    The US Nuclear Regulatory Commission (NRC) has prepared this Environmental Assessment (EA) to evaluate environmental issues associated with the renewal of licenses issued by NRC for facilities operated by Nuclear Metals, Inc. (NMI) in Concord, Massachusetts. By renewing the licenses, NRC proposes to allow the continuation of ongoing operations involving radioactive materials at NMI`s facilities. This EA focuses on the potential impacts related to air emissions at NMI during normal (incident-free) operations and accidental releases. Findings indicate that there are only two areas of potential concern. First, modeling results for sulfur dioxide (SO{sub 2}) emissions from the boilers during normalmore » operations indicate that the potential exists for exceeding the short-term National Ambient Air Quality Standards (NAAQS). NMI is prepared to undertake mitigative action to prevent potential exceedances of the short-term SO{sub 2} NAAQS, and the Massachusetts Department of Environmental Protection is prepared to resolve the issue via a permit/approval change or through a Consent Order. Second, in the unlikely event of a severe fire, predicted sulfuric acid (H{sub 2}SO{sub 4}) concentrations based on conservative (upper bound) modeling exceed the Emergency Response Planning Guideline (ERPG) levels. NMI has committed to NRC to give a briefing for local emergency response officials regarding the potential for an accidental H{sub 2}SO{sub 4} release.« less

  19. Young Learners and Lexical Awareness: Children's Engagement with Wordlists and Concordances

    ERIC Educational Resources Information Center

    MacGregor, Alex

    2014-01-01

    Sinclair (1991) found that lexical analysis can be overcomplicated, yet Johns (1994) called for investigation into whether corpus analysis can motivate beginners and near-beginners. The findings of this research suggest that young EFL learners can enjoy using corpus analysis tools (wordlists and concordances) to identify, classify, and generalize…

  20. Validation of the Web-Based IBTR! 2.0 Nomogram to Predict for Ipsilateral Breast Tumor Recurrence After Breast-Conserving Therapy

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

    Kindts, Isabelle, E-mail: Isabelle.kindts@uzleuven.be; Department of Radiation Oncology, University Hospitals Leuven, Leuven; Laenen, Annouschka

    Purpose: To evaluate the IBTR! 2.0 nomogram, which predicts 10-year ipsilateral breast tumor recurrence (IBTR) after breast-conserving therapy with and without radiation therapy for breast cancer, by using a large, external, and independent cancer center database. Methods and Materials: We retrospectively identified 1898 breast cancer cases, treated with breast-conserving therapy and radiation therapy at the University Hospital Leuven from 2000 to 2007, with requisite data for the nomogram variables. Clinicopathologic factors were assessed. Two definitions of IBTR were considered where simultaneous regional or distant recurrence were either censored (conform IBTR! 2.0) or included as event. Validity of the prediction algorithm wasmore » tested in terms of discrimination and calibration. Discrimination was assessed by the concordance probability estimate and Harrell's concordance index. The mean predicted and observed 10-year estimates were compared for the entire cohort and for 4 risk groups predefined by nomogram-predicted IBTR risks, and a calibration plot was drawn. Results: Median follow-up was 10.9 years. The 10-year IBTR rates were 1.3% and 2.1%, according to the 2 definitions of IBTR. The validation cohort differed from the development cohort with respect to the administration of hormonal therapy, surgical section margins, lymphovascular invasion, and tumor size. In univariable analysis, younger age (P=.002) and a positive nodal status (P=.048) were significantly associated with IBTR, with a trend for the omission of hormonal therapy (P=.061). The concordance probability estimate and concordance index varied between 0.57 and 0.67 for the 2 definitions of IBTR. In all 4 risk groups the model overestimated the IBTR risk. In particular, between the lowest-risk groups a limited differentiation was suggested by the calibration plot. Conclusions: The IBTR! 2.0 predictive model for IBTR in breast cancer patients shows substandard discriminative ability, with an

  1. Validation of the Web-Based IBTR! 2.0 Nomogram to Predict for Ipsilateral Breast Tumor Recurrence After Breast-Conserving Therapy.

    PubMed

    Kindts, Isabelle; Laenen, Annouschka; Peeters, Stephanie; Janssen, Hilde; Depuydt, Tom; Nevelsteen, Ines; Van Limbergen, Erik; Weltens, Caroline

    2016-08-01

    To evaluate the IBTR! 2.0 nomogram, which predicts 10-year ipsilateral breast tumor recurrence (IBTR) after breast-conserving therapy with and without radiation therapy for breast cancer, by using a large, external, and independent cancer center database. We retrospectively identified 1898 breast cancer cases, treated with breast-conserving therapy and radiation therapy at the University Hospital Leuven from 2000 to 2007, with requisite data for the nomogram variables. Clinicopathologic factors were assessed. Two definitions of IBTR were considered where simultaneous regional or distant recurrence were either censored (conform IBTR! 2.0) or included as event. Validity of the prediction algorithm was tested in terms of discrimination and calibration. Discrimination was assessed by the concordance probability estimate and Harrell's concordance index. The mean predicted and observed 10-year estimates were compared for the entire cohort and for 4 risk groups predefined by nomogram-predicted IBTR risks, and a calibration plot was drawn. Median follow-up was 10.9 years. The 10-year IBTR rates were 1.3% and 2.1%, according to the 2 definitions of IBTR. The validation cohort differed from the development cohort with respect to the administration of hormonal therapy, surgical section margins, lymphovascular invasion, and tumor size. In univariable analysis, younger age (P=.002) and a positive nodal status (P=.048) were significantly associated with IBTR, with a trend for the omission of hormonal therapy (P=.061). The concordance probability estimate and concordance index varied between 0.57 and 0.67 for the 2 definitions of IBTR. In all 4 risk groups the model overestimated the IBTR risk. In particular, between the lowest-risk groups a limited differentiation was suggested by the calibration plot. The IBTR! 2.0 predictive model for IBTR in breast cancer patients shows substandard discriminative ability, with an overestimation of the risk in all subgroups. Copyright

  2. A gp41-based heteroduplex mobility assay provides rapid and accurate assessment of intrasubtype epidemiological linkage in HIV type 1 heterosexual transmission Pairs.

    PubMed

    Manigart, Olivier; Boeras, Debrah I; Karita, Etienne; Hawkins, Paulina A; Vwalika, Cheswa; Makombe, Nathan; Mulenga, Joseph; Derdeyn, Cynthia A; Allen, Susan; Hunter, Eric

    2012-12-01

    A critical step in HIV-1 transmission studies is the rapid and accurate identification of epidemiologically linked transmission pairs. To date, this has been accomplished by comparison of polymerase chain reaction (PCR)-amplified nucleotide sequences from potential transmission pairs, which can be cost-prohibitive for use in resource-limited settings. Here we describe a rapid, cost-effective approach to determine transmission linkage based on the heteroduplex mobility assay (HMA), and validate this approach by comparison to nucleotide sequencing. A total of 102 HIV-1-infected Zambian and Rwandan couples, with known linkage, were analyzed by gp41-HMA. A 400-base pair fragment within the envelope gp41 region of the HIV proviral genome was PCR amplified and HMA was applied to both partners' amplicons separately (autologous) and as a mixture (heterologous). If the diversity between gp41 sequences was low (<5%), a homoduplex was observed upon gel electrophoresis and the transmission was characterized as having occurred between partners (linked). If a new heteroduplex formed, within the heterologous migration, the transmission was determined to be unlinked. Initial blind validation of gp-41 HMA demonstrated 90% concordance between HMA and sequencing with 100% concordance in the case of linked transmissions. Following validation, 25 newly infected partners in Kigali and 12 in Lusaka were evaluated prospectively using both HMA and nucleotide sequences. Concordant results were obtained in all but one case (97.3%). The gp41-HMA technique is a reliable and feasible tool to detect linked transmissions in the field. All identified unlinked results should be confirmed by sequence analyses.

  3. New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

    2013-10-07

    An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

  4. Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium.

    PubMed

    Ryan, Natalia; Chorley, Brian; Tice, Raymond R; Judson, Richard; Corton, J Christopher

    2016-05-01

    Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput formats. Computational methods are described here to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through chromatin immunoprecipitation coupled with DNA sequencing analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression datasets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including "very weak" agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals, the balanced accuracies were 95% and 98% for activation or suppression, respectively. These results demonstrate that the ERα gene expression biomarker can accurately identify ERα modulators in large collections of microarray data derived from MCF-7 cells. Published by Oxford University Press on behalf of the Society of Toxicology 2016. This work is written by US Government employees and is in the public domain in the US.

  5. Gender Differences in Depressive Symptoms Among HIV-Positive Concordant and Discordant Heterosexual Couples in China.

    PubMed

    Li, Li; Liang, Li-Jung; Lin, Chunqing; Ji, Guoping; Xiao, Yongkang

    2017-03-01

    HIV seropositive individuals and their heterosexual partners/spouses, either seropositive or seronegative, are facing several mental health challenges. The objective of this study was to examine gender differences in depressive symptoms among HIV-positive concordant and HIV-discordant couples. We identified heterosexual couples from participants of a randomized controlled trial conducted in Anhui province, China. A total of 265 couples, comprising 129 HIV+ male/HIV- female couples, 98 HIV- male/HIV+ female couples, and 38 HIV-positive concordant couples, were included in the analyses. We collected data using the computer-assisted personal interview method. We used a linear mixed-effects regression model to assess whether gender differences in depressive symptoms varied across couple types. HIV-positive women reported a significantly higher level of depressive symptoms than their partners/spouses. HIV-positive women with HIV-positive partners had higher depressive symptoms than those with HIV-negative partners, whereas HIV-positive men reported similar levels of depressive symptoms regardless of their partners' serostatus. Among the concordant couples, those with the highest annual family income showed the greatest gender differences in depressive symptoms. We suggest that family interventions should be gender- and couple-type specific and that mental health counseling is warranted not only for HIV-positive women but also for HIV-negative women in an HIV-affected relationship.

  6. Is there concordance in attitudes and beliefs between parents and scientists about autism spectrum disorder?

    PubMed

    Fischbach, Ruth L; Harris, Mark J; Ballan, Michelle S; Fischbach, Gerald D; Link, Bruce G

    2016-04-01

    There is no reported investigation comparing concordance in attitudes and beliefs about autism spectrum disorder between parents of children with autism spectrum disorder and scientists who research autism spectrum disorder. To investigate the level of concordance between these groups on causes of autism, priorities of research, perceived stigma, and disclosure of genetic test results, telephone interviews were conducted. Parents (n = 502) were recruited from the Simons Simplex Collection, and research scientists (n = 60) were recruited from investigators funded by the Simons Foundation. Response rates were notable (parents 91%, scientists 80%). Parents and scientists differed significantly regarding beliefs of the likely major cause of autism (p = 0.007) and priorities for further research (p < 0.001). Scientists believed in genetic causes while many parents believed in vaccines as the cause of autism. Parents (37%) were more likely to hesitate vaccinating their child (p < 0.001). In contrast, there was strong concordance regarding extent of perceived stigma (95% vs 92%) and preferences for disclosure of genetic test results, including incidental findings. While scientists believed communication important, paradoxically fewer than half reported it important for scientists to communicate directly with parents. Better communication between parents and scientists should improve mutual understanding and ultimately the health and well-being of children with autism spectrum disorder and their families. © The Author(s) 2015.

  7. Gender Differences in Depressive Symptoms Among HIV-Positive Concordant and Discordant Heterosexual Couples in China

    PubMed Central

    Li, Li; Liang, Li-Jung; Lin, Chunqing; Ji, Guoping; Xiao, Yongkang

    2016-01-01

    HIV seropositive individuals and their heterosexual partners/spouses, either seropositive or seronegative, are facing several mental health challenges. The objective of this study was to examine gender differences in depressive symptoms among HIV-positive concordant and HIV-discordant couples. We identified heterosexual couples from participants of a randomized controlled trial conducted in Anhui province, China. A total of 265 couples, comprising 129 HIV+ male/HIV− female couples, 98 HIV− male/HIV+ female couples, and 38 HIV-positive concordant couples, were included in the analyses. We collected data using the computer-assisted personal interview method. We used a linear mixed-effects regression model to assess whether gender differences in depressive symptoms varied across couple types. HIV-positive women reported a significantly higher level of depressive symptoms than their partners/spouses. HIV-positive women with HIV-positive partners had higher depressive symptoms than those with HIV-negative partners, whereas HIV-positive men reported similar levels of depressive symptoms regardless of their partners’ serostatus. Among the concordant couples, those with the highest annual family income showed the greatest gender differences in depressive symptoms. We suggest that family interventions should be gender- and couple-type specific and that mental health counseling is warranted not only for HIV-positive women but also for HIV-negative women in an HIV-affected relationship. PMID:28490832

  8. Concord Grape Juice Polyphenols and Cardiovascular Risk Factors: Dose-Response Relationships

    PubMed Central

    Blumberg, Jeffrey B.; Vita, Joseph A.; Chen, C. -Y. Oliver

    2015-01-01

    Pure fruit juices provide nutritional value with evidence suggesting some of their benefits on biomarkers of cardiovascular disease risk may be derived from their constituent polyphenols, particularly flavonoids. However, few data from clinical trials are available on the dose-response relationship of fruit juice flavonoids to these outcomes. Utilizing the results of clinical trials testing single doses, we have analyzed data from studies of 100% Concord grape juice by placing its flavonoid content in the context of results from randomized clinical trials of other polyphenol-rich foods and beverages describing the same outcomes but covering a broader range of intake. We selected established biomarkers determined by similar methods for measuring flow-mediated vasodilation (FMD), blood pressure, platelet aggregation, and the resistance of low density lipoprotein cholesterol (LDL) to oxidation. Despite differences among the clinical trials in the treatment, subjects, and duration, correlations were observed between the dose and FMD. Inverse dose-response relationships, albeit with lower correlation coefficients, were also noted for the other outcomes. These results suggest a clear relationship between consumption of even modest serving sizes of Concord grape juice, flavonoid intake, and effects on risk factors for cardiovascular disease. This approach to dose-response relationships may prove useful for testing other individual foods and beverages. PMID:26633488

  9. Identical twins concordant for pulmonary sequestration communicating with the esophagus and discordant for the VACTERL association.

    PubMed

    Becker, Julie; Hernandez, Ambrosio; Dipietro, Michael; Coran, Arnold G

    2005-07-01

    Communicating bronchopulmonary foregut malformations (CBPFMs) are unusual congenital structures composed of a segment of lung tissue connected to the foregut. We present what we believe is the first reported case of identical twins concordant for CBPFM who are discordant for the VACTERL association. Their nonfunctional lung tissue was successfully removed and the fistulae were corrected, and they are expected to live normal life spans. We review the literature concerning these malformations and the proposed theories of their etiology. This case report of concordance in identical twins suggests that a possible genetic component to CBPFMs cannot be ruled out. The discordance for the VACTERL association implies that the etiology is most likely multifactorial.

  10. Concordance among Physical Educators', Teachers', and Parents' Perceptions of Attention Problems in Children

    ERIC Educational Resources Information Center

    Efstratopoulou, Maria; Simons, Johan; Janssen, Rianne

    2013-01-01

    Objective: The study examined the concordance among rating sources on attention problems of elementary school-aged children. Method: A randomly selected sample ("N" = 841) of children was rated by the physical educators, the teachers, and the parents, using the Attention Scales of the Motor Behavior Checklist (MBC), the Teacher Report…

  11. Parent and Teacher Concordance of Child Outcomes for Youth with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Dickson, Kelsey S.; Suhrheinrich, Jessica; Rieth, Sarah R.; Stahmer, Aubyn C.

    2017-01-01

    Cross-informant ratings of are considered gold standard for child behavioral assessment. To date, little work has examined informant ratings of adaptive functioning for youth with autism spectrum disorder (ASD). In a large, diverse sample of youth with ASD, this study evaluated parent-teacher concordance of ratings of adaptive functioning and…

  12. Parent and Teacher Concordance of Child Outcomes for Youth with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Dickson, Kelsey S.; Suhrheinrich, Jessica; Rieth, Sarah R.; Stahmer, Aubyn C.

    2018-01-01

    Cross-informant ratings of are considered gold standard for child behavioral assessment. To date, little work has examined informant ratings of adaptive functioning for youth with autism spectrum disorder (ASD). In a large, diverse sample of youth with ASD, this study evaluated parent-teacher concordance of ratings of adaptive functioning and…

  13. Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA

    PubMed Central

    Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

    2017-01-01

    Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. PMID:28600436

  14. Shedding light on the variability of optical skin properties: finding a path towards more accurate prediction of light propagation in human cutaneous compartments

    PubMed Central

    Mignon, C.; Tobin, D. J.; Zeitouny, M.; Uzunbajakava, N. E.

    2018-01-01

    Finding a path towards a more accurate prediction of light propagation in human skin remains an aspiration of biomedical scientists working on cutaneous applications both for diagnostic and therapeutic reasons. The objective of this study was to investigate variability of the optical properties of human skin compartments reported in literature, to explore the underlying rational of this variability and to propose a dataset of values, to better represent an in vivo case and recommend a solution towards a more accurate prediction of light propagation through cutaneous compartments. To achieve this, we undertook a novel, logical yet simple approach. We first reviewed scientific articles published between 1981 and 2013 that reported on skin optical properties, to reveal the spread in the reported quantitative values. We found variations of up to 100-fold. Then we extracted the most trust-worthy datasets guided by a rule that the spectral properties should reflect the specific biochemical composition of each of the skin layers. This resulted in the narrowing of the spread in the calculated photon densities to 6-fold. We conclude with a recommendation to use the identified most robust datasets when estimating light propagation in human skin using Monte Carlo simulations. Alternatively, otherwise follow our proposed strategy to screen any new datasets to determine their biological relevance. PMID:29552418

  15. Comparison of low-frequency noise levels of the Concorde supersonic transport with other commercial service airplanes

    NASA Technical Reports Server (NTRS)

    Powell, C. A.; Mccurdy, D. A.

    1978-01-01

    Fifty-two airplane noise recordings, made at several locations around Dulles International Airport, were analyzed to compare the low-frequency noise levels of the Concorde supersonic transport with those of other commercial jet airplanes. Comparisons of the relative low-frequency noise levels which were produced at close and distant locations for departures and arrivals were made for three noise measures: the sound pressure level in the 1/3 octave band centered at 20 Hz, the total sound pressure level in the 1/3 octave bands with center frequencies less than or equal to 125 Hz, and the total sound pressure level in the 1/3 octave bands with center frequencies less than or equal to 500 Hz. Although the absolute noise levels for Concorde were found, in general, to be higher than those for the other airplane types, the level of low-frequency noise of the Concorde relative to the perceived noise level (PNL), effective perceived noise level (EPNL), and overall sound pressure level (OASPL) was within the range established by the other airplane types, except for the arrival operations of four-engine, narrow-body airplanes. The measure OASPL was found to be a significantly better predictor of low-frequency noise level than PNL or EPNL.

  16. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).

    PubMed

    Stacey, R Greg; Skinnider, Michael A; Scott, Nichollas E; Foster, Leonard J

    2017-10-23

    An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. We recently developed a complementary technique based on the use of protein correlation profiling (PCP) and stable isotope labeling in amino acids in cell culture (SILAC) to assess chromatographic co-elution as evidence of interacting proteins. Importantly, PCP-SILAC is also capable of measuring protein interactions simultaneously under multiple biological conditions, allowing the detection of treatment-specific changes to an interactome. Given the uniqueness and high dimensionality of co-elution data, new tools are needed to compare protein elution profiles, control false discovery rates, and construct an accurate interactome. Here we describe a freely available bioinformatics pipeline, PrInCE, for the analysis of co-elution data. PrInCE is a modular, open-source library that is computationally inexpensive, able to use label and label-free data, and capable of detecting tens of thousands of protein-protein interactions. Using a machine learning approach, PrInCE offers greatly reduced run time, more predicted interactions at the same stringency, prediction of protein complexes, and greater ease of use over previous bioinformatics tools for co-elution data. PrInCE is implemented in Matlab (version R2017a). Source code and standalone executable programs for Windows and Mac OSX are available at https://github.com/fosterlab/PrInCE , where usage instructions can be found. An example dataset and output are also provided for testing purposes. PrInCE is the first fast and easy

  17. CONCORDANCE OF TAXONOMIC RICHNESS PATTERNS ACROSS MULTIPLE ASSEMBLAGES IN LAKES OF THE NORTHEASTERN UNITED STATES

    EPA Science Inventory

    We investigated the concordance of taxonomic richness patterns and their environmental correlates for assemblages of benthic macroinvertebrates, riparian birds, sedimentary diatoms, fish, planktonic crustaceans, and planktonic rotifers in 186 northeastern U.S. lakes. Taxon counts...

  18. Noise emissions and building structural vibration levels from the Supersonic Concorde and subsconic turbojet aircraft

    DOT National Transportation Integrated Search

    1975-03-01

    Noise emissions and building structural vibration levels were measured during landing and take off operations of the Anglo/French supersonic aircraft (Concorde) and from some conventional subsonic turbojet aircraft. Measurements were made at both the...

  19. [Concordance of glomerular filtration rate with creatinine clearance in 24-hour urine and Schwartz and Schwartz updated].

    PubMed

    Salazar-Gutiérrez, María Luisa; Ochoa-Ponce, Cristina; Lona-Reyes, Juan Carlos; Gutiérrez-Íñiguez, Sara Ivonne

    Reference methods for the quantification of the glomerular filtration rate (GFR) are difficult to use in clinical practice; formulas for evaluating GFR based on serum creatinine (SCr) and/or creatinine clearance are used. The aim of this study was to quantify the correlation and concordance of GFR with creatinine clearance in 24-hour urine (GFR24) and Schwartz and Schwartz updated formulas. Cross-sectional study involving healthy pediatric patients and with chronic kidney disease (CKD) from 5 to 16.9 years. Linear correlation between GFR 24 and two formulas was evaluated with the Pearson correlation coefficient (r) and intraclass correlation coefficient (ICC). We studied 134 patients, of which 59.7% were male. Mean age was 10.8 years. The average GFR24 was 140.34ml/min/1.73m 2 ; 34.3% (n=46) had GFR <90ml/min/1.73m 2 . Moderate linear correlation between GFR24 and Schwartz (r= 0.63) and Schwartz updated (r= 0.65) formulas was observed. There was good concordance between the GFR24 and Schwartz (ICC= 0.77) and updated Schwartz (ICC= 0.77) formulas. Schwartz classical formula in patients with GFR24 ≥ 90ml/min/1.73m 2 estimated higher values, while Schwartz updated underestimated values. There is moderate correlation and good concordance between the GFR24 and Schwartz and Schwartz updated formulas. The concordance was better in patients with obesity and lower in women, patients with hyperfiltration and normal weight. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  20. 33 CFR 334.1110 - Suisun Bay at Naval Weapons Station, Concord; restricted area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Suisun Bay at Naval Weapons....1110 Suisun Bay at Naval Weapons Station, Concord; restricted area. (a) The area. Beginning at a point... his control from this area upon the request of the Commanding Officer of the Naval Weapons Station...