Reducing sojourn points from recurrence plots to improve transition detection: Application to fetal heart rate transitions.

PubMed

Zaylaa, Amira; Charara, Jamal; Girault, Jean-Marc

2015-08-01

The analysis of biomedical signals demonstrating complexity through recurrence plots is challenging. Quantification of recurrences is often biased by sojourn points that hide dynamic transitions. To overcome this problem, time series have previously been embedded at high dimensions. However, no one has quantified the elimination of sojourn points and rate of detection, nor the enhancement of transition detection has been investigated. This paper reports our on-going efforts to improve the detection of dynamic transitions from logistic maps and fetal hearts by reducing sojourn points. Three signal-based recurrence plots were developed, i.e. embedded with specific settings, derivative-based and m-time pattern. Determinism, cross-determinism and percentage of reduced sojourn points were computed to detect transitions. For logistic maps, an increase of 50% and 34.3% in sensitivity of detection over alternatives was achieved by m-time pattern and embedded recurrence plots with specific settings, respectively, and with a 100% specificity. For fetal heart rates, embedded recurrence plots with specific settings provided the best performance, followed by derivative-based recurrence plot, then unembedded recurrence plot using the determinism parameter. The relative errors between healthy and distressed fetuses were 153%, 95% and 91%. More than 50% of sojourn points were eliminated, allowing better detection of heart transitions triggered by gaseous exchange factors. This could be significant in improving the diagnosis of fetal state. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fault Detection and Severity Analysis of Servo Valves Using Recurrence Quantification Analysis

DTIC Science & Technology

2014-10-02

Fault Detection and Severity Analysis of Servo Valves Using Recurrence Quantification Analysis M. Samadani1, C. A. Kitio Kwuimy2, and C. Nataraj3...diagnostics of nonlinear systems. A detailed nonlinear math- ematical model of a servo electro-hydraulic system has been used to demonstrate the procedure...Two faults have been considered associated with the servo valve including the in- creased friction between spool and sleeve and the degradation of the

Recurrence quantification analysis of global stock markets

NASA Astrophysics Data System (ADS)

Bastos, João A.; Caiado, Jorge

2011-04-01

This study investigates the presence of deterministic dependencies in international stock markets using recurrence plots and recurrence quantification analysis (RQA). The results are based on a large set of free float-adjusted market capitalization stock indices, covering a period of 15 years. The statistical tests suggest that the dynamics of stock prices in emerging markets is characterized by higher values of RQA measures when compared to their developed counterparts. The behavior of stock markets during critical financial events, such as the burst of the technology bubble, the Asian currency crisis, and the recent subprime mortgage crisis, is analyzed by performing RQA in sliding windows. It is shown that during these events stock markets exhibit a distinctive behavior that is characterized by temporary decreases in the fraction of recurrence points contained in diagonal and vertical structures.

Quantification of C4d deposition and hepatitis C virus RNA in tissue in cases of graft rejection and hepatitis C recurrence after liver transplantation

PubMed Central

Song, Alice Tung Wan; de Mello, Evandro Sobroza; Alves, Venâncio Avancini Ferreira; Cavalheiro, Norma de Paula; Melo, Carlos Eduardo; Bonazzi, Patricia Rodrigues; Tengan, Fatima Mitiko; Freire, Maristela Pinheiro; Barone, Antonio Alci; D'Albuquerque, Luiz Augusto Carneiro; Abdala, Edson

2015-01-01

Histology is the gold standard for diagnosing acute rejection and hepatitis C recurrence after liver transplantation. However, differential diagnosis between the two can be difficult. We evaluated the role of C4d staining and quantification of hepatitis C virus (HCV) RNA levels in liver tissue. This was a retrospective study of 98 liver biopsy samples divided into four groups by histological diagnosis: acute rejection in patients undergoing liver transplant for hepatitis C (RejHCV+), HCV recurrence in patients undergoing liver transplant for hepatitis C (HCVTx+), acute rejection in patients undergoing liver transplant for reasons other than hepatitis C and chronic hepatitis C not transplanted (HCVTx-). All samples were submitted for immunohistochemical staining for C4d and HCV RNA quantification. Immunoexpression of C4d was observed in the portal vessels and was highest in the HCVTx- group. There was no difference in C4d expression between the RejHCV+ and HCVTx+ groups. However, tissue HCV RNA levels were higher in the HCVTx+ group samples than in the RejHCV+ group samples. Additionally, there was a significant correlation between tissue and serum levels of HCV RNA. The quantification of HCV RNA in liver tissue might prove to be an efficient diagnostic test for the recurrence of HCV infection. PMID:25742264

Attractor structure discriminates sleep states: recurrence plot analysis applied to infant breathing patterns.

PubMed

Terrill, Philip Ian; Wilson, Stephen James; Suresh, Sadasivam; Cooper, David M; Dakin, Carolyn

2010-05-01

Breathing patterns are characteristically different between infant active sleep (AS) and quiet sleep (QS), and statistical quantifications of interbreath interval (IBI) data have previously been used to discriminate between infant sleep states. It has also been identified that breathing patterns are governed by a nonlinear controller. This study aims to investigate whether nonlinear quantifications of infant IBI data are characteristically different between AS and QS, and whether they may be used to discriminate between these infant sleep states. Polysomnograms were obtained from 24 healthy infants at six months of age. Periods of AS and QS were identified, and IBI data extracted. Recurrence quantification analysis (RQA) was applied to each period, and recurrence calculated for a fixed radius in the range of 0-8 in steps of 0.02, and embedding dimensions of 4, 6, 8, and 16. When a threshold classifier was trained, the RQA variable recurrence was able to correctly classify 94.3% of periods in a test dataset. It was concluded that RQA of IBI data is able to accurately discriminate between infant sleep states. This is a promising step toward development of a minimal-channel automatic sleep state classification system.

Recurrence quantification analysis of heart rate variability and respiratory flow series in patients on weaning trials.

PubMed

Arcentales, Andrés; Giraldo, Beatriz F; Caminal, Pere; Benito, Salvador; Voss, Andreas

2011-01-01

Autonomic nervous system regulates the behavior of cardiac and respiratory systems. Its assessment during the ventilator weaning can provide information about physio-pathological imbalances. This work proposes a non linear analysis of the complexity of the heart rate variability (HRV) and breathing duration (T(Tot)) applying recurrence plot (RP) and their interaction joint recurrence plot (JRP). A total of 131 patients on weaning trials from mechanical ventilation were analyzed: 92 patients with successful weaning (group S) and 39 patients that failed to maintain spontaneous breathing (group F). The results show that parameters as determinism (DET), average diagonal line length (L), and entropy (ENTR), are statistically significant with RP for T(Tot) series, but not with HRV. When comparing the groups with JRP, all parameters have been relevant. In all cases, mean values of recurrence quantification analysis are higher in the group S than in the group F. The main differences between groups were found on the diagonal and vertical structures of the joint recurrence plot.

Recurrence analysis of ant activity patterns

PubMed Central

2017-01-01

In this study, we used recurrence quantification analysis (RQA) and recurrence plots (RPs) to compare the movement activity of individual workers of three ant species, as well as a gregarious beetle species. RQA and RPs quantify the number and duration of recurrences of a dynamical system, including a detailed quantification of signals that could be stochastic, deterministic, or both. First, we found substantial differences between the activity dynamics of beetles and ants, with the results suggesting that the beetles have quasi-periodic dynamics and the ants do not. Second, workers from different ant species varied with respect to their dynamics, presenting degrees of predictability as well as stochastic signals. Finally, differences were found among minor and major caste of the same (dimorphic) ant species. Our results underscore the potential of RQA and RPs in the analysis of complex behavioral patterns, as well as in general inferences on animal behavior and other biological phenomena. PMID:29016648

Application of recurrence quantification analysis to automatically estimate infant sleep states using a single channel of respiratory data.

PubMed

Terrill, Philip I; Wilson, Stephen J; Suresh, Sadasivam; Cooper, David M; Dakin, Carolyn

2012-08-01

Previous work has identified that non-linear variables calculated from respiratory data vary between sleep states, and that variables derived from the non-linear analytical tool recurrence quantification analysis (RQA) are accurate infant sleep state discriminators. This study aims to apply these discriminators to automatically classify 30 s epochs of infant sleep as REM, non-REM and wake. Polysomnograms were obtained from 25 healthy infants at 2 weeks, 3, 6 and 12 months of age, and manually sleep staged as wake, REM and non-REM. Inter-breath interval data were extracted from the respiratory inductive plethysmograph, and RQA applied to calculate radius, determinism and laminarity. Time-series statistic and spectral analysis variables were also calculated. A nested cross-validation method was used to identify the optimal feature subset, and to train and evaluate a linear discriminant analysis-based classifier. The RQA features radius and laminarity and were reliably selected. Mean agreement was 79.7, 84.9, 84.0 and 79.2 % at 2 weeks, 3, 6 and 12 months, and the classifier performed better than a comparison classifier not including RQA variables. The performance of this sleep-staging tool compares favourably with inter-human agreement rates, and improves upon previous systems using only respiratory data. Applications include diagnostic screening and population-based sleep research.

Detection of the fracture zone by the method of recurrence plot

NASA Astrophysics Data System (ADS)

Hilarov, V. L.

2017-12-01

Recurrence plots (RPs) and recurrence quantification analysis (RQA) characteristics for the normal component of the displacement vector upon excitation of a defect steel plate by a sound pulse are analyzed. Different cases of spatial distribution of defects (uniform and normal) are considered, and a difference in the RQA parameters in these cases is revealed.

Recurrence quantification analysis of electroencephalograph signals during standard tasks of Waterloo-Stanford group scale of hypnotic susceptibility.

PubMed

Yargholi, Elahe'; Nasrabadi, Ali Motie

2015-01-01

The purpose of this study was to apply RQA (recurrence quantification analysis) on hypnotic electroencephalograph (EEG) signals recorded after hypnotic induction while subjects were doing standard tasks of the Waterloo-Stanford Group Scale (WSGS) of hypnotic susceptibility. Then recurrence quantifiers were used to analyse the influence of hypnotic depth on EEGs. By the application of this method, the capability of tasks to distinguish subjects of different hypnotizability levels was determined. Besides, medium hypnotizable subjects showed the highest disposition to be inducted by hypnotizer. Similarities between brain governing dynamics during tasks of the same type were also observed. The present study demonstrated two remarkable innovations; investigating the EEGs of the hypnotized as doing mental tasks of Waterloo-Stanford Group Scale (WSGS) and applying RQA on hypnotic EEGs.

Multiscale synchrony behaviors of paired financial time series by 3D multi-continuum percolation

NASA Astrophysics Data System (ADS)

Wang, M.; Wang, J.; Wang, B. T.

2018-02-01

Multiscale synchrony behaviors and nonlinear dynamics of paired financial time series are investigated, in an attempt to study the cross correlation relationships between two stock markets. A random stock price model is developed by a new system called three-dimensional (3D) multi-continuum percolation system, which is utilized to imitate the formation mechanism of price dynamics and explain the nonlinear behaviors found in financial time series. We assume that the price fluctuations are caused by the spread of investment information. The cluster of 3D multi-continuum percolation represents the cluster of investors who share the same investment attitude. In this paper, we focus on the paired return series, the paired volatility series, and the paired intrinsic mode functions which are decomposed by empirical mode decomposition. A new cross recurrence quantification analysis is put forward, combining with multiscale cross-sample entropy, to investigate the multiscale synchrony of these paired series from the proposed model. The corresponding research is also carried out for two China stock markets as comparison.

Recurrence Quantifcation Analysis of Sentence-Level Speech Kinematics

ERIC Educational Resources Information Center

Jackson, Eric S.; Tiede, Mark; Riley, Michael A.; Whalen, D. H.

2016-01-01

Purpose: Current approaches to assessing sentence-level speech variability rely on measures that quantify variability across utterances and use normalization procedures that alter raw trajectory data. The current work tests the feasibility of a less restrictive nonlinear approach--recurrence quantification analysis (RQA)--via a procedural example…

Numerical characteristics of recurrence plots as applied to the evaluation of mechanical damage in materials

NASA Astrophysics Data System (ADS)

Hilarov, V. L.

2017-09-01

The response of a material with a random uniform distribution of pores to a sound impulse was studied. The behavior of the numerical characteristics of the recurrence plots (RP) of the normal displacement vector component depending on the degree of damage was investigated. It was shown that the recurrence quantification analysis (RQA) parameters could be very informative for sonic fault detection.

Assessing Spontaneous Combustion Instability with Recurrence Quantification Analysis

NASA Technical Reports Server (NTRS)

Eberhart, Chad J.; Casiano, Matthew J.

2016-01-01

Spontaneous instabilities can pose a significant challenge to verification of combustion stability, and characterizing its onset is an important avenue of improvement for stability assessments of liquid propellant rocket engines. Recurrence Quantification Analysis (RQA) is used here to explore nonlinear combustion dynamics that might give insight into instability. Multiple types of patterns representative of different dynamical states are identified within fluctuating chamber pressure data, and markers for impending instability are found. A class of metrics which describe these patterns is also calculated. RQA metrics are compared with and interpreted against another metric from nonlinear time series analysis, the Hurst exponent, to help better distinguish between stable and unstable operation.

Preoperative Prolapse Stage as Predictor of Failure of Sacrocolpopexy.

PubMed

Aslam, Muhammad F; Osmundsen, Blake; Edwards, Sharon R; Matthews, Catherine; Gregory, William T

2016-01-01

Our aim was to determine if there was a correlation between the preoperative prolapse stage and postoperative recurrence of prolapse 1 year after sacrocolpopexy. Our null hypothesis is that the preoperative stage of prolapse does not increase the risk of recurrence. This is a multicenter cohort study from 3 centers. We included subjects who underwent robotic-assisted sacrocolpopexy and completed a standardized 1-year follow-up from 2009-2014. All subjects underwent a complete preoperative evaluation and completed 12 months of follow-up with the pelvic organ prolapse quantification examination. We compared those subjects who met the definition of recurrence with those who did not, analyzing the following covariates: stage of prolapse using International Continence Society (ICS) definitions, individual pelvic organ prolapse quantification points, age, body mass index, race, exogenous estrogen use, menopause, smoking, vaginal parity, cesarean section, and performance of concomitant procedures. We defined recurrence as any prolapse beyond the hymen. We had 125 women from 3 centers who met our criteria, with 23.2% of them having recurrence at 1 year. We found that recurrence increased as the preoperative ICS stage of prolapse increased (P = <0.001 in the univariate model). In the multivariate model, using logistic regression, we found that the risk of recurrence of pelvic organ prolapse increased as the presurgery clinical stage increased with an odds ratio of 3.8 (95% confidence interval, 1.5-9) when controlling for age, menopausal status, and genital hiatus (P = 0.004). Much like a higher stage of disease in oncology, we found that increasing stage of prolapse preoperatively increased the risk of recurrence at 1 year after sacrocolpopexy.

Cross-evidence for hypnotic susceptibility through nonlinear measures on EEGs of non-hypnotized subjects

NASA Astrophysics Data System (ADS)

Chiarucci, Riccardo; Madeo, Dario; Loffredo, Maria I.; Castellani, Eleonora; Santarcangelo, Enrica L.; Mocenni, Chiara

2014-07-01

Assessment of hypnotic susceptibility is usually obtained through the application of psychological instruments. A satisfying classification obtained through quantitative measures is still missing, although it would be very useful for both diagnostic and clinical purposes. Aiming at investigating the relationship between the cortical brain activity and the hypnotic susceptibility level, we propose the combined use of two methodologies - Recurrence Quantification Analysis and Detrended Fluctuation Analysis - both inherited from nonlinear dynamics. Indicators obtained through the application of these techniques to EEG signals of individuals in their ordinary state of consciousness allowed us to obtain a clear discrimination between subjects with high and low susceptibility to hypnosis. Finally a neural network approach was used to perform classification analysis.

Characterization of stickiness by means of recurrence.

PubMed

Zou, Yong; Thiel, Marco; Romano, M Carmen; Kurths, Jürgen

2007-12-01

We propose recurrence plots (RPs) to characterize the stickiness of a typical area-preserving map with coexisting chaotic and regular orbits. The difference of the recurrence properties between quasiperiodic and chaotic orbits is revisited, which helps to understand the complex patterns of the corresponding RPs. Moreover, several measures from the recurrence quantification analysis are used to quantify these patterns. Among these measures, the recurrence rate, quantifying the percentage of black points in the plot, is applied to characterize the stickiness of a typical chaotic orbit. The advantage of the recurrence based method in comparison to other standard techniques is that it is possible to distinguish between quasiperiodic and chaotic orbits that are temporarily trapped in a sticky domain, from very short trajectories.

Two phase flow bifurcation due to turbulence: transition from slugs to bubbles

NASA Astrophysics Data System (ADS)

Górski, Grzegorz; Litak, Grzegorz; Mosdorf, Romuald; Rysak, Andrzej

2015-09-01

The bifurcation of slugs to bubbles within two-phase flow patterns in a minichannel is analyzed. The two-phase flow (water-air) occurring in a circular horizontal minichannel with a diameter of 1 mm is examined. The sequences of light transmission time series recorded by laser-phototransistor sensor is analyzed using recurrence plots and recurrence quantification analysis. Recurrence parameters allow the two-phase flow patterns to be found. On changing the water flow rate we identified partitioning of slugs or aggregation of bubbles.

Investigating chaotic features in solar radiation over a tropical station using recurrence quantification analysis

NASA Astrophysics Data System (ADS)

Ogunjo, Samuel T.; Adediji, Adekunle T.; Dada, Joseph B.

2017-01-01

The use of solar energy for power generation and other uses is on the increase. This demand necessitate a better understanding of the underlying dynamics for better prediction. Nonlinear dynamics and its associated tools readily lend itself for such analysis. In this paper, nonlinearity in solar radiation data is tested using recurrence plot (RP) and recurrence quantification analysis (RQA) in a tropical station. The data used was obtained from an ongoing campaign at the Federal University of Technology, Akure, Southwestern Nigeria using an Integrated Sensor Suite (Vantage2 Pro). Half hourly and daily values were tested for each month of the year. Both were found to be nonlinear. The dry months of the year exhibit higher chaoticity compared to the wet months of the year. The daily average values were found to be mildly chaotic. Using RQA, features due to external effects such as harmattan and intertropical discontinuity (ITD) on solar radiation data were uniquely identified.

Recurrence quantification analysis of human postural fluctuations in older fallers and non-fallers.

PubMed

Ramdani, Sofiane; Tallon, Guillaume; Bernard, Pierre Louis; Blain, Hubert

2013-08-01

We investigate postural sway data dynamics in older adult fallers and non-fallers. Center of pressure (COP) signals were recorded during quiet standing in 28 older adults. The subjects were divided in two groups: with and without history of falls. COP time series were analyzed using recurrence quantification analysis (RQA) in both anteroposterior and mediolateral (ML) directions. Classical stabilometric variables (path length and range) were also computed. The results showed that RQA outputs quantifying predictability of COP fluctuations and Shannon entropy of recurrence plot diagonal line length distribution, were significantly higher in fallers, only for ML direction. In addition, the range of ML COP signals was also significantly higher in fallers. This result is in accordance with some findings of the literature and could be interpreted as an increased hip strategy in fallers. The RQA results seem coherent with the theory of loss of complexity with aging and disease. Our results suggest that RQA is a promising approach for the investigation of COP fluctuations in a frail population.

Characterising non-linear dynamics in nocturnal breathing patterns of healthy infants using recurrence quantification analysis.

PubMed

Terrill, Philip I; Wilson, Stephen J; Suresh, Sadasivam; Cooper, David M; Dakin, Carolyn

2013-05-01

Breathing dynamics vary between infant sleep states, and are likely to exhibit non-linear behaviour. This study applied the non-linear analytical tool recurrence quantification analysis (RQA) to 400 breath interval periods of REM and N-REM sleep, and then using an overlapping moving window. The RQA variables were different between sleep states, with REM radius 150% greater than N-REM radius, and REM laminarity 79% greater than N-REM laminarity. RQA allowed the observation of temporal variations in non-linear breathing dynamics across a night's sleep at 30s resolution, and provides a basis for quantifying changes in complex breathing dynamics with physiology and pathology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

PubMed

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

An online sleep apnea detection method based on recurrence quantification analysis.

PubMed

Nguyen, Hoa Dinh; Wilkins, Brek A; Cheng, Qi; Benjamin, Bruce Allen

2014-07-01

This paper introduces an online sleep apnea detection method based on heart rate complexity as measured by recurrence quantification analysis (RQA) statistics of heart rate variability (HRV) data. RQA statistics can capture nonlinear dynamics of a complex cardiorespiratory system during obstructive sleep apnea. In order to obtain a more robust measurement of the nonstationarity of the cardiorespiratory system, we use different fixed amount of neighbor thresholdings for recurrence plot calculation. We integrate a feature selection algorithm based on conditional mutual information to select the most informative RQA features for classification, and hence, to speed up the real-time classification process without degrading the performance of the system. Two types of binary classifiers, i.e., support vector machine and neural network, are used to differentiate apnea from normal sleep. A soft decision fusion rule is developed to combine the results of these classifiers in order to improve the classification performance of the whole system. Experimental results show that our proposed method achieves better classification results compared with the previous recurrence analysis-based approach. We also show that our method is flexible and a strong candidate for a real efficient sleep apnea detection system.

Spatial recurrence analysis: A sensitive and fast detection tool in digital mammography

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

Prado, T. L.; Galuzio, P. P.; Lopes, S. R.

Efficient diagnostics of breast cancer requires fast digital mammographic image processing. Many breast lesions, both benign and malignant, are barely visible to the untrained eye and requires accurate and reliable methods of image processing. We propose a new method of digital mammographic image analysis that meets both needs. It uses the concept of spatial recurrence as the basis of a spatial recurrence quantification analysis, which is the spatial extension of the well-known time recurrence analysis. The recurrence-based quantifiers are able to evidence breast lesions in a way as good as the best standard image processing methods available, but with amore » better control over the spurious fragments in the image.« less

Measure of the electroencephalographic effects of sevoflurane using recurrence dynamics.

PubMed

Li, Xiaoli; Sleigh, Jamie W; Voss, Logan J; Ouyang, Gaoxiang

2007-08-31

This paper proposes a novel method to interpret the effect of anesthetic agents (sevoflurane) on the neural activity, by using recurrence quantification analysis of EEG data. First, we reduce the artefacts in the scalp EEG using a novel filter that combines wavelet transforms and empirical mode decomposition. Then, the determinism in the recurrence plot is calculated. It is found that the determinism increases gradually with increasing the concentration of sevoflurane. Finally, a pharmacokinetic and pharmacodynamic (PKPD) model is built to describe the relationship between the concentration of sevoflurane and the processed EEG measure ('determinism' of the recurrence plot). A test sample of nine patients shows the recurrence in EEG data may track the effect of the sevoflurane on the brain.

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action

PubMed Central

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels—from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures. PMID:27920748

Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action.

PubMed

Wallot, Sebastian; Roepstorff, Andreas; Mønster, Dan

2016-01-01

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels-from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures.

Reliability of recurrence quantification analysis measures of the center of pressure during standing in individuals with musculoskeletal disorders.

PubMed

Mazaheri, Masood; Negahban, Hossein; Salavati, Mahyar; Sanjari, Mohammad Ali; Parnianpour, Mohamad

2010-09-01

Although the application of nonlinear tools including recurrence quantification analysis (RQA) has increasingly grown in the recent years especially in balance-disordered populations, there have been few studies which determine their measurement properties. Therefore, a methodological study was performed to estimate the intersession and intrasession reliability of some dynamic features provided by RQA for nonlinear analysis of center of pressure (COP) signals recorded during quiet standing in a sample of patients with musculoskeletal disorders (MSDs) including low back pain (LBP), anterior cruciate ligament (ACL) injury and functional ankle instability (FAI). The subjects completed postural measurements with three levels of difficulty (rigid surface-eyes open, rigid surface-eyes closed, and foam surface-eyes closed). Four RQA measures (% recurrence, % determinism, entropy, and trend) were extracted from the recurrence plot. Relative reliability of these measures was assessed using intraclass correlation coefficient and absolute reliability using standard error of measurement and coefficient of variation. % Determinism and entropy were the most reliable features of RQA for the both intersession and intrasession reliability measures. High level of reliability of % determinism and entropy in this preliminary investigation may show their clinical promise for discriminative and evaluative purposes of balance performance. 2010 IPEM. Published by Elsevier Ltd. All rights reserved.

Recurrence Quantification of Fractal Structures

PubMed Central

Webber, Charles L.

2012-01-01

By definition, fractal structures possess recurrent patterns. At different levels repeating patterns can be visualized at higher magnifications. The purpose of this chapter is threefold. First, general characteristics of dynamical systems are addressed from a theoretical mathematical perspective. Second, qualitative and quantitative recurrence analyses are reviewed in brief, but the reader is directed to other sources for explicit details. Third, example mathematical systems that generate strange attractors are explicitly defined, giving the reader the ability to reproduce the rich dynamics of continuous chaotic flows or discrete chaotic iterations. The challenge is then posited for the reader to study for themselves the recurrent structuring of these different dynamics. With a firm appreciation of the power of recurrence analysis, the reader will be prepared to turn their sights on real-world systems (physiological, psychological, mechanical, etc.). PMID:23060808

Optimal estimation of recurrence structures from time series

NASA Astrophysics Data System (ADS)

beim Graben, Peter; Sellers, Kristin K.; Fröhlich, Flavio; Hutt, Axel

2016-05-01

Recurrent temporal dynamics is a phenomenon observed frequently in high-dimensional complex systems and its detection is a challenging task. Recurrence quantification analysis utilizing recurrence plots may extract such dynamics, however it still encounters an unsolved pertinent problem: the optimal selection of distance thresholds for estimating the recurrence structure of dynamical systems. The present work proposes a stochastic Markov model for the recurrent dynamics that allows for the analytical derivation of a criterion for the optimal distance threshold. The goodness of fit is assessed by a utility function which assumes a local maximum for that threshold reflecting the optimal estimate of the system's recurrence structure. We validate our approach by means of the nonlinear Lorenz system and its linearized stochastic surrogates. The final application to neurophysiological time series obtained from anesthetized animals illustrates the method and reveals novel dynamic features of the underlying system. We propose the number of optimal recurrence domains as a statistic for classifying an animals' state of consciousness.

Application of Concepts from Cross-Recurrence Analysis in Speech Production: An Overview and Comparison with Other Nonlinear Methods

ERIC Educational Resources Information Center

Lancia, Leonardo; Fuchs, Susanne; Tiede, Mark

2014-01-01

Purpose: The aim of this article was to introduce an important tool, cross-recurrence analysis, to speech production applications by showing how it can be adapted to evaluate the similarity of multivariate patterns of articulatory motion. The method differs from classical applications of cross-recurrence analysis because no phase space…

Application of recurrence quantification analysis for the automated identification of epileptic EEG signals.

PubMed

Acharya, U Rajendra; Sree, S Vinitha; Chattopadhyay, Subhagata; Yu, Wenwei; Ang, Peng Chuan Alvin

2011-06-01

Epilepsy is a common neurological disorder that is characterized by the recurrence of seizures. Electroencephalogram (EEG) signals are widely used to diagnose seizures. Because of the non-linear and dynamic nature of the EEG signals, it is difficult to effectively decipher the subtle changes in these signals by visual inspection and by using linear techniques. Therefore, non-linear methods are being researched to analyze the EEG signals. In this work, we use the recorded EEG signals in Recurrence Plots (RP), and extract Recurrence Quantification Analysis (RQA) parameters from the RP in order to classify the EEG signals into normal, ictal, and interictal classes. Recurrence Plot (RP) is a graph that shows all the times at which a state of the dynamical system recurs. Studies have reported significantly different RQA parameters for the three classes. However, more studies are needed to develop classifiers that use these promising features and present good classification accuracy in differentiating the three types of EEG segments. Therefore, in this work, we have used ten RQA parameters to quantify the important features in the EEG signals.These features were fed to seven different classifiers: Support vector machine (SVM), Gaussian Mixture Model (GMM), Fuzzy Sugeno Classifier, K-Nearest Neighbor (KNN), Naive Bayes Classifier (NBC), Decision Tree (DT), and Radial Basis Probabilistic Neural Network (RBPNN). Our results show that the SVM classifier was able to identify the EEG class with an average efficiency of 95.6%, sensitivity and specificity of 98.9% and 97.8%, respectively.

Extended quantification of the generalized recurrence plot

NASA Astrophysics Data System (ADS)

Riedl, Maik; Marwan, Norbert; Kurths, Jürgen

2016-04-01

The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing structures, turbulent spatial plankton patterns, and fractals. But, it is also successfully applied to the description of spatio-temporal dynamics and the detection of regime shifts, such as in the complex Ginzburg-Landau- equation. The recurrence plot based determinism is a central measure in this framework quantifying the level of regularities in temporal and spatial structures. We extend this measure for the generalized recurrence plot considering additional operations of symmetry than the simple translation. It is tested not only on two-dimensional regular patterns and noise but also on complex spatial patterns reconstructing the parameter space of the complex Ginzburg-Landau-equation. The extended version of the determinism resulted in values which are consistent to the original recurrence plot approach. Furthermore, the proposed method allows a split of the determinism into parts which based on laminar and non-laminar regions of the two-dimensional pattern of the complex Ginzburg-Landau-equation. A comparison of these parts with a standard method of image classification, the co-occurrence matrix approach, shows differences especially in the description of patterns associated with turbulence. In that case, it seems that the extended version of the determinism allows a distinction of phase turbulence and defect turbulence by means of their spatial patterns. This ability of the proposed method promise new insights in other systems with turbulent dynamics coming from climatology, biology, ecology, and social sciences, for example.

Recurrence quantification analysis and support vector machines for golf handicap and low back pain EMG classification.

PubMed

Silva, Luís; Vaz, João Rocha; Castro, Maria António; Serranho, Pedro; Cabri, Jan; Pezarat-Correia, Pedro

2015-08-01

The quantification of non-linear characteristics of electromyography (EMG) must contain information allowing to discriminate neuromuscular strategies during dynamic skills. There are a lack of studies about muscle coordination under motor constrains during dynamic contractions. In golf, both handicap (Hc) and low back pain (LBP) are the main factors associated with the occurrence of injuries. The aim of this study was to analyze the accuracy of support vector machines SVM on EMG-based classification to discriminate Hc (low and high handicap) and LBP (with and without LPB) in the main phases of golf swing. For this purpose recurrence quantification analysis (RQA) features of the trunk and the lower limb muscles were used to feed a SVM classifier. Recurrence rate (RR) and the ratio between determinism (DET) and RR showed a high discriminant power. The Hc accuracy for the swing, backswing, and downswing were 94.4±2.7%, 97.1±2.3%, and 95.3±2.6%, respectively. For LBP, the accuracy was 96.9±3.8% for the swing, and 99.7±0.4% in the backswing. External oblique (EO), biceps femoris (BF), semitendinosus (ST) and rectus femoris (RF) showed high accuracy depending on the laterality within the phase. RQA features and SVM showed a high muscle discriminant capacity within swing phases by Hc and by LBP. Low back pain golfers showed different neuromuscular coordination strategies when compared with asymptomatic. Copyright © 2015 Elsevier Ltd. All rights reserved.

Errors in the estimation of approximate entropy and other recurrence-plot-derived indices due to the finite resolution of RR time series.

PubMed

García-González, Miguel A; Fernández-Chimeno, Mireya; Ramos-Castro, Juan

2009-02-01

An analysis of the errors due to the finite resolution of RR time series in the estimation of the approximate entropy (ApEn) is described. The quantification errors in the discrete RR time series produce considerable errors in the ApEn estimation (bias and variance) when the signal variability or the sampling frequency is low. Similar errors can be found in indices related to the quantification of recurrence plots. An easy way to calculate a figure of merit [the signal to resolution of the neighborhood ratio (SRN)] is proposed in order to predict when the bias in the indices could be high. When SRN is close to an integer value n, the bias is higher than when near n - 1/2 or n + 1/2. Moreover, if SRN is close to an integer value, the lower this value, the greater the bias is.

Automated Detection of Stereotypical Motor Movements in Autism Spectrum Disorder Using Recurrence Quantification Analysis

PubMed Central

Großekathöfer, Ulf; Manyakov, Nikolay V.; Mihajlović, Vojkan; Pandina, Gahan; Skalkin, Andrew; Ness, Seth; Bangerter, Abigail; Goodwin, Matthew S.

2017-01-01

A number of recent studies using accelerometer features as input to machine learning classifiers show promising results for automatically detecting stereotypical motor movements (SMM) in individuals with Autism Spectrum Disorder (ASD). However, replicating these results across different types of accelerometers and their position on the body still remains a challenge. We introduce a new set of features in this domain based on recurrence plot and quantification analyses that are orientation invariant and able to capture non-linear dynamics of SMM. Applying these features to an existing published data set containing acceleration data, we achieve up to 9% average increase in accuracy compared to current state-of-the-art published results. Furthermore, we provide evidence that a single torso sensor can automatically detect multiple types of SMM in ASD, and that our approach allows recognition of SMM with high accuracy in individuals when using a person-independent classifier. PMID:28261082

Automated Detection of Stereotypical Motor Movements in Autism Spectrum Disorder Using Recurrence Quantification Analysis.

PubMed

Großekathöfer, Ulf; Manyakov, Nikolay V; Mihajlović, Vojkan; Pandina, Gahan; Skalkin, Andrew; Ness, Seth; Bangerter, Abigail; Goodwin, Matthew S

2017-01-01

A number of recent studies using accelerometer features as input to machine learning classifiers show promising results for automatically detecting stereotypical motor movements (SMM) in individuals with Autism Spectrum Disorder (ASD). However, replicating these results across different types of accelerometers and their position on the body still remains a challenge. We introduce a new set of features in this domain based on recurrence plot and quantification analyses that are orientation invariant and able to capture non-linear dynamics of SMM. Applying these features to an existing published data set containing acceleration data, we achieve up to 9% average increase in accuracy compared to current state-of-the-art published results. Furthermore, we provide evidence that a single torso sensor can automatically detect multiple types of SMM in ASD, and that our approach allows recognition of SMM with high accuracy in individuals when using a person-independent classifier.

Extended generalized recurrence plot quantification of complex circular patterns

NASA Astrophysics Data System (ADS)

Riedl, Maik; Marwan, Norbert; Kurths, Jürgen

2017-03-01

The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing patterns, turbulent spatial plankton patterns, and fractals. Determinism is a central measure in this framework quantifying the level of regularity of spatial structures. We show by basic examples of fully regular patterns of different symmetries that this measure underestimates the orderliness of circular patterns resulting from rotational symmetries. We overcome this crucial problem by checking additional structural elements of the generalized recurrence plot which is demonstrated with the examples. Furthermore, we show the potential of the extended quantity of determinism applying it to more irregular circular patterns which are generated by the complex Ginzburg-Landau-equation and which can be often observed in real spatially extended dynamical systems. So, we are able to reconstruct the main separations of the system's parameter space analyzing single snapshots of the real part only, in contrast to the use of the original quantity. This ability of the proposed method promises also an improved description of other systems with complicated spatio-temporal dynamics typically occurring in fluid dynamics, climatology, biology, ecology, social sciences, etc.

Recurrence Quantification Analysis of Sentence-Level Speech Kinematics.

PubMed

Jackson, Eric S; Tiede, Mark; Riley, Michael A; Whalen, D H

2016-12-01

Current approaches to assessing sentence-level speech variability rely on measures that quantify variability across utterances and use normalization procedures that alter raw trajectory data. The current work tests the feasibility of a less restrictive nonlinear approach-recurrence quantification analysis (RQA)-via a procedural example and subsequent analysis of kinematic data. To test the feasibility of RQA, lip aperture (i.e., the Euclidean distance between lip-tracking sensors) was recorded for 21 typically developing adult speakers during production of a simple utterance. The utterance was produced in isolation and in carrier structures differing just in length or in length and complexity. Four RQA indices were calculated: percent recurrence (%REC), percent determinism (%DET), stability (MAXLINE), and stationarity (TREND). Percent determinism (%DET) decreased only for the most linguistically complex sentence; MAXLINE decreased as a function of linguistic complexity but increased for the longer-only sentence; TREND decreased as a function of both length and linguistic complexity. This research note demonstrates the feasibility of using RQA as a tool to compare speech variability across speakers and groups. RQA offers promise as a technique to assess effects of potential stressors (e.g., linguistic or cognitive factors) on the speech production system.

Recurrence Quantification Analysis of Sentence-Level Speech Kinematics

PubMed Central

Tiede, Mark; Riley, Michael A.; Whalen, D. H.

2016-01-01

Purpose Current approaches to assessing sentence-level speech variability rely on measures that quantify variability across utterances and use normalization procedures that alter raw trajectory data. The current work tests the feasibility of a less restrictive nonlinear approach—recurrence quantification analysis (RQA)—via a procedural example and subsequent analysis of kinematic data. Method To test the feasibility of RQA, lip aperture (i.e., the Euclidean distance between lip-tracking sensors) was recorded for 21 typically developing adult speakers during production of a simple utterance. The utterance was produced in isolation and in carrier structures differing just in length or in length and complexity. Four RQA indices were calculated: percent recurrence (%REC), percent determinism (%DET), stability (MAXLINE), and stationarity (TREND). Results Percent determinism (%DET) decreased only for the most linguistically complex sentence; MAXLINE decreased as a function of linguistic complexity but increased for the longer-only sentence; TREND decreased as a function of both length and linguistic complexity. Conclusions This research note demonstrates the feasibility of using RQA as a tool to compare speech variability across speakers and groups. RQA offers promise as a technique to assess effects of potential stressors (e.g., linguistic or cognitive factors) on the speech production system. PMID:27824987

Quantification of scaling exponent with Crossover type phenomena for different types of forcing in DC glow discharge plasma

NASA Astrophysics Data System (ADS)

Saha, Debajyoti; Shaw, Pankaj Kumar; Ghosh, Sabuj; Janaki, M. S.; Sekar Iyengar, A. N.

2018-01-01

We have carried out a detailed study of scaling region using detrended fractal analysis test by applying different forcing likewise noise, sinusoidal, square on the floating potential fluctuations acquired under different pressures in a DC glow discharge plasma. The transition in the dynamics is observed through recurrence plot techniques which is an efficient method to observe the critical regime transitions in dynamics. The complexity of the nonlinear fluctuation has been revealed with the help of recurrence quantification analysis which is a suitable tool for investigating recurrence, an ubiquitous feature providing a deep insight into the dynamics of real dynamical system. An informal test for stationarity which checks for the compatibility of nonlinear approximations to the dynamics made in different segments in a time series has been proposed. In case of sinusoidal, noise, square forcing applied on fluctuation acquired at P = 0.12 mbar only one dominant scaling region is observed whereas the forcing applied on fluctuation (P = 0.04 mbar) two prominent scaling regions have been explored reliably using different forcing amplitudes indicating the signature of crossover phenomena. Furthermore a persistence long range behavior has been observed in one of these scaling regions. A comprehensive study of the quantification of scaling exponents has been carried out with the increase in amplitude and frequency of sinusoidal, square type of forcings. The scalings exponent is envisaged to be the roughness of the time series. The method provides a single quantitative idea of the scaling exponent to quantify the correlation properties of a signal.

Recurrence quantity analysis based on singular value decomposition

NASA Astrophysics Data System (ADS)

Bian, Songhan; Shang, Pengjian

2017-05-01

Recurrence plot (RP) has turned into a powerful tool in many different sciences in the last three decades. To quantify the complexity and structure of RP, recurrence quantification analysis (RQA) has been developed based on the measures of recurrence density, diagonal lines, vertical lines and horizontal lines. This paper will study the RP based on singular value decomposition which is a new perspective of RP study. Principal singular value proportion (PSVP) will be proposed as one new RQA measure and bigger PSVP means higher complexity for one system. In contrast, smaller PSVP reflects a regular and stable system. Considering the advantage of this method in detecting the complexity and periodicity of systems, several simulation and real data experiments are chosen to examine the performance of this new RQA.

Silent Reading Fluency and Comprehension in Bilingual Children

PubMed Central

O'Brien, Beth A.; Wallot, Sebastian

2016-01-01

This paper focuses on reading fluency by bilingual primary school students, and the relation of text fluency to their reading comprehension. Group differences were examined in a cross-sectional design across the age range when fluency is posed to shift from word-level to text-level. One hundred five bilingual children from primary grades 3, 4, and 5 were assessed for English word reading and decoding fluency, phonological awareness, rapid symbol naming, and oral language proficiency with standardized measures. These skills were correlated with their silent reading fluency on a self-paced story reading task. Text fluency was quantified using non-linear analytic methods: recurrence quantification and fractal analyses. Findings indicate that more fluent text reading appeared by grade 4, similar to monolingual findings, and that different aspects of fluency characterized passage reading performance at different grade levels. Text fluency and oral language proficiency emerged as significant predictors of reading comprehension. PMID:27630590

Applying the recurrence quantification analysis method for analyzing the recurrence of simulated multiple African easterly waves in 2006

NASA Astrophysics Data System (ADS)

Reyes, T.; Shen, B. W.; Wu, Y.; Faghih-Naini, S.; Li, J.

2017-12-01

In late August, 2006, six African easterly waves (AEWs) appeared sequentially over the African continent during a 30-day period. With a global model of 1/4 degree resolution, statistics of these AEWs were realistically captured. More interestingly, the formation, subsequent intensification, and movement of Hurricane Helene (2006) were simulated to a degree of satisfaction during the model integration from Day 22 to 30 (Shen et al., 2010). We then developed a parallel ensemble empirical mode decomposition method (PEEMD; Shen et al. 2012; 2017; Cheung et al. 2013) to reveal the role of downscaling processes associated with the environmental flows in determining the timing and location of Helene's formation (Wu and Shen, 2016), supporting its practical predictability at extended-range time scales. Recently, further analysis of the correlation coefficients (CCs) between the simulated temperature and reanalysis data showed that CCs are above 0.65 during the 30 day simulations but display oscillations. While high CCs are consistent with the accurate simulations of the AEWs and Hurricane Helene, oscillations may indicate the inaccurate simulations of moving speeds (i.e., an inaccurate phase) as compared to observations. The observed AEWs have comparable but slightly different periods. To quantitatively examine this space-varying feature in observations and the temporal oscillations in the CCs of the simulations, we select recurrence quantification analysis (RQA) methods and the recurrence plot (RP) in order to account for the local nature of these features. A recurrence is defined when the trajectory returns back to the neighborhood of a previously visited state. With the RQA methods, we can compute the "recurrence rate" and "determinism" present in the RP in order to reveal the degree of recurrence and determinism (or "predictability") of the recurrent solutions. To verify of our implementations in Python, we applied our methods to analyze idealized solutions (e.g., quasi-periodic solutions and limit torus) from the three-dimensional and five-dimensional dissipative or non-dissipative Lorenz Models (Shen and Faghih-Naini, 2017). Post verification, we apply the RQA methods to analyze the 30-days reanalysis and simulation data. In this talk, we will present preliminary but promising results.

Main-channel slopes of selected streams in Iowa for estimation of flood-frequency discharges

USGS Publications Warehouse

Eash, David A.

2003-01-01

This report describes a statewide study conducted to develop main-channel slope (MCS) curves for 138 selected streams in Iowa with drainage areas greater than 100 square miles. MCS values determined from the curves can be used in regression equations for estimating floodfrequency discharges. Multivariable regression equations previously developed for two of the three hydrologic regions defined for Iowa require the measurement of MCS. Main-channel slope is a difficult measurement to obtain for large streams using 1:24,000-scale topographic maps. The curves developed in this report provide a simplified method for determining MCS values for sites located along large streams in Iowa within hydrologic Regions 2 and 3. The curves were developed using MCS values quantified for 2,058 selected sites along 138 selected streams in Iowa. A geographic information system (GIS) technique and 1:24,000-scale topographic data were used to quantify MCS values for the stream sites. The sites were selected at about 5-mile intervals along the streams. River miles were quantified for each stream site using a GIS program. Data points for river-mile and MCS values were plotted and a best-fit curve was developed for each stream. An adjustment was applied to all 138 curves to compensate for differences in MCS values between manual measurements and GIS quantifications. The multivariable equations for Regions 2 and 3 were developed using manual measurements of MCS. A comparison of manual measurements and GIS quantifications of MCS indicates that manual measurements typically produce greater values of MCS compared to GIS quantifications. Median differences between manual measurements and GIS quantifications of MCS are 14.8 and 17.7 percent for Regions 2 and 3, respectively. Comparisons of percentage differences between flood-frequency discharges calculated using MCS values of manual measurements and GIS quantifications indicate that use of GIS values of MCS for Region 3 substantially underestimate flood discharges. Mean and median percentage differences for 2- to 500-year recurrence- interval flood discharges ranged from 5.0 to 5.3 and 4.3 to 4.5 percent, respectively, for Region 2 and ranged from 18.3 to 27.1 and 12.3 to 17.3 percent for Region 3. The MCS curves developed from GIS quantifications were adjusted by 14.8 percent for streams located in Region 2 and by 17.7 percent for streams located in Region 3. Comparisons of percentage differences between flood discharges calculated using MCS values of manual measurements and adjusted-GIS quantifications for Regions 2 and 3 indicate that the flood-discharge estimates are comparable. For Region 2, mean percentage differences for 2- to 500-year recurrence- interval flood discharges ranged between 0.6 and 0.8 percent and median differences were 0.0 percent. For Region 3, mean and median differences ranged between 5.4 to 8.4 and 0.0 to 0.3 percent, respectively. A list of selected stream sites presented with each curve provides information about the sites including river miles, drainage areas, the location of U.S. Geological Survey streamflowgaging stations, and the location of streams crossing hydrologic region boundaries or the Des Moines Lobe landform region boundary. Two examples are presented for determining river-mile and MCS values, and two techniques are presented for computing flood-frequency discharges.

Detection of traffic incidents using nonlinear time series analysis

NASA Astrophysics Data System (ADS)

Fragkou, A. D.; Karakasidis, T. E.; Nathanail, E.

2018-06-01

In this study, we present results of the application of nonlinear time series analysis on traffic data for incident detection. More specifically, we analyze daily volume records of Attica Tollway (Greece) collected from sensors located at various locations. The analysis was performed using the Recurrence Plot (RP) and Recurrence Quantification Analysis (RQA) method of the volume data of the lane closest to the median. The results show that it is possible to identify, through the abrupt change of the dynamics of the system revealed by RPs and RQA, the occurrence of incidents on the freeway and differentiate from recurrent traffic congestion. The proposed methodology could be of interest for big data traffic analysis.

Evaluation of selected recurrence measures in discriminating pre-ictal and inter-ictal periods from epileptic EEG data

NASA Astrophysics Data System (ADS)

Ngamga, Eulalie Joelle; Bialonski, Stephan; Marwan, Norbert; Kurths, Jürgen; Geier, Christian; Lehnertz, Klaus

2016-04-01

We investigate the suitability of selected measures of complexity based on recurrence quantification analysis and recurrence networks for an identification of pre-seizure states in multi-day, multi-channel, invasive electroencephalographic recordings from five epilepsy patients. We employ several statistical techniques to avoid spurious findings due to various influencing factors and due to multiple comparisons and observe precursory structures in three patients. Our findings indicate a high congruence among measures in identifying seizure precursors and emphasize the current notion of seizure generation in large-scale epileptic networks. A final judgment of the suitability for field studies, however, requires evaluation on a larger database.

Recurrence plot statistics and the effect of embedding

NASA Astrophysics Data System (ADS)

March, T. K.; Chapman, S. C.; Dendy, R. O.

2005-01-01

Recurrence plots provide a graphical representation of the recurrent patterns in a timeseries, the quantification of which is a relatively new field. Here we derive analytical expressions which relate the values of key statistics, notably determinism and entropy of line length distribution, to the correlation sum as a function of embedding dimension. These expressions are obtained by deriving the transformation which generates an embedded recurrence plot from an unembedded plot. A single unembedded recurrence plot thus provides the statistics of all possible embedded recurrence plots. If the correlation sum scales exponentially with embedding dimension, we show that these statistics are determined entirely by the exponent of the exponential. This explains the results of Iwanski and Bradley [J.S. Iwanski, E. Bradley, Recurrence plots of experimental data: to embed or not to embed? Chaos 8 (1998) 861-871] who found that certain recurrence plot statistics are apparently invariant to embedding dimension for certain low-dimensional systems. We also examine the relationship between the mutual information content of two timeseries and the common recurrent structure seen in their recurrence plots. This allows time-localized contributions to mutual information to be visualized. This technique is demonstrated using geomagnetic index data; we show that the AU and AL geomagnetic indices share half their information, and find the timescale on which mutual features appear.

Characterization of high-intensity, long-duration continuous auroral activity (HILDCAA) events using recurrence quantification analysis

NASA Astrophysics Data System (ADS)

Mendes, Odim; Oliveira Domingues, Margarete; Echer, Ezequiel; Hajra, Rajkumar; Everton Menconi, Varlei

2017-08-01

Considering the magnetic reconnection and the viscous interaction as the fundamental mechanisms for transfer particles and energy into the magnetosphere, we study the dynamical characteristics of auroral electrojet (AE) index during high-intensity, long-duration continuous auroral activity (HILDCAA) events, using a long-term geomagnetic database (1975-2012), and other distinct interplanetary conditions (geomagnetically quiet intervals, co-rotating interaction regions (CIRs)/high-speed streams (HSSs) not followed by HILDCAAs, and events of AE comprised in global intense geomagnetic disturbances). It is worth noting that we also study active but non-HILDCAA intervals. Examining the geomagnetic AE index, we apply a dynamics analysis composed of the phase space, the recurrence plot (RP), and the recurrence quantification analysis (RQA) methods. As a result, the quantification finds two distinct clusterings of the dynamical behaviours occurring in the interplanetary medium: one regarding a geomagnetically quiet condition regime and the other regarding an interplanetary activity regime. Furthermore, the HILDCAAs seem unique events regarding a visible, intense manifestations of interplanetary Alfvénic waves; however, they are similar to the other kinds of conditions regarding a dynamical signature (based on RQA), because it is involved in the same complex mechanism of generating geomagnetic disturbances. Also, by characterizing the proper conditions of transitions from quiescent conditions to weaker geomagnetic disturbances inside the magnetosphere and ionosphere system, the RQA method indicates clearly the two fundamental dynamics (geomagnetically quiet intervals and HILDCAA events) to be evaluated with magneto-hydrodynamics simulations to understand better the critical processes related to energy and particle transfer into the magnetosphere-ionosphere system. Finally, with this work, we have also reinforced the potential applicability of the RQA method for characterizing nonlinear geomagnetic processes related to the magnetic reconnection and the viscous interaction affecting the magnetosphere.

Recurrence Plots: a New Tool for Quantification of Cardiac Autonomic Nervous System Recovery after Transplant.

PubMed

Takakura, Isabela Thomaz; Hoshi, Rosangela Akemi; Santos, Márcio Antonio; Pivatelli, Flávio Correa; Nóbrega, João Honorato; Guedes, Débora Linhares; Nogueira, Victor Freire; Frota, Tuane Queiroz; Castelo, Gabriel Castro; Godoy, Moacir Fernandes de

2017-01-01

To evaluate a possible evolutionary post-heart transplant return of autonomic function using quantitative and qualitative information from recurrence plots. Using electrocardiography, 102 RR tachograms of 45 patients (64.4% male) who underwent heart transplantation and that were available in the database were analyzed at different follow-up periods. The RR tachograms were collected from patients in the supine position for about 20 minutes. A time series with 1000 RR intervals was analyzed, a recurrence plot was created, and the following quantitative variables were evaluated: percentage of determinism, percentage of recurrence, average diagonal length, Shannon entropy, and sample entropy, as well as the visual qualitative aspect. Quantitative and qualitative signs of heart rate variability recovery were observed after transplantation. There is evidence that autonomic innervation of the heart begins to happen gradually after transplantation. Quantitative and qualitative analyses of recurrence can be useful tools for monitoring cardiac transplant patients and detecting the gradual return of heart rate variability.

In Search of Determinism-Sensitive Region to Avoid Artefacts in Recurrence Plots

NASA Astrophysics Data System (ADS)

Wendi, Dadiyorto; Marwan, Norbert; Merz, Bruno

As an effort to reduce parameter uncertainties in constructing recurrence plots, and in particular to avoid potential artefacts, this paper presents a technique to derive artefact-safe region of parameter sets. This technique exploits both deterministic (incl. chaos) and stochastic signal characteristics of recurrence quantification (i.e. diagonal structures). It is useful when the evaluated signal is known to be deterministic. This study focuses on the recurrence plot generated from the reconstructed phase space in order to represent many real application scenarios when not all variables to describe a system are available (data scarcity). The technique involves random shuffling of the original signal to destroy its original deterministic characteristics. Its purpose is to evaluate whether the determinism values of the original and the shuffled signal remain closely together, and therefore suggesting that the recurrence plot might comprise artefacts. The use of such determinism-sensitive region shall be accompanied by standard embedding optimization approaches, e.g. using indices like false nearest neighbor and mutual information, to result in a more reliable recurrence plot parameterization.

Recurrence quantity analysis based on matrix eigenvalues

NASA Astrophysics Data System (ADS)

Yang, Pengbo; Shang, Pengjian

2018-06-01

Recurrence plots is a powerful tool for visualization and analysis of dynamical systems. Recurrence quantification analysis (RQA), based on point density and diagonal and vertical line structures in the recurrence plots, is considered to be alternative measures to quantify the complexity of dynamical systems. In this paper, we present a new measure based on recurrence matrix to quantify the dynamical properties of a given system. Matrix eigenvalues can reflect the basic characteristics of the complex systems, so we show the properties of the system by exploring the eigenvalues of the recurrence matrix. Considering that Shannon entropy has been defined as a complexity measure, we propose the definition of entropy of matrix eigenvalues (EOME) as a new RQA measure. We confirm that EOME can be used as a metric to quantify the behavior changes of the system. As a given dynamical system changes from a non-chaotic to a chaotic regime, the EOME will increase as well. The bigger EOME values imply higher complexity and lower predictability. We also study the effect of some factors on EOME,including data length, recurrence threshold, the embedding dimension, and additional noise. Finally, we demonstrate an application in physiology. The advantage of this measure lies in a high sensitivity and simple computation.

Cross over of recurrence networks to random graphs and random geometric graphs

NASA Astrophysics Data System (ADS)

Jacob, Rinku; Harikrishnan, K. P.; Misra, R.; Ambika, G.

2017-02-01

Recurrence networks are complex networks constructed from the time series of chaotic dynamical systems where the connection between two nodes is limited by the recurrence threshold. This condition makes the topology of every recurrence network unique with the degree distribution determined by the probability density variations of the representative attractor from which it is constructed. Here we numerically investigate the properties of recurrence networks from standard low-dimensional chaotic attractors using some basic network measures and show how the recurrence networks are different from random and scale-free networks. In particular, we show that all recurrence networks can cross over to random geometric graphs by adding sufficient amount of noise to the time series and into the classical random graphs by increasing the range of interaction to the system size. We also highlight the effectiveness of a combined plot of characteristic path length and clustering coefficient in capturing the small changes in the network characteristics.

Recurrence quantification analysis applied to spatiotemporal pattern analysis in high-density mapping of human atrial fibrillation.

PubMed

Zeemering, Stef; Bonizzi, Pietro; Maesen, Bart; Peeters, Ralf; Schotten, Ulrich

2015-01-01

Spatiotemporal complexity of atrial fibrillation (AF) patterns is often quantified by annotated intracardiac contact mapping. We introduce a new approach that applies recurrence plot (RP) construction followed by recurrence quantification analysis (RQA) to epicardial atrial electrograms, recorded with a high-density grid of electrodes. In 32 patients with no history of AF (aAF, n=11), paroxysmal AF (PAF, n=12) and persistent AF (persAF, n=9), RPs were constructed using a phase space electrogram embedding dimension equal to the estimated AF cycle length. Spatial information was incorporated by 1) averaging the recurrence over all electrodes, and 2) by applying principal component analysis (PCA) to the matrix of embedded electrograms and selecting the first principal component as a representation of spatial diversity. Standard RQA parameters were computed on the constructed RPs and correlated to the number of fibrillation waves per AF cycle (NW). Averaged RP RQA parameters showed no correlation with NW. Correlations improved when applying PCA, with maximum correlation achieved between RP threshold and NW (RR1%, r=0.68, p <; 0.001) and RP determinism (DET, r=-0.64, p <; 0.001). All studied RQA parameters based on the PCA RP were able to discriminate between persAF and aAF/PAF (DET persAF 0.40 ± 0.11 vs. 0.59 ± 0.14/0.62 ± 0.16, p <; 0.01). RP construction and RQA combined with PCA provide a quick and reliable tool to visualize dynamical behaviour and to assess the complexity of contact mapping patterns in AF.

Application of the new Cross Recurrence Plots to multivariate data

NASA Astrophysics Data System (ADS)

Thiel, M.; Romano, C.; Kurths, J.

2003-04-01

We extend and then apply the method of the new Cross Recurrence Plots (XRPs) to multivariate data. After introducing the new method we carry out an analysis of spatiotemporal ecological data. We compute not only the Rényi entropies and cross entropies by XRP, that allow to draw conclusions about the coupling of the systems, but also find a prediction horizon for intermediate time scales.

Dynamics of a two-phase flow through a minichannel: Transition from churn to slug flow

NASA Astrophysics Data System (ADS)

Górski, Grzegorz; Litak, Grzegorz; Mosdorf, Romuald; Rysak, Andrzej

2016-04-01

The churn-to-slug flow bifurcations of two-phase (air-water) flow patterns in a 2mm diameter minichannel were investigated. With increasing a water flow rate, we observed the transition of slugs to bubbles of different sizes. The process was recorded by a digital camera. The sequences of light transmission time series were recorded by a laser-phototransistor sensor, and then analyzed using the recurrence plots and recurrence quantification analysis (RQA). Due to volume dependence of bubbles velocities, we observed the formation of periodic modulations in the laser signal.

Recurrence Quantification Analysis of Processes and Products of Discourse: A Tutorial in R

ERIC Educational Resources Information Center

Wallot, Sebastian

2017-01-01

Processes of naturalistic reading and writing are based on complex linguistic input, stretch-out over time, and rely on an integrated performance of multiple perceptual, cognitive, and motor processes. Hence, naturalistic reading and writing performance is nonstationary and exhibits fluctuations and transitions. However, instead of being just…

Predicting termination of atrial fibrillation based on the structure and quantification of the recurrence plot.

PubMed

Sun, Rongrong; Wang, Yuanyuan

2008-11-01

Predicting the spontaneous termination of the atrial fibrillation (AF) leads to not only better understanding of mechanisms of the arrhythmia but also the improved treatment of the sustained AF. A novel method is proposed to characterize the AF based on structure and the quantification of the recurrence plot (RP) to predict the termination of the AF. The RP of the electrocardiogram (ECG) signal is firstly obtained and eleven features are extracted to characterize its three basic patterns. Then the sequential forward search (SFS) algorithm and Davies-Bouldin criterion are utilized to select the feature subset which can predict the AF termination effectively. Finally, the multilayer perceptron (MLP) neural network is applied to predict the AF termination. An AF database which includes one training set and two testing sets (A and B) of Holter ECG recordings is studied. Experiment results show that 97% of testing set A and 95% of testing set B are correctly classified. It demonstrates that this algorithm has the ability to predict the spontaneous termination of the AF effectively.

Multiscale recurrence analysis of spatio-temporal data

NASA Astrophysics Data System (ADS)

Riedl, M.; Marwan, N.; Kurths, J.

2015-12-01

The description and analysis of spatio-temporal dynamics is a crucial task in many scientific disciplines. In this work, we propose a method which uses the mapogram as a similarity measure between spatially distributed data instances at different time points. The resulting similarity values of the pairwise comparison are used to construct a recurrence plot in order to benefit from established tools of recurrence quantification analysis and recurrence network analysis. In contrast to other recurrence tools for this purpose, the mapogram approach allows the specific focus on different spatial scales that can be used in a multi-scale analysis of spatio-temporal dynamics. We illustrate this approach by application on mixed dynamics, such as traveling parallel wave fronts with additive noise, as well as more complicate examples, pseudo-random numbers and coupled map lattices with a semi-logistic mapping rule. Especially the complicate examples show the usefulness of the multi-scale consideration in order to take spatial pattern of different scales and with different rhythms into account. So, this mapogram approach promises new insights in problems of climatology, ecology, or medicine.

Multiscale recurrence analysis of spatio-temporal data.

PubMed

Riedl, M; Marwan, N; Kurths, J

2015-12-01

The description and analysis of spatio-temporal dynamics is a crucial task in many scientific disciplines. In this work, we propose a method which uses the mapogram as a similarity measure between spatially distributed data instances at different time points. The resulting similarity values of the pairwise comparison are used to construct a recurrence plot in order to benefit from established tools of recurrence quantification analysis and recurrence network analysis. In contrast to other recurrence tools for this purpose, the mapogram approach allows the specific focus on different spatial scales that can be used in a multi-scale analysis of spatio-temporal dynamics. We illustrate this approach by application on mixed dynamics, such as traveling parallel wave fronts with additive noise, as well as more complicate examples, pseudo-random numbers and coupled map lattices with a semi-logistic mapping rule. Especially the complicate examples show the usefulness of the multi-scale consideration in order to take spatial pattern of different scales and with different rhythms into account. So, this mapogram approach promises new insights in problems of climatology, ecology, or medicine.

Recurrence Methods for the Identification of Morphogenetic Patterns

PubMed Central

Facchini, Angelo; Mocenni, Chiara

2013-01-01

This paper addresses the problem of identifying the parameters involved in the formation of spatial patterns in nonlinear two dimensional systems. To this aim, we perform numerical experiments on a prototypical model generating morphogenetic Turing patterns, by changing both the spatial frequency and shape of the patterns. The features of the patterns and their relationship with the model parameters are characterized by means of the Generalized Recurrence Quantification measures. We show that the recurrence measures Determinism and Recurrence Entropy, as well as the distribution of the line lengths, allow for a full characterization of the patterns in terms of power law decay with respect to the parameters involved in the determination of their spatial frequency and shape. A comparison with the standard two dimensional Fourier transform is performed and the results show a better performance of the recurrence indicators in identifying a reliable connection with the spatial frequency of the patterns. Finally, in order to evaluate the robustness of the estimation of the power low decay, extensive simulations have been performed by adding different levels of noise to the patterns. PMID:24066062

Comparative study of chaotic features in hourly wind speed using recurrence quantification analysis

NASA Astrophysics Data System (ADS)

Adeniji, A. E.; Olusola, O. I.; Njah, A. N.

2018-02-01

Due to the shortage in electricity supply in Nigeria, there is a need to improve the alternative power generation from wind energy by analysing the wind speed data available in some parts of the country, for a better understanding of its underlying dynamics for the purpose of good prediction and modelling. The wind speed data used in this study were collected over a period of two years by National Space Research and Development Agency (NASRDA) from five different stations in the tropics namely; Abuja (7050'02.09"N and 6004'29.97"E), Akungba (6059'05.40"N and 5035'52.23"E), Nsukka (6051'28.14"N and 7024'28.15"E), Port Harcourt (4047'05.41"N and 6059'30.62"E), and Yola (9017'33.58"N and 12023'26.69"E). In this paper, recurrence plot (RP) and recurrence quantification analysis (RQA) are applied to investigate a non-linear deterministic dynamical process and non-stationarity in hourly wind speed data from the study areas. Using RQA for each month of the two years, it is observed that wind speed data for the wet months exhibit higher chaoticity than that of the dry months for all the stations, due to strong and weak monsoonal effect during the wet and dry seasons respectively. The results show that recurrence techniques are able to identify areas and periods for which the harvest of wind energy for power generation is good (high predictability) and poor (low predictability) in the study areas. This work also validates the RQA measures (Lmax, DET and ENT) used and establishes that they are similar/related as they give similar results for the dynamical characterization of the wind speed data.

Detecting intrinsic dynamics of traffic flow with recurrence analysis and empirical mode decomposition

NASA Astrophysics Data System (ADS)

Xiong, Hui; Shang, Pengjian; Bian, Songhan

2017-05-01

In this paper, we apply the empirical mode decomposition (EMD) method to the recurrence plot (RP) and recurrence quantification analysis (RQA), to evaluate the frequency- and time-evolving dynamics of the traffic flow. Based on the cumulative intrinsic mode functions extracted by the EMD, the frequency-evolving RP regarding different oscillation of modes suggests that apparent dynamics of the data considered are mainly dominated by its components of medium- and low-frequencies while severely affected by fast oscillated noises contained in the signal. Noises are then eliminated to analyze the intrinsic dynamics and consequently, the denoised time-evolving RQA diversely characterizes the properties of the signal and marks crucial points more accurately where white bands in the RP occur, whereas a strongly qualitative agreement exists between all the non-denoised RQA measures. Generally, the EMD combining with the recurrence analysis sheds more reliable, abundant and inherent lights into the traffic flow, which is meaningful to the empirical analysis of complex systems.

Uncertainty quantification in fission cross section measurements at LANSCE

DOE PAGES

Tovesson, F.

2015-01-09

Neutron-induced fission cross sections have been measured for several isotopes of uranium and plutonium at the Los Alamos Neutron Science Center (LANSCE) over a wide range of incident neutron energies. The total uncertainties in these measurements are in the range 3–5% above 100 keV of incident neutron energy, which results from uncertainties in the target, neutron source, and detector system. The individual sources of uncertainties are assumed to be uncorrelated, however correlation in the cross section across neutron energy bins are considered. The quantification of the uncertainty contributions will be described here.

Responses of bistable piezoelectric-composite energy harvester by means of recurrences

NASA Astrophysics Data System (ADS)

Syta, Arkadiusz; Bowen, Christopher R.; Kim, H. Alicia; Rysak, Andrzej; Litak, Grzegorz

2016-08-01

In this paper we examine the modal response of a bistable electro-mechanical energy harvesting device based on characterization of the experimental time-series. A piezoelectric element attached to a vibrating bistable carbon-fibre reinforced polymer laminate plate was used for the conversion of mechanical vibrations to electrical energy under harmonic excitations at a variety of frequencies and amplitudes. The inherent bistability of the mechanical resonator and snap-through phenomenon between stable states were exploited for energy harvesting. To identify the dynamics of the response of the studied harvesting structure and the associated output power generation we used the Fourier spectrum and Recurrence Quantification Analysis (RQA).

RP and RQA Analysis for Floating Potential Fluctuations in a DC Magnetron Sputtering Plasma

NASA Astrophysics Data System (ADS)

Sabavath, Gopikishan; Banerjee, I.; Mahapatra, S. K.

2016-04-01

The nonlinear dynamics of a direct current magnetron sputtering plasma is visualized using recurrence plot (RP) technique. RP comprises the recurrence quantification analysis (RQA) which is an efficient method to observe critical regime transitions in dynamics. Further, RQA provides insight information about the system’s behavior. We observed the floating potential fluctuations of the plasma as a function of discharge voltage by using Langmuir probe. The system exhibits quasi-periodic-chaotic-quasi-periodic-chaotic transitions. These transitions are quantified from determinism, Lmax, and entropy of RQA. Statistical investigations like kurtosis and skewness also studied for these transitions which are in well agreement with RQA results.

Development of next-generation mapping populations: Multi-parent Advanced Generation Inter-Cross (MAGIC) and Marker-Assisted Recurrent Selection (MARS) populations in peanut

USDA-ARS?s Scientific Manuscript database

Generation Inter-Cross (MAGIC) and Marker-Assisted Recurrent Selection (MARS) have been proposed and used in many crops to dissect complex traits or QTL. MAGIC allows for dissecting genomic structure, and for improving breeding populations by integrating multiple alleles from different parents. MAR...

Illness perceptions or recurrence risk perceptions: What comes first? A longitudinal cross-lagged examination among cardiac patients.

PubMed

Peleg, Shira; Drori, Erga; Banai, Shmuel; Finkelstein, Ariel; Shiloh, Shoshana

2016-05-01

Previous research suggested that illness perceptions provide the basis for illness risk perceptions through an inductive reasoning process. This study aimed to assess the direction of relationships between illness and recurrence risk perceptions over time, among cardiac patients. A longitudinal study was conducted among 138 patients undergoing coronary angioplasty. Self-report questionnaires measured perceived recurrence risk and illness perceptions one day and one month after catheterisation. Cross-lagged Panel Model Analyses revealed that higher perceptions of timeline, consequences and emotional representations of illness at hospitalisation were associated with higher recurrence risk perceptions one month later. Perceived personal control was the only illness perception with bi-directional associations: higher perceived personal control at hospitalisation was associated with higher recurrence risk perceptions one month later; and higher recurrence risk perceptions at hospitalisation was associated with lower personal control one month later. The findings suggest that the associations between recurrence risk and illness perceptions can only partly be explained by inductive reasoning. Halo effects and defensive processes are suggested as complementary explanations for the observed associations between risk and illness perceptions.

Nucleic Acid-Based Cross-Linking Assay for Detection and Quantification of Hepatitis B Virus DNA

PubMed Central

Lai, Vicky C. H.; Guan, Richard; Wood, Michael L.; Lo, Su Kong; Yuen, Man-Fung; Lai, Ching-Lung

1999-01-01

A nucleic acid photo-cross-linking technology was used to develop a direct assay for the quantification of hepatitis B virus (HBV) DNA levels in serum. Cross-linker-modified DNA probes complementary to the viral genomes of the major HBV subtypes were synthesized and used in an assay that could be completed in less than 6 h. The quantification range of the assay, as determined by testing serial dilutions of Eurohep HBV reference standards and cloned HBV DNA, was 5 × 105 to 3 × 109 molecules of HBV DNA/ml of serum. Within-run and between-run coefficients of variation (CVs) for the assay were 4.3 and 4.0%, respectively. The assay was used to determine HBV DNA levels in 302 serum samples, and the results were compared to those obtained after testing the same samples with the Chiron branched-DNA (bDNA) assay for HBV DNA. Of the samples tested, 218 were positive for HBV DNA by both assays and 72 gave results below the cutoff for both assays. Of the remaining 12 samples, 10 were positive for HBV DNA by the cross-linking assay only; the 2 other samples were positive by the bDNA assay only. Twenty-eight samples had to be retested by the bDNA assay (CV, >20% between the results obtained from the testing of each sample in duplicate), whereas only three samples required retesting by the cross-linking assay. The correlation between the HBV DNA levels, as measured by the two tests, was very high (r = 0.902; P = 0.01). We conclude that the cross-linking assay is a sensitive and reproducible method for the detection and quantification of HBV DNA levels in serum. PMID:9854083

The Role of Recurrence Plots in Characterizing the Output-Unemployment Relationship: An Analysis

PubMed Central

Caraiani, Petre; Haven, Emmanuel

2013-01-01

We analyse the output-unemployment relationship using an approach based on cross-recurrence plots and quantitative recurrence analysis. We use post-war period quarterly U.S. data. The results obtained show the emergence of a complex and interesting relationship. PMID:23460814

A School-Based Survey of Recurrent Non-Specific Low-Back Pain Prevalence and Consequences in Children

ERIC Educational Resources Information Center

Jones, M. A.; Stratton, G.; Reilly, T.; Unnithan, V. B.

2004-01-01

The aim of this investigation was to provide evidence of the prevalence and consequences of recurrent low-back pain in children from Northwest England. A cross-sectional survey was conducted involving a standardized questionnaire with established reliability and validity. A cross-sectional sample of 500 boys (n = 249) and girls (n = 251) aged…

Macrophyte succession in Swedish lakes caused by deposition of airborne acid substances

Treesearch

Olle Grahn

1976-01-01

Recurrent biological investigations have been made in six lakes in two areas in western Sweden. It has been found that the supply of acid substances induces long-term biological perturbations at all trophic levels in the lake ecosystem. Among these changes, the sphagnum expansion is believed to strongly affect the dynamics in the lake. A quantification of the Sphagnum...

The Impact of Social-Cognitive Stress on Speech Variability, Determinism, and Stability in Adults Who Do and Do Not Stutter

ERIC Educational Resources Information Center

Jackson, Eric S.; Tiede, Mark; Beal, Deryk; Whalen, D. H.

2016-01-01

Purpose: This study examined the impact of social-cognitive stress on sentence-level speech variability, determinism, and stability in adults who stutter (AWS) and adults who do not stutter (AWNS). We demonstrated that complementing the spatiotemporal index (STI) with recurrence quantification analysis (RQA) provides a novel approach to both…

[Performance evaluation of Abbott RealTime HBV Quantification Kit for HBV viral load by real-time PCR].

PubMed

Kim, Myeong Hee; Cha, Choong Hwan; An, Dongheui; Choi, Sung Eun; Oh, Heung Bum

2008-04-01

Hepatitis B virus (HBV) DNA quantification is necessary for starting and monitoring of antiviral therapy in patients with chronic hepatitis B. This study was intended to assess the clinical performance of Abbott RealTime HBV Quantification kit (Abbott Laboratories, USA). The performance was evaluated in terms of precision, linearity, detection sensitivity, cross-reactivity, and carry-over. A correlation with the Real-Q HBV Quantification kit (BioSewoom Inc., Korea) was also examined using serum samples from 64 patients diagnosed with chronic hepatitis B and underwent lamivudine therapy in Asan Medical Center. We verified the trueness of the system by comparing the outputs with the assigned values of the BBI panel (BBI Diagnostics, USA). Within-run and between-run coefficients of variation (CV) were 3.56-4.71% and 3.03-4.98%, respectively. Linearity was manifested ranging from 53 to 10(9)copies/mL and the detection sensitivity was verified to be 51 copies/mL. None of hepatitis C virus showed cross-reactivity. No cross-contamination occurred when negative and positive samples were alternatively placed in a row. It showed a good correlation with the Real-Q HBV (r(2)=0.9609) and the test results for the BBI panel were also well agreed to the assigned values (r(2)=0.9933). The performance of Abbott RealTime HBV Quantification kit was excellent; thus, it should be widely used in starting and monitoring of antiviral therapy in Korean patients with chronic hepatitis B.

A novel approach to the dynamical complexity of the Earth's magnetosphere at geomagnetic storm time-scales based on recurrences

NASA Astrophysics Data System (ADS)

Donner, Reik; Balasis, Georgios; Stolbova, Veronika; Wiedermann, Marc; Georgiou, Marina; Kurths, Jürgen

2016-04-01

Magnetic storms are the most prominent global manifestations of out-of-equilibrium magnetospheric dynamics. Investigating the dynamical complexity exhibited by geomagnetic observables can provide valuable insights into relevant physical processes as well as temporal scales associated with this phenomenon. In this work, we introduce several innovative data analysis techniques enabling a quantitative analysis of the Dst index non-stationary behavior. Using recurrence quantification analysis (RQA) and recurrence network analysis (RNA), we obtain a variety of complexity measures serving as markers of quiet- and storm-time magnetospheric dynamics. We additionally apply these techniques to the main driver of Dst index variations, the V BSouth coupling function and interplanetary medium parameters Bz and Pdyn in order to discriminate internal processes from the magnetosphere's response directly induced by the external forcing by the solar wind. The derived recurrence-based measures allow us to improve the accuracy with which magnetospheric storms can be classified based on ground-based observations. The new methodology presented here could be of significant interest for the space weather research community working on time series analysis for magnetic storm forecasts.

Complexity in congestive heart failure: A time-frequency approach

NASA Astrophysics Data System (ADS)

Banerjee, Santo; Palit, Sanjay K.; Mukherjee, Sayan; Ariffin, MRK; Rondoni, Lamberto

2016-03-01

Reconstruction of phase space is an effective method to quantify the dynamics of a signal or a time series. Various phase space reconstruction techniques have been investigated. However, there are some issues on the optimal reconstructions and the best possible choice of the reconstruction parameters. This research introduces the idea of gradient cross recurrence (GCR) and mean gradient cross recurrence density which shows that reconstructions in time frequency domain preserve more information about the dynamics than the optimal reconstructions in time domain. This analysis is further extended to ECG signals of normal and congestive heart failure patients. By using another newly introduced measure—gradient cross recurrence period density entropy, two classes of aforesaid ECG signals can be classified with a proper threshold. This analysis can be applied to quantifying and distinguishing biomedical and other nonlinear signals.

Movement dynamics reflect a functional role for weak coupling and role structure in dyadic problem solving.

PubMed

Abney, Drew H; Paxton, Alexandra; Dale, Rick; Kello, Christopher T

2015-11-01

Successful interaction requires complex coordination of body movements. Previous research has suggested a functional role for coordination and especially synchronization (i.e., time-locked movement across individuals) in different types of human interaction contexts. Although such coordination has been shown to be nearly ubiquitous in human interaction, less is known about its function. One proposal is that synchrony supports and facilitates communication (Topics Cogn Sci 1:305-319, 2009). However, questions still remain about what the properties of coordination for optimizing communication might look like. In the present study, dyads worked together to construct towers from uncooked spaghetti and marshmallows. Using cross-recurrence quantification analysis, we found that dyads with loosely coupled gross body movements performed better, supporting recent work suggesting that simple synchrony may not be the key to effective performance (Riley et al. 2011). We also found evidence that leader-follower dynamics-when sensitive to the specific role structure of the interaction-impact task performance. We discuss our results with respect to the functional role of coordination in human interaction.

Cross-sectional study on comorbidities and adverse events in patients with advanced and recurrent ovarian cancer in France.

PubMed

Le Saux, Olivia; Taylor, Aliki; Chia, Victoria; Pillas, Demetris; Kaur, Moninder; Freyer, Gilles

2015-01-01

The purpose of this study was to evaluate the prevalence of comorbidities and adverse events (AEs), and determine the treatment patterns according to platinum-sensitivity status in patients with advanced (stage IIIB-IV) or recurrent epithelial ovarian cancer (EOC). A cross-sectional study was carried out in France with patients over 18 years, diagnosed with advanced (stage IIIB-IV) or recurrent EOC between 2009 and 2012. A total of 23 physicians (oncologists and gynecologists) participated, contributing 127 patients. Data were abstracted by participating physicians into a case report form. Of the 127 patients included, 92 (72.4%) had advanced EOC and 35 (27.6%) had recurrent EOC. A total of 73 comorbidities were reported in 44 patients (34.6%). Vascular (10.2%), metabolic (7.1%), respiratory (5.5%), and psychiatric disorders (5.5%) were the most common types of comorbidities reported. Prevalence of AEs was 74.8%, of which 12.6% were classified as serious. The most common AEs were anemia (16.5%), hematologic events (12.6%), taste change (11.8%), and headache (7.1%). Throughout the follow-up period, twelve patient deaths were reported (six due to disease progression). Of 35 patients with recurrent disease, 16 were highly platinum sensitive (recurrence >12 months after stopping platinum-based therapy), eleven were partially platinum sensitive (recurrence 6-12 months after stopping platinum-based therapy), seven were platinum resistant (recurrence within 6 months of stopping platinum-based therapy or progression while receiving second- or later-line platinum-based therapy), and one was platinum refractory (recurrence within 6 months from the start of first-line platinum-based therapy). In this cross-sectional study of advanced and metastatic ovarian cancer patients, approximately one-third of patients were diagnosed with comorbidities, and approximately three-quarters were diagnosed with AEs (12.6% with severe AEs).

Cardiovascular regulation during sleep quantified by symbolic coupling traces

NASA Astrophysics Data System (ADS)

Suhrbier, A.; Riedl, M.; Malberg, H.; Penzel, T.; Bretthauer, G.; Kurths, J.; Wessel, N.

2010-12-01

Sleep is a complex regulated process with short periods of wakefulness and different sleep stages. These sleep stages modulate autonomous functions such as blood pressure and heart rate. The method of symbolic coupling traces (SCT) is used to analyze and quantify time-delayed coupling of these measurements during different sleep stages. The symbolic coupling traces, defined as the symmetric and diametric traces of the bivariate word distribution matrix, allow the quantification of time-delayed coupling. In this paper, the method is applied to heart rate and systolic blood pressure time series during different sleep stages for healthy controls as well as for normotensive and hypertensive patients with sleep apneas. Using the SCT, significant different cardiovascular mechanisms not only between the deep sleep and the other sleep stages but also between healthy subjects and patients can be revealed. The SCT method is applied to model systems, compared with established methods, such as cross correlation, mutual information, and cross recurrence analysis and demonstrates its advantages especially for nonstationary physiological data. As a result, SCT proves to be more specific in detecting delays of directional interactions than standard coupling analysis methods and yields additional information which cannot be measured by standard parameters of heart rate and blood pressure variability. The proposed method may help to indicate the pathological changes in cardiovascular regulation and also the effects of continuous positive airway pressure therapy on the cardiovascular system.

What'd You Say Again? Recurrence Quantification Analysis as a Method for Analyzing the Dynamics of Discourse in a Reading Strategy Tutor

ERIC Educational Resources Information Center

Allen, Laura K.; Perret, Cecile; Likens, Aaron; McNamara, Danielle S.

2017-01-01

In this study, we investigated the degree to which the cognitive processes in which students engage during reading comprehension could be examined through dynamical analyses of their natural language responses to texts. High school students (n = 142) generated typed self-explanations while reading a science text. They then completed a…

Electrogram morphology recurrence patterns during atrial fibrillation.

PubMed

Ng, Jason; Gordon, David; Passman, Rod S; Knight, Bradley P; Arora, Rishi; Goldberger, Jeffrey J

2014-11-01

Traditional mapping of atrial fibrillation (AF) is limited by changing electrogram morphologies and variable cycle lengths. We tested the hypothesis that morphology recurrence plot analysis would identify sites of stable and repeatable electrogram morphology patterns. AF electrograms recorded from left atrial (LA) and right atrial (RA) sites in 19 patients (10 men; mean age 59 ± 10 years) before AF ablation were analyzed. Morphology recurrence plots for each electrogram recording were created by cross-correlation of each automatically detected activation with every other activation in the recording. A recurrence percentage, the percentage of the most common morphology, and the mean cycle length of activations with the most recurrent morphology were computed. The morphology recurrence plots commonly showed checkerboard patterns of alternating high and low cross-correlation values, indicating periodic recurrences in morphologies. The mean recurrence percentage for all sites and all patients was 38 ± 25%. The highest recurrence percentage per patient averaged 83 ± 17%. The highest recurrence percentage was located in the RA in 5 patients and in the LA in 14 patients. Patients with sites of shortest mean cycle length of activations with the most recurrent morphology in the LA and RA had ablation failure rates of 25% and 100%, respectively (hazard ratio 4.95; P = .05). A new technique to characterize electrogram morphology recurrence demonstrated that there is a distribution of sites with high and low repeatability of electrogram morphologies. Sites with rapid activation of highly repetitive morphology patterns may be critical to sustaining AF. Further testing of this approach to map and ablate AF sources is warranted. Copyright © 2014 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Quantification of intestinal bacterial populations by real-time PCR with a universal primer set and minor groove binder probes: a global approach to the enteric flora.

PubMed

Ott, Stephan J; Musfeldt, Meike; Ullmann, Uwe; Hampe, Jochen; Schreiber, Stefan

2004-06-01

The composition of the human intestinal flora is important for the health status of the host. The global composition and the presence of specific pathogens are relevant to the effects of the flora. Therefore, accurate quantification of all major bacterial populations of the enteric flora is needed. A TaqMan real-time PCR-based method for the quantification of 20 dominant bacterial species and groups of the intestinal flora has been established on the basis of 16S ribosomal DNA taxonomy. A PCR with conserved primers was used for all reactions. In each real-time PCR, a universal probe for quantification of total bacteria and a specific probe for the species in question were included. PCR with conserved primers and the universal probe for total bacteria allowed relative and absolute quantification. Minor groove binder probes increased the sensitivity of the assays 10- to 100-fold. The method was evaluated by cross-reaction experiments and quantification of bacteria in complex clinical samples from healthy patients. A sensitivity of 10(1) to 10(3) bacterial cells per sample was achieved. No significant cross-reaction was observed. The real-time PCR assays presented may facilitate understanding of the intestinal bacterial flora through a normalized global estimation of the major contributing species.

Quantitative proteomics analysis of early recurrence/metastasis of huge hepatocellular carcinoma following radical resection

PubMed Central

2014-01-01

Background Hepatic resection is the preferred treatment for huge hepatocellular carcinoma (>10 cm in diameter; H-HCC). However, the patients with H-HCC suffer from poor prognosis due to the early recurrence/metastasis. The underlying mechanism of H-HCC’s early recurrence/metastasis is currently not well understood. Results Here, we describe an Isobaric Tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics approach to analyze the early recurrence/metastasis related proteins of H-HCC after radical resection through multidimensional chromatography coupled with tandem mass spectrometry (2DLC-MS/MS). The different protein expression profiles between the early recurrence/metastasis within 6 months(R/M≤6months) and late recurrence/metastasis within 6–12 months after surgery (R/M6-12months) were confirmed and might reveal different underlying molecular mechanisms. We identified 44 and 49 significantly differentially expressed proteins in the R/M≤6months group and the R/M6-12months group compared to the group who had no recurrence within 2 years post surgery (the NR/M group), respectively. Moreover, among those proteins, S100A12 and AMACR were down regulated in the R/M≤6months group but up-regulated in the R/M6-12months group; and this regulation was further confirmed in mRNA and protein level by Q-PCR, Western-Blot and Immunohistochemistry (IHC). Conclusions This current study presents the first proteomic profile of the early recurrence/metastasis of H-HCC. The results suggest that S100A12 and AMACR might be potential prognostic markers for predicting the early recurrence/metastasis of H-HCC after hepatectomy. PMID:24839399

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

PubMed

Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

2016-09-02

Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNP(xl) for UV-induced peptide-RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark ( Ramus, C.; J. Proteomics 2016 , 132 , 51 - 62 ). The second workflow, RNP(xl), represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

Electrogram Morphology Recurrence Patterns during Atrial Fibrillation

PubMed Central

Ng, Jason; Gordon, David; Passman, Rod S.; Knight, Bradley P.; Arora, Rishi; Goldberger, Jeffrey J.

2014-01-01

Background Traditional mapping of atrial fibrillation (AF) is limited by changing electrogram morphologies and variable cycle lengths. Objective We tested the hypothesis that morphology recurrence plot analysis would identify sites of stable and repeatable electrogram morphology patterns. Methods AF electrograms recorded from left atrial (LA) and right atrial (RA) sites in 19 patients (10 male, 59±10 years old) prior to AF ablation were analyzed. Morphology recurrence plots for each electrogram recording were created by cross-correlation of each automatically detected activation with every other activation in the recording. A recurrence percentage, the percentage of the most common morphology, and the mean cycle length of activations with the most common morphology (CLR) were computed. Results The morphology recurrence plots commonly showed checkerboard patterns of alternating high and low cross correlation values indicating periodic recurrences in morphologies. The mean recurrence percentage for all sites and all patients was 38±25%. The highest recurrence percentage per patient averaged 83±17%. The highest recurrence percentage was located in the RA in 5 patients and in the LA in 14 patients. Patients with sites of shortest CLR in the LA and RA had ablation failure rates of 25% and 100%, respectively (HR=4.95; p=0.05). Conclusions A new technique to characterize electrogram morphology recurrence demonstrated that there is a distribution of sites with high and low repeatability of electrogram morphologies. Sites with rapid activation of highly repetitive morphology patterns may be critical to sustaining AF. Further testing of this approach to map and ablate AF sources is warranted. PMID:25101485

Exact solutions for rate and synchrony in recurrent networks of coincidence detectors.

PubMed

Mikula, Shawn; Niebur, Ernst

2008-11-01

We provide analytical solutions for mean firing rates and cross-correlations of coincidence detector neurons in recurrent networks with excitatory or inhibitory connectivity, with rate-modulated steady-state spiking inputs. We use discrete-time finite-state Markov chains to represent network state transition probabilities, which are subsequently used to derive exact analytical solutions for mean firing rates and cross-correlations. As illustrated in several examples, the method can be used for modeling cortical microcircuits and clarifying single-neuron and population coding mechanisms. We also demonstrate that increasing firing rates do not necessarily translate into increasing cross-correlations, though our results do support the contention that firing rates and cross-correlations are likely to be coupled. Our analytical solutions underscore the complexity of the relationship between firing rates and cross-correlations.

Combinatorics and synchronization in natural semiotics

NASA Astrophysics Data System (ADS)

Orsucci, Franco; Giuliani, Alessandro; Webber, Charles; Zbilut, Joseph; Fonagy, Peter; Mazza, Marianna

2006-03-01

In this study the derivation of an objective metrics to appreciate the degree of structuring of written and spoken texts is presented. The proposed metrics is based on the scoring of recurrences inside a text by means of the application of recurrence quantification analysis (RQA), a nonlinear technique widely used in other fields of sciences. The adopted approach allowed us to create a ranking of different poems strictly related to their prosodic structure and, more importantly, the possibility to recognize the same structure across different languages, to define a level of structuring typical of spoken texts and identifying the progressive synchronization of a dyadic relation between two speakers in terms of relative complexity of their speeches. These results suggest the possibility of introducing objective measurement methods into humanities studies.

Analysis of Brain Recurrence

NASA Astrophysics Data System (ADS)

Frilot, Clifton; Kim, Paul Y.; Carrubba, Simona; McCarty, David E.; Chesson, Andrew L.; Marino, Andrew A.

Analysis of Brain Recurrence (ABR) is a method for extracting physiologically significant information from the electroencephalogram (EEG), a non-stationary electrical output of the brain, the ultimate complex dynamical system. ABR permits quantification of temporal patterns in the EEG produced by the non-autonomous differential laws that govern brain metabolism. In the context of appropriate experimental and statistical designs, ABR is ideally suited to the task of interpreting the EEG. Present applications of ABR include discovery of a human magnetic sense, increased mechanistic understanding of neuronal membrane processes, diagnosis of degenerative neurological disease, detection of changes in brain metabolism caused by weak environmental electromagnetic fields, objective characterization of the quality of human sleep, and evaluation of sleep disorders. ABR has important beneficial implications for the development of clinical and experimental neuroscience.

Non-random nature of spontaneous mIPSCs in mouse auditory brainstem neurons revealed by recurrence quantification analysis

PubMed Central

Leao, Richardson N; Leao, Fabricio N; Walmsley, Bruce

2005-01-01

A change in the spontaneous release of neurotransmitter is a useful indicator of processes occurring within presynaptic terminals. Linear techniques (e.g. Fourier transform) have been used to analyse spontaneous synaptic events in previous studies, but such methods are inappropriate if the timing pattern is complex. We have investigated spontaneous glycinergic miniature synaptic currents (mIPSCs) in principal cells of the medial nucleus of the trapezoid body. The random versus deterministic (or periodic) nature of mIPSCs was assessed using recurrence quantification analysis. Nonlinear methods were then used to quantify any detected determinism in spontaneous release, and to test for chaotic or fractal patterns. Modelling demonstrated that this procedure is much more sensitive in detecting periodicities than conventional techniques. mIPSCs were found to exhibit periodicities that were abolished by blockade of internal calcium stores with ryanodine, suggesting calcium oscillations in the presynaptic inhibitory terminals. Analysis indicated that mIPSC occurrences were chaotic in nature. Furthermore, periodicities were less evident in congenitally deaf mice than in normal mice, indicating that appropriate neural activity during development is necessary for the expression of deterministic chaos in mIPSC patterns. We suggest that chaotic oscillations of mIPSC occurrences play a physiological role in signal processing in the auditory brainstem. PMID:16271982

Dynamical characteristics of surface EMG signals of hand grasps via recurrence plot.

PubMed

Ouyang, Gaoxiang; Zhu, Xiangyang; Ju, Zhaojie; Liu, Honghai

2014-01-01

Recognizing human hand grasp movements through surface electromyogram (sEMG) is a challenging task. In this paper, we investigated nonlinear measures based on recurrence plot, as a tool to evaluate the hidden dynamical characteristics of sEMG during four different hand movements. A series of experimental tests in this study show that the dynamical characteristics of sEMG data with recurrence quantification analysis (RQA) can distinguish different hand grasp movements. Meanwhile, adaptive neuro-fuzzy inference system (ANFIS) is applied to evaluate the performance of the aforementioned measures to identify the grasp movements. The experimental results show that the recognition rate (99.1%) based on the combination of linear and nonlinear measures is much higher than those with only linear measures (93.4%) or nonlinear measures (88.1%). These results suggest that the RQA measures might be a potential tool to reveal the sEMG hidden characteristics of hand grasp movements and an effective supplement for the traditional linear grasp recognition methods.

Recurrence-plot-based measures of complexity and their application to heart-rate-variability data.

PubMed

Marwan, Norbert; Wessel, Niels; Meyerfeldt, Udo; Schirdewan, Alexander; Kurths, Jürgen

2002-08-01

The knowledge of transitions between regular, laminar or chaotic behaviors is essential to understand the underlying mechanisms behind complex systems. While several linear approaches are often insufficient to describe such processes, there are several nonlinear methods that, however, require rather long time observations. To overcome these difficulties, we propose measures of complexity based on vertical structures in recurrence plots and apply them to the logistic map as well as to heart-rate-variability data. For the logistic map these measures enable us not only to detect transitions between chaotic and periodic states, but also to identify laminar states, i.e., chaos-chaos transitions. The traditional recurrence quantification analysis fails to detect the latter transitions. Applying our measures to the heart-rate-variability data, we are able to detect and quantify the laminar phases before a life-threatening cardiac arrhythmia occurs thereby facilitating a prediction of such an event. Our findings could be of importance for the therapy of malignant cardiac arrhythmias.

Long-range correlations and patterns of recurrence in children and adults' attention to hierarchical displays

PubMed Central

Castillo, Ramon D.; Kloos, Heidi; Holden, John G.; Richardson, Michael J.

2015-01-01

In order to make sense of a scene, a person must pay attention to several levels of nested order, ranging from the most differentiated details of the display to the integrated whole. In adults, research shows that the processes of integration and differentiation have the signature of self-organization. Does the same hold for children? The current study addresses this question with children between 6 and 9 years of age, using two tasks that require attention to hierarchical displays. A group of adults were tested as well, for control purposes. To get at the question of self-organization, reaction times were submitted to a detrended fluctuation analysis and a recurrence quantification analysis. H exponents show a long-range correlations (1/f noise), and recurrence measures (percent determinism, maximum line, entropy, and trend), show a deterministic structure of variability being characteristic of self-organizing systems. Findings are discussed in terms of organism-environment coupling that gives rise to fluid attention to hierarchical displays. PMID:25999862

Application of concepts from cross-recurrence analysis in speech production: an overview and comparison with other nonlinear methods.

PubMed

Lancia, Leonardo; Fuchs, Susanne; Tiede, Mark

2014-06-01

The aim of this article was to introduce an important tool, cross-recurrence analysis, to speech production applications by showing how it can be adapted to evaluate the similarity of multivariate patterns of articulatory motion. The method differs from classical applications of cross-recurrence analysis because no phase space reconstruction is conducted, and a cleaning algorithm removes the artifacts from the recurrence plot. The main features of the proposed approach are robustness to nonstationarity and efficient separation of amplitude variability from temporal variability. The authors tested these claims by applying their method to synthetic stimuli whose variability had been carefully controlled. The proposed method was also demonstrated in a practical application: It was used to investigate the role of biomechanical constraints in articulatory reorganization as a consequence of speeded repetition of CVCV utterances containing a labial and a coronal consonant. Overall, the proposed approach provided more reliable results than other methods, particularly in the presence of high variability. The proposed method is a useful and appropriate tool for quantifying similarity and dissimilarity in patterns of speech articulator movement, especially in such research areas as speech errors and pathologies, where unpredictable divergent behavior is expected.

Levator hiatal area as a risk factor for cystocele recurrence after surgery: a prospective study.

PubMed

Vergeldt, T F M; Notten, K J B; Weemhoff, M; van Kuijk, S M J; Mulder, F E M; Beets-Tan, R G; Vliegen, R F A; Gondrie, E T C M; Bergmans, M G M; Roovers, J P W R; Kluivers, K B

2015-07-01

To investigate whether increased levator hiatal area, measured preoperatively, was independently associated with anatom-ical cystocele recurrence 12 months after anterior colporrhaphy. Multicentre prospective cohort study. Nine teaching hospitals in the Netherlands. Women planned for conventional anterior colporrhaphy without mesh. Women underwent physical examination, translabial three-dimensional (3D) ultrasound and magnetic resonance imaging (MRI) prior to surgery. At 12 months after surgery the physical examination was repeated. Women with and without anatomical cystocele recurrence were compared to assess the association with levator hiatal area on 3D ultrasound, levator hiatal area on MRI, and potential confounding factors. The receiver operating characteristic (ROC) curve was created to quantify the discriminative ability of using levator hiatal area to predict anatomical cystocele recurrence. Of 139 included women, 76 (54.7%) had anatomical cystocele recurrence. Preoperative stage 3 or 4 and increased levator hiatal area during Valsalva on ultrasound were significantly associated with cystocele recurrence, with odds ratios of 3.47 (95% confidence interval, 95% CI 1.66-7.28) and 1.06 (95% CI 1.01-1.11) respectively. The area under the ROC curve was 0.60 (95% CI 0.51-0.70) for levator hiatal area during Valsalva on ultrasound, and 0.65 (95% CI 0.55-0.71) for preoperative Pelvic Organ Prolapse Quantification (POP-Q) stage. Increased levator hiatal area during Valsalva on ultrasound prior to surgery and preoperative stage 3 or 4 are independent risk factors for anatomical cystocele recurrence after anterior colporrhaphy; however, increased levator hiatal area as the sole factor for predicting anatomical cystocele recurrence after surgery shows poor test characteristics. © 2015 Royal College of Obstetricians and Gynaecologists.

A regression tree for identifying combinations of fall risk factors associated to recurrent falling: a cross-sectional elderly population-based study.

PubMed

Kabeshova, A; Annweiler, C; Fantino, B; Philip, T; Gromov, V A; Launay, C P; Beauchet, O

2014-06-01

Regression tree (RT) analyses are particularly adapted to explore the risk of recurrent falling according to various combinations of fall risk factors compared to logistic regression models. The aims of this study were (1) to determine which combinations of fall risk factors were associated with the occurrence of recurrent falls in older community-dwellers, and (2) to compare the efficacy of RT and multiple logistic regression model for the identification of recurrent falls. A total of 1,760 community-dwelling volunteers (mean age ± standard deviation, 71.0 ± 5.1 years; 49.4 % female) were recruited prospectively in this cross-sectional study. Age, gender, polypharmacy, use of psychoactive drugs, fear of falling (FOF), cognitive disorders and sad mood were recorded. In addition, the history of falls within the past year was recorded using a standardized questionnaire. Among 1,760 participants, 19.7 % (n = 346) were recurrent fallers. The RT identified 14 nodes groups and 8 end nodes with FOF as the first major split. Among participants with FOF, those who had sad mood and polypharmacy formed the end node with the greatest OR for recurrent falls (OR = 6.06 with p < 0.001). Among participants without FOF, those who were male and not sad had the lowest OR for recurrent falls (OR = 0.25 with p < 0.001). The RT correctly classified 1,356 from 1,414 non-recurrent fallers (specificity = 95.6 %), and 65 from 346 recurrent fallers (sensitivity = 18.8 %). The overall classification accuracy was 81.0 %. The multiple logistic regression correctly classified 1,372 from 1,414 non-recurrent fallers (specificity = 97.0 %), and 61 from 346 recurrent fallers (sensitivity = 17.6 %). The overall classification accuracy was 81.4 %. Our results show that RT may identify specific combinations of risk factors for recurrent falls, the combination most associated with recurrent falls involving FOF, sad mood and polypharmacy. The FOF emerged as the risk factor strongly associated with recurrent falls. In addition, RT and multiple logistic regression were not sensitive enough to identify the majority of recurrent fallers but appeared efficient in detecting individuals not at risk of recurrent falls.

Exact Solutions for Rate and Synchrony in Recurrent Networks of Coincidence Detectors

PubMed Central

Mikula, Shawn; Niebur, Ernst

2009-01-01

We provide analytical solutions for mean firing rates and cross-correlations of coincidence detector neurons in recurrent networks with excitatory or inhibitory connectivity with rate-modulated steady-state spiking inputs. We use discrete-time finite-state Markov chains to represent network state transition probabilities, which are subsequently used to derive exact analytical solutions for mean firing rates and cross-correlations. As illustrated in several examples, the method can be used for modeling cortical microcircuits and clarifying single-neuron and population coding mechanisms. We also demonstrate that increasing firing rates do not necessarily translate into increasing cross-correlations, though our results do support the contention that firing rates and cross-correlations are likely to be coupled. Our analytical solutions underscore the complexity of the relationship between firing rates and cross-correlations. PMID:18439133

Application of cross recurrence plot for identification of temperature fluctuations synchronization in parallel minichannels

NASA Astrophysics Data System (ADS)

Grzybowski, H.; Mosdorf, R.

2016-09-01

The temperature fluctuations occurring in flow boiling in parallel minichannels with diameter of 1 mm have been experimentally investigated and analysed. The wall temperature was recorded at each minichannel outlet by thermocouple with 0.08 mm diameter probe. The time series where recorded during dynamic two-phase flow instabilities which are accompanied by chaotic temperature fluctuations. Time series were denoised using wavelet decomposition and were analysed using cross recurrence plots (CRP) which enables the study of two time series synchronization.

Principal Components of Recurrence Quantification Analysis of EMG

DTIC Science & Technology

2001-10-25

Springer, 1981, pp. 366-381. 4. M. Fraser and H. L. Swinney, “ Independent coordinates for strange attractors from mutual information ,” Phys. Rev. A...autocorrelation function of s(n), although it has also been argued that the first local minimum of the auto mutual information function is more appropriate [4...recordings from a given subject. T was taken as the lag corresponding to the first minimum of the auto mutual information function, calculated as

Non Linear Assessment of Musical Consonance

NASA Astrophysics Data System (ADS)

Trulla, Lluis Lligoña; Guiliani, Alessandro; Zimatore, Giovanna; Colosimo, Alfredo; Zbilut, Joseph P.

2005-12-01

The position of intervals and the degree of musical consonance can be objectively explained by temporal series formed by mixing two pure sounds covering an octave. This result is achieved by means of Recurrence Quantification Analysis (RQA) without considering neither overtones nor physiological hypotheses. The obtained prediction of a consonance can be considered a novel solution to Galileo's conjecture on the nature of consonance. It constitutes an objective link between musical performance and listeners' hearing activity..

Moderating effects of perceived growth on the association between fear of cancer recurrence and health-related quality of life among adolescent and young adult cancer survivors.

PubMed

Cho, Dalnim; Park, Crystal L

2017-01-01

We examined whether (1) fear of cancer recurrence was related to lower health-related quality of life and (2) perceived growth moderated the link between fear of recurrence and health-related quality of life. About 292 adolescent and young adult cancer survivors (diagnosed with cancer at ages 15-34) completed a cross-sectional survey. Fear of recurrence was related to poorer physical and mental health-related quality of life. The negative association between fear of recurrence and mental health-related quality of life was moderated by perceived growth. Fostering perceived growth may mitigate the adverse associations of fear of recurrence and health-related quality of life.

Children’s looking preference for biological motion may be related to an affinity for mathematical chaos

PubMed Central

Haworth, Joshua L.; Kyvelidou, Anastasia; Fisher, Wayne; Stergiou, Nicholas

2015-01-01

Recognition of biological motion is pervasive in early child development. Further, viewing the movement behavior of others is a primary component of a child’s acquisition of complex, robust movement repertoires, through imitation and real-time coordinated action. We theorize that inherent to biological movements are particular qualities of mathematical chaos and complexity. We further posit that this character affords the rich and complex inter-dynamics throughout early motor development. Specifically, we explored whether children’s preference for biological motion may be related to an affinity for mathematical chaos. Cross recurrence quantification analysis (cRQA) was used to investigate the coordination of gaze and posture with various temporal structures (periodic, chaotic, and aperiodic) of the motion of an oscillating visual stimulus. Children appear to competently perceive and respond to chaotic motion, both in rate (cRQA-percent determinism) and duration (cRQA-maxline) of coordination. We interpret this to indicate that children not only recognize chaotic motion structures, but also have a preference for coordination with them. Further, stratification of our sample (by age) uncovers the suggestion that this preference may become refined with age. PMID:25852600

What Factors Influence Women's Perceptions of their Systemic Recurrence Risk after Breast Cancer Treatment?

PubMed

Lee, Kamaria L; Janz, Nancy K; Zikmund-Fisher, Brian J; Jagsi, Reshma; Wallner, Lauren P; Kurian, Allison W; Katz, Steven J; Abrahamse, Paul; Hawley, Sarah T

2018-01-01

Breast cancer patients' misunderstanding of their systemic cancer recurrence risk has consequences on decision-making and quality of life. Little is known about how women derive their risk estimates. Using Los Angeles and Georgia's SEER registries (2014-2015), a random sample of early-stage breast cancer patients was sent surveys about 2 to 3 months after surgery ( N = 3930; RR, 68%). We conducted an inductive thematic analysis of open-ended responses about why women chose their risk estimates in a uniquely large sub-sample ( N = 1,754). Clinician estimates of systemic recurrence risk were provided for patient sub-groups with DCIS and with low-, intermediate-, and high-risk invasive disease. Women's perceived risk of systemic recurrence (0% to 100%) was categorized as overestimation, reasonably accurate estimation, or underestimation (0% for invasive disease) and was compared across identified factors and by clinical presentation. Women identified 9 main factors related to their clinical experience (e.g., diagnosis and testing; treatment) and non-clinical beliefs (e.g., uncertainty; spirituality). Women who mentioned at least one clinical experience factor were significantly less likely to overestimate their risk (12% v. 43%, P < 0.001). Most women who were influenced by "communication with a clinician" had reasonably accurate recurrence estimates (68%). "Uncertainty" and "family and personal history" were associated with overestimation, particularly for women with DCIS (75%; 84%). "Spirituality, religion, and faith" was associated with an underestimation of risk (63% v. 20%, P < 0.001). The quantification of our qualitative results is subject to any biases that may have occurred during the coding process despite rigorous methodology. Patient-clinician communication is important for breast cancer patients' understanding of their numeric risk of systemic recurrence. Clinician discussions about recurrence risk should address uncertainty and relevance of family and personal history.

Accurate determination of Brillouin frequency based on cross recurrence plot analysis in Brillouin distributed fiber sensor

NASA Astrophysics Data System (ADS)

Haneef, Shahna M.; Srijith, K.; Venkitesh, D.; Srinivasan, B.

2017-04-01

We propose and demonstrate the use of cross recurrence plot analysis (CRPA) to accurately determine the Brillouin shift due to strain and temperature in a Brillouin distributed fiber sensor. This signal processing technique, which is implemented in Brillouin sensors for the first time relies on apriori data i.e, the lineshape of the Brillouin gain spectrum and its similarity with the spectral features measured at different locations along the fiber. Analytical and experimental investigation of the proposed scheme is presented in this paper.

Combining Recurrence Analysis and Automatic Movement Extraction from Video Recordings to Study Behavioral Coupling in Face-to-Face Parent-Child Interactions.

PubMed

López Pérez, David; Leonardi, Giuseppe; Niedźwiecka, Alicja; Radkowska, Alicja; Rączaszek-Leonardi, Joanna; Tomalski, Przemysław

2017-01-01

The analysis of parent-child interactions is crucial for the understanding of early human development. Manual coding of interactions is a time-consuming task, which is a limitation in many projects. This becomes especially demanding if a frame-by-frame categorization of movement needs to be achieved. To overcome this, we present a computational approach for studying movement coupling in natural settings, which is a combination of a state-of-the-art automatic tracker, Tracking-Learning-Detection (TLD), and nonlinear time-series analysis, Cross-Recurrence Quantification Analysis (CRQA). We investigated the use of TLD to extract and automatically classify movement of each partner from 21 video recordings of interactions, where 5.5-month-old infants and mothers engaged in free play in laboratory settings. As a proof of concept, we focused on those face-to-face episodes, where the mother animated an object in front of the infant, in order to measure the coordination between the infants' head movement and the mothers' hand movement. We also tested the feasibility of using such movement data to study behavioral coupling between partners with CRQA. We demonstrate that movement can be extracted automatically from standard definition video recordings and used in subsequent CRQA to quantify the coupling between movement of the parent and the infant. Finally, we assess the quality of this coupling using an extension of CRQA called anisotropic CRQA and show asymmetric dynamics between the movement of the parent and the infant. When combined these methods allow automatic coding and classification of behaviors, which results in a more efficient manner of analyzing movements than manual coding.

Combining Recurrence Analysis and Automatic Movement Extraction from Video Recordings to Study Behavioral Coupling in Face-to-Face Parent-Child Interactions

PubMed Central

López Pérez, David; Leonardi, Giuseppe; Niedźwiecka, Alicja; Radkowska, Alicja; Rączaszek-Leonardi, Joanna; Tomalski, Przemysław

2017-01-01

The analysis of parent-child interactions is crucial for the understanding of early human development. Manual coding of interactions is a time-consuming task, which is a limitation in many projects. This becomes especially demanding if a frame-by-frame categorization of movement needs to be achieved. To overcome this, we present a computational approach for studying movement coupling in natural settings, which is a combination of a state-of-the-art automatic tracker, Tracking-Learning-Detection (TLD), and nonlinear time-series analysis, Cross-Recurrence Quantification Analysis (CRQA). We investigated the use of TLD to extract and automatically classify movement of each partner from 21 video recordings of interactions, where 5.5-month-old infants and mothers engaged in free play in laboratory settings. As a proof of concept, we focused on those face-to-face episodes, where the mother animated an object in front of the infant, in order to measure the coordination between the infants' head movement and the mothers' hand movement. We also tested the feasibility of using such movement data to study behavioral coupling between partners with CRQA. We demonstrate that movement can be extracted automatically from standard definition video recordings and used in subsequent CRQA to quantify the coupling between movement of the parent and the infant. Finally, we assess the quality of this coupling using an extension of CRQA called anisotropic CRQA and show asymmetric dynamics between the movement of the parent and the infant. When combined these methods allow automatic coding and classification of behaviors, which results in a more efficient manner of analyzing movements than manual coding. PMID:29312075

Changes in matrix metalloproteinase network in a spontaneous autoimmune uveitis model.

PubMed

Hofmaier, Florian; Hauck, Stefanie M; Amann, Barbara; Degroote, Roxane L; Deeg, Cornelia A

2011-04-08

Autoimmune uveitis is a sight-threatening disease in which autoreactive T cells cross the blood-retinal barrier. Molecular mechanisms contributing to the loss of eye immune privilege in this autoimmune disease are not well understood. In this study, the authors investigated the changes in the matrix metalloproteinase network in spontaneous uveitis. Matrix metalloproteinase (MMP) MMP2, MMP9, and MMP14 expression and tissue inhibitor of metalloproteinase (TIMP)-2 and lipocalin 2 (LCN2) expression were analyzed using Western blot quantification. Enzyme activities were examined with zymography. Expression patterns of network candidates were revealed with immunohistochemistry, comparing physiological appearance and changes in a spontaneous recurrent uveitis model. TIMP2 protein expression was found to be decreased in both the vitreous and the retina of a spontaneous model for autoimmune uveitis (equine recurrent uveitis [ERU]), and TIMP2 activity was significantly reduced in ERU vitreous. Functionally associated MMPs such as MMP2, MMP14, and MMP9 were found to show altered or shifted expression and activity. Although MMP2 decreased in ERU vitreous, MMP9 expression and activity were found to be increased. These changes were reflected by profound changes within uveitic target tissue, where TIMP2, MMP9, and MMP14 decreased in expression, whereas MMP2 displayed a shifted expression pattern. LCN2, a potential stabilizer of MMP9, was found prominently expressed in equine healthy retina and displayed notable changes in expression patterns accompanied by significant upregulation in autoimmune conditions. Invading cells expressed MMP9 and LCN2. This study implicates a dysregulation or a change in functional protein-protein interactions in this TIMP2-associated protein network, together with altered expression of functionally related MMPs.

Tracking Normalization of Brain Tumor Vasculature by Magnetic Imaging and Proangiogenic Biomarkers

PubMed Central

Hormigo, Adília; Gutin, Philip H.; Rafii, Shahin

2010-01-01

Clinical assessment of the response to antiangiogenic therapy has been cumbersome. A study in this issue of Cancer Cell demonstrates that a combination of magnetic resonance imaging (MRI) for quantification of normalized vessels with measurements of circulating levels of proangiogenic factors, including FGF2, SDF1, and viable circulating endothelial cells, provides an effective means to evaluate the response of recurrent glioblastoma to a prototypical pan-VEGF receptor tyrosine kinase inhibitor, AZD2171. PMID:17222788

Identification and quantification analysis of nonlinear dynamics properties of combustion instability in a diesel engine.

PubMed

Yang, Li-Ping; Ding, Shun-Liang; Litak, Grzegorz; Song, En-Zhe; Ma, Xiu-Zhen

2015-01-01

The cycling combustion instabilities in a diesel engine have been analyzed based on chaos theory. The objective was to investigate the dynamical characteristics of combustion in diesel engine. In this study, experiments were performed under the entire operating range of a diesel engine (the engine speed was changed from 600 to 1400 rpm and the engine load rate was from 0% to 100%), and acquired real-time series of in-cylinder combustion pressure using a piezoelectric transducer installed on the cylinder head. Several methods were applied to identify and quantitatively analyze the combustion process complexity in the diesel engine including delay-coordinate embedding, recurrence plot (RP), Recurrence Quantification Analysis, correlation dimension (CD), and the largest Lyapunov exponent (LLE) estimation. The results show that the combustion process exhibits some determinism. If LLE is positive, then the combustion system has a fractal dimension and CD is no more than 1.6 and within the diesel engine operating range. We have concluded that the combustion system of diesel engine is a low-dimensional chaotic system and the maximum values of CD and LLE occur at the lowest engine speed and load. This means that combustion system is more complex and sensitive to initial conditions and that poor combustion quality leads to the decrease of fuel economy and the increase of exhaust emissions.

Cross-national Epidemiology of Panic Disorder and Panic Attacks in the World Mental Health Surveys

PubMed Central

de Jonge, Peter; Roest, Annelieke M.; Lim, Carmen C.W.; Florescu, Silvia E.; Bromet, Evelyn; Stein, Dan; Harris, Meredith; Nakov, Vladimir; Caldas-de-Almeida, Jose Miguel; Levinson, Daphna; Al-Hamzawi, Ali O.; Haro, Josep Maria; Viana, Maria Carmen; Borges, Gui; O’Neill, Siobhan; de Girolamo, Giovanni; Demyttenaere, Koen; Gureje, Oye; Iwata, Noboru; Lee, Sing; Hu, Chiyi; Karam, Aimee; Moskalewicz, Jacek; Kovess-Masfety, Viviane; Navarro-Mateu, Fernando; Browne, Mark Oakley; Piazza, Maria; Posada-Villa, José; Torres, Yolanda; ten Have, Margreet L.; Kessler, Ronald C.; Scott, Kate M.

2016-01-01

Context The scarcity of cross-national reports and the changes in DSM-5 regarding panic disorder (PD) and panic attacks (PAs) call for new epidemiological data on PD and PAs and its subtypes in the general population. Objective To present representative data about the cross-national epidemiology of PD and PAs in accordance with DSM-5 definitions. Design and Setting Nationally representative cross-sectional surveys using the World Health Organization Composite International Diagnostic Interview version 3.0. Participants Respondents (n=142,949) from 25 high, middle and lower-middle income countries across the world aged 18 years or older. Main Outcome Measures PD and presence of single and recurrent PAs. Results Lifetime prevalence of PAs was 13.2% (s.e. 0.1%). Among persons that ever had a PA, the majority had recurrent PAs (66.5%; s.e. 0.5%), while only 12.8% fulfilled DSM-5 criteria for PD. Recurrent PAs were associated with a subsequent onset of a variety of mental disorders (OR 2.0; 95% CI 1.8–2.2) and their course (OR 1.3; 95% CI 1.2–2.4) whereas single PAs were not (OR 1.1; 95% CI 0.9–1.3 and OR 0.7; 95% CI 0.6–0.8). Cross-national lifetime prevalence estimates were 1.7% (s.e. 0.0%) for PD with a median age of onset of 32 (IQR 20–47). Some 80.4% of persons with lifetime PD had a lifetime comorbid mental disorder. Conclusions We extended previous epidemiological data to a cross-national context. The presence of recurrent PAs in particular is associated with subsequent onset and course of mental disorders beyond agoraphobia and PD, and might serve as a generic risk marker for psychopathology. PMID:27775828

Short-term outcomes of the transvaginal minimal mesh procedure for pelvic organ prolapse.

PubMed

Takazawa, Naoko; Fujisaki, Akiko; Yoshimura, Yasukuni; Tsujimura, Akira; Horie, Shigeo

2018-03-01

This study aimed to evaluate the clinical outcomes and complications of transvaginal minimal mesh repair without using commercially available kits for treatment of pelvic organ prolapse (POP). This retrospective cohort study involved 91 women who underwent surgical management of POP with originally designed small mesh between July 2014 and August 2015. This mesh is 56% smaller than the mesh widely used in Japan, and it has only two arms delivered into each right and left sacrospinous ligament. The main study outcome was the anatomic cure rate defined as recurrence of POP quantification (POP-Q) stage II or more. We also assessed changes in the overactive bladder symptom score (OABSS) and prolapse quality of life questionnaire (P-QOL) and evaluated adverse events. Finally, we compared patient backgrounds between the patients with and without recurrence. Prolapse recurred in 10 of 91 patients (11.0%), and all patients with recurrence were diagnosed as POP-Q stage II. As adverse events, only mesh erosion occurred in two (2.2%) and pelvic pain in one (1.1%) of the 91 patients. The OABSS and P-QOL were significantly improved by the operation. When we compared patient backgrounds between the patients with and without recurrence, body mass index was the only factor influencing affecting recurrence. Transvaginal minimal mesh repair resulted in successful outcomes with low mesh-related complications and anatomic recurrence at one year. Furthermore, significant improvement in QOL was offered by this procedure. Our minimal mesh technique should be considered as one treatment option for the management of POP.

Short-term outcomes of the transvaginal minimal mesh procedure for pelvic organ prolapse

PubMed Central

Takazawa, Naoko; Fujisaki, Akiko; Yoshimura, Yasukuni; Tsujimura, Akira

2018-01-01

Purpose This study aimed to evaluate the clinical outcomes and complications of transvaginal minimal mesh repair without using commercially available kits for treatment of pelvic organ prolapse (POP). Materials and Methods This retrospective cohort study involved 91 women who underwent surgical management of POP with originally designed small mesh between July 2014 and August 2015. This mesh is 56% smaller than the mesh widely used in Japan, and it has only two arms delivered into each right and left sacrospinous ligament. The main study outcome was the anatomic cure rate defined as recurrence of POP quantification (POP-Q) stage II or more. We also assessed changes in the overactive bladder symptom score (OABSS) and prolapse quality of life questionnaire (P-QOL) and evaluated adverse events. Finally, we compared patient backgrounds between the patients with and without recurrence. Results Prolapse recurred in 10 of 91 patients (11.0%), and all patients with recurrence were diagnosed as POP-Q stage II. As adverse events, only mesh erosion occurred in two (2.2%) and pelvic pain in one (1.1%) of the 91 patients. The OABSS and P-QOL were significantly improved by the operation. When we compared patient backgrounds between the patients with and without recurrence, body mass index was the only factor influencing affecting recurrence. Conclusions Transvaginal minimal mesh repair resulted in successful outcomes with low mesh-related complications and anatomic recurrence at one year. Furthermore, significant improvement in QOL was offered by this procedure. Our minimal mesh technique should be considered as one treatment option for the management of POP. PMID:29520390

Chaos in brake squeal noise

NASA Astrophysics Data System (ADS)

Oberst, S.; Lai, J. C. S.

2011-02-01

Brake squeal has become an increasing concern to the automotive industry because of warranty costs and the requirement for continued interior vehicle noise reduction. Most research has been directed to either analytical and experimental studies of brake squeal mechanisms or the prediction of brake squeal propensity using finite element methods. By comparison, there is a lack of systematic analysis of brake squeal data obtained from a noise dynamometer. It is well known that brake squeal is a nonlinear transient phenomenon and a number of studies using analytical and experimental models of brake systems (e.g., pin-on-disc) indicate that it could be treated as a chaotic phenomenon. Data obtained from a full brake system on a noise dynamometer were examined with nonlinear analysis techniques. The application of recurrence plots reveals chaotic structures even in noisy data from the squealing events. By separating the time series into different regimes, lower dimensional attractors are isolated and quantified by dynamic invariants such as correlation dimension estimates or Lyapunov exponents. Further analysis of the recurrence plot of squealing events by means of recurrence quantification analysis measures reveals different regimes of laminar and random behaviour, periodicity and chaos-forming recurrent transitions. These results help to classify brake squeal mechanisms and to enhance understanding of friction-related noise phenomena.

Low-molecular-weight model study of peroxide cross-linking of ethylene-propylene-diene rubber using gas chromatography and mass spectrometry II. Addition and combination reactions.

PubMed

Peters, R; van Duin, M; Tonoli, D; Kwakkenbos, G; Mengerink, Y; van Benthem, R A T M; de Koster, C G; Schoenmakers, P J; van der Wal, Sj

2008-08-08

The dicumyl-peroxide-initiated addition and combination reactions of mixtures of alkanes (n-octane, n-decane) and alkenes [5,6-dihydrodicyclopentadiene (DCPDH), 5-ethylidene-2-norbornane (ENBH) and 5-vinylidene-2-norbornane (VNBH)] were studied to mimic the peroxide cross-linking reactions of terpolymerised ethylene, propylene and a diene monomer (EPDM). The reaction products of the mixtures were separated by both gas chromatography (GC) and comprehensive two-dimensional gas chromatography (GCxGC). The separated compounds were identified from their mass spectra and their GC and GCxGC elution pattern. Quantification of the various alkyl/alkyl, alkyl/allyl and allyl/allyl combination products shows that allylic-radicals comprise approximately 60% of the substrate radicals formed. The total concentration of the products formed by combination is found to be independent of the concentration and the type of alkene. The total concentration of the products formed by addition to the alkene increases with increasing concentration of alkene. In addition, the total concentration of the formed addition products depends strongly on the type of the alkene used, viz. VNBH>ENBH approximately DCPDH, which is a consequence of differences in steric hindrance of the unsaturation. The peroxide curing efficiency, defined as the number of moles of cross-linked products formed per mol of peroxide, is 173% using 9% (w/w) 5-vinylidene-2-norbornane (VNBH). This indicates that the addition reaction is recurrent. All these findings are consistent with experimental studies on peroxide curing of EPDM rubber. In addition, the present results provide more-detailed structural information, increasing the understanding of the mechanism of peroxide curing of EPDM. The described approach to use low-molecular-weight model compounds followed by GC-mass spectrometry (MS) and GCxGC-MS analysis is proven to be a very powerful tool to study the cross-linking of EPDM.

A Short Interspersed Nuclear Element (SINE)-Based Real-Time PCR Approach to Detect and Quantify Porcine Component in Meat Products.

PubMed

Zhang, Chi; Fang, Xin; Qiu, Haopu; Li, Ning

2015-01-01

Real-time PCR amplification of mitochondria gene could not be used for DNA quantification, and that of single copy DNA did not allow an ideal sensitivity. Moreover, cross-reactions among similar species were commonly observed in the published methods amplifying repetitive sequence, which hindered their further application. The purpose of this study was to establish a short interspersed nuclear element (SINE)-based real-time PCR approach having high specificity for species detection that could be used in DNA quantification. After massive screening of candidate Sus scrofa SINEs, one optimal combination of primers and probe was selected, which had no cross-reaction with other common meat species. LOD of the method was 44 fg DNA/reaction. Further, quantification tests showed this approach was practical in DNA estimation without tissue variance. Thus, this study provided a new tool for qualitative detection of porcine component, which could be promising in the QC of meat products.

Electrochemical Quantification of the Antioxidant Capacity of Medicinal Plants Using Biosensors

PubMed Central

Rodríguez-Sevilla, Erika; Ramírez-Silva, María-Teresa; Romero-Romo, Mario; Ibarra-Escutia, Pedro; Palomar-Pardavé, Manuel

2014-01-01

The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr) using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA), cross-linking using glutaraldehyde (GA), and cross-linking using GA and human serum albumin (HSA); the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km′, of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km′ (57 ± 7) μM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC) was determined from infusions prepared with “mirto” (Salvia microphylla), “hHierba dulce” (Lippia dulcis) and “salve real” (Lippia alba), medicinal plants commonly used in Mexico. PMID:25111237

Electrochemical quantification of the antioxidant capacity of medicinal plants using biosensors.

PubMed

Rodríguez-Sevilla, Erika; Ramírez-Silva, María-Teresa; Romero-Romo, Mario; Ibarra-Escutia, Pedro; Palomar-Pardavé, Manuel

2014-08-08

The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr) using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA), cross-linking using glutaraldehyde (GA), and cross-linking using GA and human serum albumin (HSA); the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km', of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km' (57 ± 7) µM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC) was determined from infusions prepared with "mirto" (Salvia microphylla), "hHierba dulce" (Lippia dulcis) and "salve real" (Lippia alba), medicinal plants commonly used in Mexico.

Cross-Participant EEG-Based Assessment of Cognitive Workload Using Multi-Path Convolutional Recurrent Neural Networks.

PubMed

Hefron, Ryan; Borghetti, Brett; Schubert Kabban, Christine; Christensen, James; Estepp, Justin

2018-04-26

Applying deep learning methods to electroencephalograph (EEG) data for cognitive state assessment has yielded improvements over previous modeling methods. However, research focused on cross-participant cognitive workload modeling using these techniques is underrepresented. We study the problem of cross-participant state estimation in a non-stimulus-locked task environment, where a trained model is used to make workload estimates on a new participant who is not represented in the training set. Using experimental data from the Multi-Attribute Task Battery (MATB) environment, a variety of deep neural network models are evaluated in the trade-space of computational efficiency, model accuracy, variance and temporal specificity yielding three important contributions: (1) The performance of ensembles of individually-trained models is statistically indistinguishable from group-trained methods at most sequence lengths. These ensembles can be trained for a fraction of the computational cost compared to group-trained methods and enable simpler model updates. (2) While increasing temporal sequence length improves mean accuracy, it is not sufficient to overcome distributional dissimilarities between individuals’ EEG data, as it results in statistically significant increases in cross-participant variance. (3) Compared to all other networks evaluated, a novel convolutional-recurrent model using multi-path subnetworks and bi-directional, residual recurrent layers resulted in statistically significant increases in predictive accuracy and decreases in cross-participant variance.

Cross-Participant EEG-Based Assessment of Cognitive Workload Using Multi-Path Convolutional Recurrent Neural Networks

PubMed Central

Hefron, Ryan; Borghetti, Brett; Schubert Kabban, Christine; Christensen, James; Estepp, Justin

2018-01-01

Applying deep learning methods to electroencephalograph (EEG) data for cognitive state assessment has yielded improvements over previous modeling methods. However, research focused on cross-participant cognitive workload modeling using these techniques is underrepresented. We study the problem of cross-participant state estimation in a non-stimulus-locked task environment, where a trained model is used to make workload estimates on a new participant who is not represented in the training set. Using experimental data from the Multi-Attribute Task Battery (MATB) environment, a variety of deep neural network models are evaluated in the trade-space of computational efficiency, model accuracy, variance and temporal specificity yielding three important contributions: (1) The performance of ensembles of individually-trained models is statistically indistinguishable from group-trained methods at most sequence lengths. These ensembles can be trained for a fraction of the computational cost compared to group-trained methods and enable simpler model updates. (2) While increasing temporal sequence length improves mean accuracy, it is not sufficient to overcome distributional dissimilarities between individuals’ EEG data, as it results in statistically significant increases in cross-participant variance. (3) Compared to all other networks evaluated, a novel convolutional-recurrent model using multi-path subnetworks and bi-directional, residual recurrent layers resulted in statistically significant increases in predictive accuracy and decreases in cross-participant variance. PMID:29701668

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

Recurrence predictive models for patients with hepatocellular carcinoma after radiofrequency ablation using support vector machines with feature selection methods.

PubMed

Liang, Ja-Der; Ping, Xiao-Ou; Tseng, Yi-Ju; Huang, Guan-Tarn; Lai, Feipei; Yang, Pei-Ming

2014-12-01

Recurrence of hepatocellular carcinoma (HCC) is an important issue despite effective treatments with tumor eradication. Identification of patients who are at high risk for recurrence may provide more efficacious screening and detection of tumor recurrence. The aim of this study was to develop recurrence predictive models for HCC patients who received radiofrequency ablation (RFA) treatment. From January 2007 to December 2009, 83 newly diagnosed HCC patients receiving RFA as their first treatment were enrolled. Five feature selection methods including genetic algorithm (GA), simulated annealing (SA) algorithm, random forests (RF) and hybrid methods (GA+RF and SA+RF) were utilized for selecting an important subset of features from a total of 16 clinical features. These feature selection methods were combined with support vector machine (SVM) for developing predictive models with better performance. Five-fold cross-validation was used to train and test SVM models. The developed SVM-based predictive models with hybrid feature selection methods and 5-fold cross-validation had averages of the sensitivity, specificity, accuracy, positive predictive value, negative predictive value, and area under the ROC curve as 67%, 86%, 82%, 69%, 90%, and 0.69, respectively. The SVM derived predictive model can provide suggestive high-risk recurrent patients, who should be closely followed up after complete RFA treatment. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Assessing nonlinear structures in real exchange rates using recurrence plot strategies

NASA Astrophysics Data System (ADS)

Belaire-Franch, Jorge; Contreras, Dulce; Tordera-Lledó, Lorena

2002-11-01

Purchasing power parity (PPP) is an important theory at the basis of a large number of economic models. However, the implication derived from the theory that real exchange rates must follow stationary processes is not conclusively supported by empirical studies. In a recent paper, Serletis and Gogas [Appl. Finance Econ. 10 (2000) 615] show evidence of deterministic chaos in several OECD exchange rates. As a consequence, PPP rejections could be spurious. In this work, we follow a two-stage testing procedure to test for nonlinearities and chaos in real exchange rates, using a new set of techniques designed by Webber and Zbilut [J. Appl. Physiol. 76 (1994) 965], called recurrence quantification analysis (RQA). Our conclusions differ slightly from Serletis and Gogas [Appl. Finance Econ. 10 (2000) 615], but they are also supportive of chaos for some exchange rates.

Chaos-chaos transition of left hemisphere EEGs during standard tasks of Waterloo-Stanford Group Scale of hypnotic susceptibility.

PubMed

Yargholi, Elahe'; Nasrabadi, Ali Motie

2015-01-01

A recent study, recurrence quantification analysis of EEG signals during standard tasks of Waterloo-Stanford Group Scale of hypnotic susceptibility investigated recurrence quantifiers (RQs) of hypnotic electroencephalograph (EEG) signals recorded after hypnotic induction while subjects were doing standard tasks of Waterloo-Stanford Group Scale (WSGS) of hypnotic susceptibility to distinguish subjects of different hypnotizability levels. Following the same analysis, the current study determines the capability of different RQs to distinguish subjects of low, medium and high hypnotizability level and studies the influence of hypnotizability level on underlying dynamic of tasks. Besides, EEG channels were sorted according to the number of their RQs, which differed significantly among subjects of different hypnotizability levels. Another valuable result was determination of major brain regions in observing significant differences in various task types (ideomotors, hallucination, challenge and memory).

Recurrent urethral obstruction secondary to idiopathic renal hematuria in a puppy.

PubMed

Hawthorne, J C; deHaan, J J; Goring, R L; Randall, S R; Kennedy, F S; Stone, E; Zimmerman, K M; McAbee, S W

1998-01-01

A seven-month-old, neutered male Catahoula leopard dog cross was presented for recurrent urethral obstruction and intermittent hematuria. After exploratory laparotomy and ventral cystotomy, unilateral idiopathic renal hematuria was diagnosed based on gross observation of hematuria from the left ureteral catheter. The hematuria resolved after nephrectomy of the left kidney. The histopathological diagnosis was multifocal, acute congestion and intratubular hemorrhage. Although idiopathic renal hematuria has been described previously, this puppy was unique because the hematuria caused recurrent, complete urethral obstruction.

Patterns of recurrence after surgery alone versus preoperative chemoradiotherapy and surgery in the CROSS trials.

PubMed

Oppedijk, Vera; van der Gaast, Ate; van Lanschot, Jan J B; van Hagen, Pieter; van Os, Rob; van Rij, Caroline M; van der Sangen, Maurice J; Beukema, Jannet C; Rütten, Heidi; Spruit, Patty H; Reinders, Janny G; Richel, Dick J; van Berge Henegouwen, Mark I; Hulshof, Maarten C C M

2014-02-10

To analyze recurrence patterns in patients with cancer of the esophagus or gastroesophageal junction treated with either preoperative chemoradiotherapy (CRT) plus surgery or surgery alone. Recurrence pattern was analyzed in patients from the previously published CROSS I and II trials in relation to radiation target volumes. CRT consisted of five weekly courses of paclitaxel and carboplatin combined with a concurrent radiation dose of 41.4 Gy in 1.8-Gy fractions to the tumor and pathologic lymph nodes with margin. Of the 422 patients included from 2001 to 2008, 418 were available for analysis. Histology was mostly adenocarcinoma (75%). Of the 374 patients who underwent resection, 86% were allocated to surgery and 92% to CRT plus surgery. On January 1, 2011, after a minimum follow-up of 24 months (median, 45 months), the overall recurrence rate in the surgery arm was 58% versus 35% in the CRT plus surgery arm. Preoperative CRT reduced locoregional recurrence (LRR) from 34% to 14% (P < .001) and peritoneal carcinomatosis from 14% to 4% (P < .001). There was a small but significant effect on hematogenous dissemination in favor of the CRT group (35% v 29%; P = .025). LRR occurred in 5% within the target volume, in 2% in the margins, and in 6% outside the radiation target volume. In 1%, the exact site in relation to the target volume was unclear. Only 1% had an isolated infield recurrence after CRT plus surgery. Preoperative CRT in patients with esophageal cancer reduced LRR and peritoneal carcinomatosis. Recurrence within the radiation target volume occurred in only 5%, mostly combined with outfield failures.

Distributed multisensory integration in a recurrent network model through supervised learning

NASA Astrophysics Data System (ADS)

Wang, He; Wong, K. Y. Michael

Sensory integration between different modalities has been extensively studied. It is suggested that the brain integrates signals from different modalities in a Bayesian optimal way. However, how the Bayesian rule is implemented in a neural network remains under debate. In this work we propose a biologically plausible recurrent network model, which can perform Bayesian multisensory integration after trained by supervised learning. Our model is composed of two modules, each for one modality. We assume that each module is a recurrent network, whose activity represents the posterior distribution of each stimulus. The feedforward input on each module is the likelihood of each modality. Two modules are integrated through cross-links, which are feedforward connections from the other modality, and reciprocal connections, which are recurrent connections between different modules. By stochastic gradient descent, we successfully trained the feedforward and recurrent coupling matrices simultaneously, both of which resembles the Mexican-hat. We also find that there are more than one set of coupling matrices that can approximate the Bayesian theorem well. Specifically, reciprocal connections and cross-links will compensate each other if one of them is removed. Even though trained with two inputs, the network's performance with only one input is in good accordance with what is predicted by the Bayesian theorem.

A multicenter cohort study of spinal osteoid osteomas: results of surgical treatment and analysis of local recurrence.

PubMed

Quraishi, Nasir A; Boriani, Stefano; Sabou, Silviu; Varga, Peter P; Luzzati, Alessandro; Gokaslan, Ziya L; Fehlings, Michael G; Fisher, Charles G; Dekutoski, Mark B; Rhines, Laurence D; Reynolds, Jeremy J; Germscheid, Niccole M; Bettegowda, Chetan; Williams, Richard P

2017-03-01

Spinal osteoid osteomas are benign primary tumors arising predominantly from the posterior column of the spine. These "osteoblastic" lesions have traditionally been treated with intralesional excision. The purpose of the present study was to review the treatment and local recurrence rates for symptomatic spinal osteoid osteomas. Multicenter ambispective cross-sectional observational cohort study. During the study period, a total of 84 patients (65 males, 19 females) were diagnosed with a spinal osteoid osteoma and received surgical treatment. The mean age at surgery was 21.8 ± 9.0 years (range: 6.7-52.4 years) and the mean follow-up was 2.7 years (13 days-14.5 years). Local recurrence, perioperative morbidity, and cross-sectional survival. Using the AOSpine Knowledge Forum Tumor multicenter ambispective database, surgically treated osteoid osteoma cases were identified. Patient demographic, clinical and diagnostic, treatment, local recurrence, perioperative morbidity, and cross-sectional survival data were collected and retrieved. Descriptive statistics were summarized using mean/standard deviation or frequency/percentage. In our study, most of the tumors were localized in the mobile spine (81 of 84 [96%]); all patients reported pain as a symptom. According to the postoperative assessment, 10 (12%) patients received an en bloc resection with marginal or wide margins, whereas two (2%) patients received en bloc resections with intralesional margins, 69 (82%) patients were treated by piecemeal "intralesional" resection, and three (4%) patients were not assessed. A total of six patients (7%) experienced a local recurrence, all of which occurred in patients who had received an intralesional resection. Benign bone-forming tumors of the spine are uncommon. Most patients in our series underwent a piecemeal resection with intralesional margins. This remains safe with a low local recurrence rate. En bloc excision may provide more chance of complete excision of the nidus but is not mandatory. The importance of complete excision of the nidus cannot be overemphasized. Copyright © 2016 Elsevier Inc. All rights reserved.

Prostate cancer outcome and tissue levels of metal ions

USGS Publications Warehouse

Sarafanov, A.G.; Todorov, T.I.; Centeno, J.A.; MacIas, V.; Gao, W.; Liang, W.-M.; Beam, C.; Gray, Marion A.; Kajdacsy-Balla, A.

2011-01-01

BACKGROUNDThere are several studies examining prostate cancer and exposure to cadmium, iron, selenium, and zinc. Less data are available on the possible influence of these metal ions on prostate cancer outcome. This study measured levels of these ions in prostatectomy samples in order to examine possible associations between metal concentrations and disease outcome.METHODSWe obtained formalin fixed paraffin embedded tissue blocks of prostatectomy samples of 40 patients with PSA recurrence, matched 1:1 (for year of surgery, race, age, Gleason grading, and pathology TNM classification) with tissue blocks from 40 patients without recurrence (n = 80). Case–control pairs were compared for the levels of metals in areas adjacent to tumors. Inductively coupled plasma-mass spectrometry (ICP-MS) was used for quantification of Cd, Fe, Zn, and Se.RESULTSPatients with biochemical (PSA) recurrence of disease had 12% lower median iron (95 µg/g vs. 111 µg/g; P = 0.04) and 21% lower zinc (279 µg/g vs. 346 µg/g; P = 0.04) concentrations in the normal-appearing tissue immediately adjacent to cancer areas. Differences in cadmium (0.489 µg/g vs. 0.439 µg/g; 4% higher) and selenium (1.68 µg/g vs. 1.58 µg/g; 5% higher) levels were not statistically significant in recurrence cases, when compared to non-recurrences (P = 0.40 and 0.21, respectively).CONCLUSIONSThere is an association between low zinc and low iron prostate tissue levels and biochemical recurrence in prostate cancer. Whether these novel findings are a cause or effect of more aggressive tumors, or whether low zinc and iron prostatic levels raise implications for therapy, remains to be investigated. 

Dynamics of intracranial electroencephalographic recordings from epilepsy patients using univariate and bivariate recurrence networks.

PubMed

Subramaniyam, Narayan Puthanmadam; Hyttinen, Jari

2015-02-01

Recently Andrezejak et al. combined the randomness and nonlinear independence test with iterative amplitude adjusted Fourier transform (iAAFT) surrogates to distinguish between the dynamics of seizure-free intracranial electroencephalographic (EEG) signals recorded from epileptogenic (focal) and nonepileptogenic (nonfocal) brain areas of epileptic patients. However, stationarity is a part of the null hypothesis for iAAFT surrogates and thus nonstationarity can violate the null hypothesis. In this work we first propose the application of the randomness and nonlinear independence test based on recurrence network measures to distinguish between the dynamics of focal and nonfocal EEG signals. Furthermore, we combine these tests with both iAAFT and truncated Fourier transform (TFT) surrogate methods, which also preserves the nonstationarity of the original data in the surrogates along with its linear structure. Our results indicate that focal EEG signals exhibit an increased degree of structural complexity and interdependency compared to nonfocal EEG signals. In general, we find higher rejections for randomness and nonlinear independence tests for focal EEG signals compared to nonfocal EEG signals. In particular, the univariate recurrence network measures, the average clustering coefficient C and assortativity R, and the bivariate recurrence network measure, the average cross-clustering coefficient C(cross), can successfully distinguish between the focal and nonfocal EEG signals, even when the analysis is restricted to nonstationary signals, irrespective of the type of surrogates used. On the other hand, we find that the univariate recurrence network measures, the average path length L, and the average betweenness centrality BC fail to distinguish between the focal and nonfocal EEG signals when iAAFT surrogates are used. However, these two measures can distinguish between focal and nonfocal EEG signals when TFT surrogates are used for nonstationary signals. We also report an improvement in the performance of nonlinear prediction error N and nonlinear interdependence measure L used by Andrezejak et al., when TFT surrogates are used for nonstationary EEG signals. We also find that the outcome of the nonlinear independence test based on the average cross-clustering coefficient C(cross) is independent of the outcome of the randomness test based on the average clustering coefficient C. Thus, the univariate and bivariate recurrence network measures provide independent information regarding the dynamics of the focal and nonfocal EEG signals. In conclusion, recurrence network analysis combined with nonstationary surrogates can be applied to derive reliable biomarkers to distinguish between epileptogenic and nonepileptogenic brain areas using EEG signals.

Improving the understanding of sleep apnea characterization using Recurrence Quantification Analysis by defining overall acceptable values for the dimensionality of the system, the delay, and the distance threshold

PubMed Central

Navarro-Mesa, Juan L.; Juliá-Serdá, Gabriel; Ramírez-Ávila, G. Marcelo; Ravelo-García, Antonio G.

2018-01-01

Our contribution focuses on the characterization of sleep apnea from a cardiac rate point of view, using Recurrence Quantification Analysis (RQA), based on a Heart Rate Variability (HRV) feature selection process. Three parameters are crucial in RQA: those related to the embedding process (dimension and delay) and the threshold distance. There are no overall accepted parameters for the study of HRV using RQA in sleep apnea. We focus on finding an overall acceptable combination, sweeping a range of values for each of them simultaneously. Together with the commonly used RQA measures, we include features related to recurrence times, and features originating in the complex network theory. To the best of our knowledge, no author has used them all for sleep apnea previously. The best performing feature subset is entered into a Linear Discriminant classifier. The best results in the “Apnea-ECG Physionet database” and the “HuGCDN2014 database” are, according to the area under the receiver operating characteristic curve, 0.93 (Accuracy: 86.33%) and 0.86 (Accuracy: 84.18%), respectively. Our system outperforms, using a relatively small set of features, previously existing studies in the context of sleep apnea. We conclude that working with dimensions around 7–8 and delays about 4–5, and using for the threshold distance the Fixed Amount of Nearest Neighbours (FAN) method with 5% of neighbours, yield the best results. Therefore, we would recommend these reference values for future work when applying RQA to the analysis of HRV in sleep apnea. We also conclude that, together with the commonly used vertical and diagonal RQA measures, there are newly used features that contribute valuable information for apnea minutes discrimination. Therefore, they are especially interesting for characterization purposes. Using two different databases supports that the conclusions reached are potentially generalizable, and are not limited by database variability. PMID:29621264

Improving the understanding of sleep apnea characterization using Recurrence Quantification Analysis by defining overall acceptable values for the dimensionality of the system, the delay, and the distance threshold.

PubMed

Martín-González, Sofía; Navarro-Mesa, Juan L; Juliá-Serdá, Gabriel; Ramírez-Ávila, G Marcelo; Ravelo-García, Antonio G

2018-01-01

Our contribution focuses on the characterization of sleep apnea from a cardiac rate point of view, using Recurrence Quantification Analysis (RQA), based on a Heart Rate Variability (HRV) feature selection process. Three parameters are crucial in RQA: those related to the embedding process (dimension and delay) and the threshold distance. There are no overall accepted parameters for the study of HRV using RQA in sleep apnea. We focus on finding an overall acceptable combination, sweeping a range of values for each of them simultaneously. Together with the commonly used RQA measures, we include features related to recurrence times, and features originating in the complex network theory. To the best of our knowledge, no author has used them all for sleep apnea previously. The best performing feature subset is entered into a Linear Discriminant classifier. The best results in the "Apnea-ECG Physionet database" and the "HuGCDN2014 database" are, according to the area under the receiver operating characteristic curve, 0.93 (Accuracy: 86.33%) and 0.86 (Accuracy: 84.18%), respectively. Our system outperforms, using a relatively small set of features, previously existing studies in the context of sleep apnea. We conclude that working with dimensions around 7-8 and delays about 4-5, and using for the threshold distance the Fixed Amount of Nearest Neighbours (FAN) method with 5% of neighbours, yield the best results. Therefore, we would recommend these reference values for future work when applying RQA to the analysis of HRV in sleep apnea. We also conclude that, together with the commonly used vertical and diagonal RQA measures, there are newly used features that contribute valuable information for apnea minutes discrimination. Therefore, they are especially interesting for characterization purposes. Using two different databases supports that the conclusions reached are potentially generalizable, and are not limited by database variability.

Low-Energy Defibrillation Failure Correction is Possible Through Nonlinear Analysis of Spatiotemporal Arrhythmia Data

NASA Astrophysics Data System (ADS)

Simonotto, Jennifer; Furman, Michael; Beaver, Thomas; Spano, Mark; Kavanagh, Katherine; Iden, Jason; Hu, Gang; Ditto, William

2004-03-01

Explanted Porcine hearts were Langendorff-perfused, administered a voltage-sensitive fluorescent dye (Di-4-ANEPPS) and illuminated with a ND:Yag laser (532 nm); the change in fluorescence resulting from electrical activity on the heart surface was recorded with an 80 x 80 pixel CCD camera at 1000 frames per second. The heart was put into fibrillation with rapid ventricular pacing and shocks were administered close to the defibrillation threshold. Defibrillation failure data was analyzed using synchronization, space-time volume plots and recurrence quantification. Preliminary spatiotemporal synchronization results reveal a short window of time ( 1 second) after defibrillation failure in which the disordered electrical activity becomes ordered; this ordered period occurs 4-5 seconds after the defibrillation shock. Recurrence analysis of a single time series confirmed these results, thus opening the avenue for dynamic defibrillators that can detect an optimal window for cardioversion.

Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation.

PubMed

Yang, Jian-Yi; Peng, Zhen-Ling; Yu, Zu-Guo; Zhang, Rui-Jie; Anh, Vo; Wang, Desheng

2009-04-21

In this paper, we intend to predict protein structural classes (alpha, beta, alpha+beta, or alpha/beta) for low-homology data sets. Two data sets were used widely, 1189 (containing 1092 proteins) and 25PDB (containing 1673 proteins) with sequence homology being 40% and 25%, respectively. We propose to decompose the chaos game representation of proteins into two kinds of time series. Then, a novel and powerful nonlinear analysis technique, recurrence quantification analysis (RQA), is applied to analyze these time series. For a given protein sequence, a total of 16 characteristic parameters can be calculated with RQA, which are treated as feature representation of protein sequences. Based on such feature representation, the structural class for each protein is predicted with Fisher's linear discriminant algorithm. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies with step-by-step procedure are 65.8% and 64.2% for 1189 and 25PDB data sets, respectively. With one-against-others procedure used widely, we compare our method with five other existing methods. Especially, the overall accuracies of our method are 6.3% and 4.1% higher for the two data sets, respectively. Furthermore, only 16 parameters are used in our method, which is less than that used by other methods. This suggests that the current method may play a complementary role to the existing methods and is promising to perform the prediction of protein structural classes.

Radiomic signature of infiltration in peritumoral edema predicts subsequent recurrence in glioblastoma: implications for personalized radiotherapy planning.

PubMed

Rathore, Saima; Akbari, Hamed; Doshi, Jimit; Shukla, Gaurav; Rozycki, Martin; Bilello, Michel; Lustig, Robert; Davatzikos, Christos

2018-04-01

Standard surgical resection of glioblastoma, mainly guided by the enhancement on postcontrast T1-weighted magnetic resonance imaging (MRI), disregards infiltrating tumor within the peritumoral edema region (ED). Subsequent radiotherapy typically delivers uniform radiation to peritumoral FLAIR-hyperintense regions, without attempting to target areas likely to be infiltrated more heavily. Noninvasive in vivo delineation of the areas of tumor infiltration and prediction of early recurrence in peritumoral ED could assist in targeted intensification of local therapies, thereby potentially delaying recurrence and prolonging survival. This paper presents a method for estimating peritumoral edema infiltration using radiomic signatures determined via machine learning methods, and tests it on 90 patients with de novo glioblastoma. The generalizability of the proposed predictive model was evaluated via cross-validation in a discovery cohort ([Formula: see text]) and was subsequently evaluated in a replication cohort ([Formula: see text]). Spatial maps representing the likelihood of tumor infiltration and future early recurrence were compared with regions of recurrence on postresection follow-up studies with pathology confirmation. The cross-validated accuracy of our predictive infiltration model on the discovery and replication cohorts was 87.51% (odds ratio = 10.22, sensitivity = 80.65, and specificity = 87.63) and 89.54% (odds ratio = 13.66, sensitivity = 97.06, and specificity = 76.73), respectively. The radiomic signature of the recurrent tumor region revealed higher vascularity and cellularity when compared with the nonrecurrent region. The proposed model shows evidence that multiparametric pattern analysis from clinical MRI sequences can assist in in vivo estimation of the spatial extent and pattern of tumor recurrence in peritumoral edema, which may guide supratotal resection and/or intensification of postoperative radiation therapy.

Intratumoral stromal morphometry predicts disease recurrence but not response to 5-fluorouracil-results from the QUASAR trial of colorectal cancer.

PubMed

Hutchins, Gordon G A; Treanor, Darren; Wright, Alexander; Handley, Kelly; Magill, Laura; Tinkler-Hundal, Emma; Southward, Katie; Seymour, Matthew; Kerr, David; Gray, Richard; Quirke, Philip

2018-02-01

The biological importance of tumour-associated stroma is becoming increasingly apparent, but its clinical utility remains ill-defined. For stage II/Dukes B colorectal cancer (CRC), clinical biomarkers are urgently required to direct therapeutic options. We report here prognostic/predictive analyses, and molecular associations, of stromal morphometric quantification in the Quick and Simple and Reliable (QUASAR) trial of CRC. Relative proportions of tumour epithelium (PoT) or stroma (PoS) were morphometrically quantified on digitised haematoxylin and eosin (H&E) sections derived from 1800 patients enrolled in QUASAR, which randomised 3239 (91% stage II) CRC patients between adjuvant fluorouracil/folinic acid (FUFA) chemotherapy and observation. The prognostic and predictive values of PoT/PoS measurements were determined by the use of stratified log-rank analyses. A high proportion of tumour stroma (≥50%) was associated with an increased recurrence risk: 31.3% (143/457) recurrence for ≥50% versus 21.9% (294/1343) for <50% [rate ratio (RR) 1.62; 95% confidence interval (CI) 1.30-2.02; P < 0.0001]. Of patients with stromal proportions of ≥65%, 40% (46/115) had recurrent disease within 10 years. The adverse prognostic effect of a high stromal proportion was independent of established prognostic variables, and was maintained in stage II/Dukes B patients (RR 1.62; 95% CI 1.26-2.08; P = 0.0002). KRAS mutation in the presence of a high stromal proportion augmented recurrence risk (RR 2.93; 95% CI 1.87-4.59; P = 0.0005). Stromal morphometry did not predict response to FUFA chemotherapy. Simple digital morphometry applied to a single representative H&E section identifies CRC patients with a >50% higher risk of disease recurrence. This technique can reliably partition patients into subpopulations with different risks of tumour recurrence in a simple and cost-effective manner. Further prospective validation is warranted. © 2017 John Wiley & Sons Ltd.

Evaluation of quantification methods for real-time PCR minor groove binding hybridization probe assays.

PubMed

Durtschi, Jacob D; Stevenson, Jeffery; Hymas, Weston; Voelkerding, Karl V

2007-02-01

Real-time PCR data analysis for quantification has been the subject of many studies aimed at the identification of new and improved quantification methods. Several analysis methods have been proposed as superior alternatives to the common variations of the threshold crossing method. Notably, sigmoidal and exponential curve fit methods have been proposed. However, these studies have primarily analyzed real-time PCR with intercalating dyes such as SYBR Green. Clinical real-time PCR assays, in contrast, often employ fluorescent probes whose real-time amplification fluorescence curves differ from those of intercalating dyes. In the current study, we compared four analysis methods related to recent literature: two versions of the threshold crossing method, a second derivative maximum method, and a sigmoidal curve fit method. These methods were applied to a clinically relevant real-time human herpes virus type 6 (HHV6) PCR assay that used a minor groove binding (MGB) Eclipse hybridization probe as well as an Epstein-Barr virus (EBV) PCR assay that used an MGB Pleiades hybridization probe. We found that the crossing threshold method yielded more precise results when analyzing the HHV6 assay, which was characterized by lower signal/noise and less developed amplification curve plateaus. In contrast, the EBV assay, characterized by greater signal/noise and amplification curves with plateau regions similar to those observed with intercalating dyes, gave results with statistically similar precision by all four analysis methods.

Structure-related statistical singularities along protein sequences: a correlation study.

PubMed

Colafranceschi, Mauro; Colosimo, Alfredo; Zbilut, Joseph P; Uversky, Vladimir N; Giuliani, Alessandro

2005-01-01

A data set composed of 1141 proteins representative of all eukaryotic protein sequences in the Swiss-Prot Protein Knowledge base was coded by seven physicochemical properties of amino acid residues. The resulting numerical profiles were submitted to correlation analysis after the application of a linear (simple mean) and a nonlinear (Recurrence Quantification Analysis, RQA) filter. The main RQA variables, Recurrence and Determinism, were subsequently analyzed by Principal Component Analysis. The RQA descriptors showed that (i) within protein sequences is embedded specific information neither present in the codes nor in the amino acid composition and (ii) the most sensitive code for detecting ordered recurrent (deterministic) patterns of residues in protein sequences is the Miyazawa-Jernigan hydrophobicity scale. The most deterministic proteins in terms of autocorrelation properties of primary structures were found (i) to be involved in protein-protein and protein-DNA interactions and (ii) to display a significantly higher proportion of structural disorder with respect to the average data set. A study of the scaling behavior of the average determinism with the setting parameters of RQA (embedding dimension and radius) allows for the identification of patterns of minimal length (six residues) as possible markers of zones specifically prone to inter- and intramolecular interactions.

Regenerating time series from ordinal networks.

PubMed

McCullough, Michael; Sakellariou, Konstantinos; Stemler, Thomas; Small, Michael

2017-03-01

Recently proposed ordinal networks not only afford novel methods of nonlinear time series analysis but also constitute stochastic approximations of the deterministic flow time series from which the network models are constructed. In this paper, we construct ordinal networks from discrete sampled continuous chaotic time series and then regenerate new time series by taking random walks on the ordinal network. We then investigate the extent to which the dynamics of the original time series are encoded in the ordinal networks and retained through the process of regenerating new time series by using several distinct quantitative approaches. First, we use recurrence quantification analysis on traditional recurrence plots and order recurrence plots to compare the temporal structure of the original time series with random walk surrogate time series. Second, we estimate the largest Lyapunov exponent from the original time series and investigate the extent to which this invariant measure can be estimated from the surrogate time series. Finally, estimates of correlation dimension are computed to compare the topological properties of the original and surrogate time series dynamics. Our findings show that ordinal networks constructed from univariate time series data constitute stochastic models which approximate important dynamical properties of the original systems.

Regenerating time series from ordinal networks

NASA Astrophysics Data System (ADS)

McCullough, Michael; Sakellariou, Konstantinos; Stemler, Thomas; Small, Michael

2017-03-01

Recently proposed ordinal networks not only afford novel methods of nonlinear time series analysis but also constitute stochastic approximations of the deterministic flow time series from which the network models are constructed. In this paper, we construct ordinal networks from discrete sampled continuous chaotic time series and then regenerate new time series by taking random walks on the ordinal network. We then investigate the extent to which the dynamics of the original time series are encoded in the ordinal networks and retained through the process of regenerating new time series by using several distinct quantitative approaches. First, we use recurrence quantification analysis on traditional recurrence plots and order recurrence plots to compare the temporal structure of the original time series with random walk surrogate time series. Second, we estimate the largest Lyapunov exponent from the original time series and investigate the extent to which this invariant measure can be estimated from the surrogate time series. Finally, estimates of correlation dimension are computed to compare the topological properties of the original and surrogate time series dynamics. Our findings show that ordinal networks constructed from univariate time series data constitute stochastic models which approximate important dynamical properties of the original systems.

Clinical and Histopathologic Assessment of Facial Melasma After Low-Fluence Q-Switched Neodymium-Doped Yttrium Aluminium Garnet Laser.

PubMed

Hofbauer Parra, Camila Anna; Careta, Mariana Figueroa; Valente, Neusa Yuriko Sakai; de Sanches Osório, Nuno Eduardo Guimaraes; Torezan, Luis Antonio Ribeiro

2016-04-01

Melasma is a frequent and difficult to treat skin disorder. Results of laser therapy are inconsistent. To determine the safety and efficacy of low-fluence Q-switched neodymium-doped yttrium aluminum garnet (QS Nd:YAG) laser for melasma treatment and assess recurrence rates and histopathologic findings before and after treatment. Twenty patients were treated with 10 weekly sessions of low-fluence 1064-nm QS Nd:YAG laser at 1-week intervals. The modified Melasma Area and Severity Index (mMASI) score was evaluated at baseline; 1 week; and 1, 3, and 6 months after treatment. Epidermal melanin quantification was performed on 10 biopsy samples and compared before and after treatment. All patients showed improvement by mMASI scores, range (21%-75%) compared with that at baseline. No permanent side effects occurred. The recurrence rate was 81%. By histopathology, a slight, nonsignificant (p = .305) decrease in melanin deposition was seen in all layers of the epidermis 1 week after the laser treatments ended. The results confirm the safety and effectiveness of low-fluence QS Nd:YAG laser for treating melasma; however, the high recurrence suggests poor long-term results when the laser is used as a monotherapy.

Tumor-treating fields plus chemotherapy versus chemotherapy alone for glioblastoma at first recurrence: a post hoc analysis of the EF-14 trial

PubMed Central

Kesari, Santosh; Ram, Zvi

2017-01-01

Background: This post hoc analysis of the EF-14 trial (NCT00916409) of tumor-treating fields (TTFields) plus temozolomide versus temozolomide alone in newly diagnosed glioblastoma compared the efficacy of TTFields plus chemotherapy (physician’s choice) versus chemotherapy alone after first recurrence. Methods: Patients on TTFields plus temozolomide continued TTFields plus second-line chemotherapy after first recurrence. Some patients on temozolomide alone crossed over after approval of TTFields for recurrent GBM. The primary efficacy outcome was overall survival (OS). Results: After disease progression, 131 patients received TTFields plus chemotherapy and 73 chemotherapy alone. Thirteen patients in the original temozolomide-alone group crossed over to receive TTFields plus chemotherapy after disease progression, resulting in 144 patients receiving TTFields plus chemotherapy and 60 chemotherapy alone. Median follow-up was 12.6 months. Bevacizumab, alone or with cytotoxic chemotherapy, was the most frequent treatment. Median OS in the TTFields plus chemotherapy group was significantly longer versus chemotherapy alone (11.8 vs 9.2 months; HR: 0.70; 95% CI, 0.48–1.00; p=0.049). TTFields showed a low toxicity safety profile, as previously reported, with no grade 3/4 device-related adverse events. Conclusion: TTFields plus chemotherapy after first disease recurrence on TTFields plus temozolomide or temozolomide alone prolonged OS in patients in the EF-14 trial. PMID:28399638

The Stance Leads the Dance: The Emergence of Role in a Joint Supra-Postural Task

PubMed Central

Davis, Tehran J.; Pinto, Gabriela B.; Kiefer, Adam W.

2017-01-01

Successfully meeting a shared goal usually requires co-actors to adopt complementary roles. However, in many cases, who adopts what role is not explicitly predetermined, but instead emerges as a consequence of the differences in the individual abilities and constraints imposed upon each actor. Perhaps the most basic of roles are leader and follower. Here, we investigated the emergence of “leader-follower” dynamics in inter-personal coordination using a joint supra-postural task paradigm (Ramenzoni et al., 2011; Athreya et al., 2014). Pairs of actors were tasked with holding two objects in alignment (each actor manually controlled one of the objects) as they faced different demands for stance (stable vs. difficult) and control (which actor controlled the larger or smaller object). Our results indicate that when actors were in identical stances, neither led the inter-personal (between actors) coordination by any systematic fashion. Alternatively, when asymmetries in postural demands were introduced, the actor with the more difficult stance led the coordination (as determined using cross-recurrence quantification analysis). Moreover, changes in individual stance difficulty resulted in similar changes in the structure of both intra-personal (individual) and inter-personal (dyadic) coordination, suggesting a scale invariance of the task dynamics. Implications for the study of interpersonal coordination are discussed. PMID:28536547

Verbal interactional dominance and coordinative structure of speech rhythms of staff and clients with an intellectual disability.

PubMed

Reuzel, Ellen; Embregts, Petri J C M; Bosman, Anna M T; Cox, Ralf F A; van Nieuwenhuijzen, Maroesjka; Jahoda, Andrew

2014-10-01

Social interactions between staff and clients with an intellectual disability contain synchronized turn-taking patterns. Synchrony can increase rapport and cooperation between individuals. This study investigated whether verbal interactional dominance and balance, an indication of attunement between staff and clients with ID, are associated with synchrony of turn-taking patterns during staff-client interactions and whether the level of dominance and balance is related to the observed quality of the social interactions. Nineteen staff members video-recorded a social interaction with one of their clients in which the client asked for support. The recordings were analyzed using Cross Recurrence Quantification Analysis and Initiative Response Analysis. Fifteen staff observers as well as client observers completed a questionnaire on the quality of the video-recorded interactions. Staff and clients' patterns of verbal interactional dominance and balance were associated with the synchrony of their turn-taking behaviors. Staff's dominance was associated with a higher level of synchrony of turn taking, whereas client's dominance was associated with a lower level of synchrony. The patterns of verbal interactional dominance and balance were associated with staff observer reports about the quality of the interactions. The study suggested that staff and clients have a tendency to be sensitive to different aspects of interactions, which in turn may have different functions.

Multilevel Boundary Crossing in a Professional Development School Partnership

ERIC Educational Resources Information Center

Akkerman, Sanne; Bruining, Ton

2016-01-01

This study aims to understand the recurrent challenges of professional development school (PDS) partnerships experienced by many countries. It does so by conceptualizing PDS partnerships as endeavors to cross institutionally and epistemologically developed boundaries between teacher education, schooling, and academic research. After introducing…

An evaluation of dynamic mutuality measurements and methods in cyclic time series

NASA Astrophysics Data System (ADS)

Xia, Xiaohua; Huang, Guitian; Duan, Na

2010-12-01

Several measurements and techniques have been developed to detect dynamic mutuality and synchronicity of time series in econometrics. This study aims to compare the performances of five methods, i.e., linear regression, dynamic correlation, Markov switching models, concordance index and recurrence quantification analysis, through numerical simulations. We evaluate the abilities of these methods to capture structure changing and cyclicity in time series and the findings of this paper would offer guidance to both academic and empirical researchers. Illustration examples are also provided to demonstrate the subtle differences of these techniques.

Quantification of susceptibility change at high-concentrated SPIO-labeled target by characteristic phase gradient recognition.

PubMed

Zhu, Haitao; Nie, Binbin; Liu, Hua; Guo, Hua; Demachi, Kazuyuki; Sekino, Masaki; Shan, Baoci

2016-05-01

Phase map cross-correlation detection and quantification may produce highlighted signal at superparamagnetic iron oxide nanoparticles, and distinguish them from other hypointensities. The method may quantify susceptibility change by performing least squares analysis between a theoretically generated magnetic field template and an experimentally scanned phase image. Because characteristic phase recognition requires the removal of phase wrap and phase background, additional steps of phase unwrapping and filtering may increase the chance of computing error and enlarge the inconsistence among algorithms. To solve problem, phase gradient cross-correlation and quantification method is developed by recognizing characteristic phase gradient pattern instead of phase image because phase gradient operation inherently includes unwrapping and filtering functions. However, few studies have mentioned the detectable limit of currently used phase gradient calculation algorithms. The limit may lead to an underestimation of large magnetic susceptibility change caused by high-concentrated iron accumulation. In this study, mathematical derivation points out the value of maximum detectable phase gradient calculated by differential chain algorithm in both spatial and Fourier domain. To break through the limit, a modified quantification method is proposed by using unwrapped forward differentiation for phase gradient generation. The method enlarges the detectable range of phase gradient measurement and avoids the underestimation of magnetic susceptibility. Simulation and phantom experiments were used to quantitatively compare different methods. In vivo application performs MRI scanning on nude mice implanted by iron-labeled human cancer cells. Results validate the limit of detectable phase gradient and the consequent susceptibility underestimation. Results also demonstrate the advantage of unwrapped forward differentiation compared with differential chain algorithms for susceptibility quantification at high-concentrated iron accumulation. Copyright © 2015 Elsevier Inc. All rights reserved.

Flood profiles for lower Brooker Creek, west-central Florida

USGS Publications Warehouse

Murphy, W.R.

1978-01-01

Flood heights are computed for a range of recurrence intervals for a 12.6 mile reach of Brooker Creek, beginning at the mouth at Lake Tarpon. A Geological Survey step-backwater computer program, E431, was used in these analyses using: (1) Stream and valley cross-section geometry and roughness data; (2) Recurrence interval flood-peak discharges; (3) Recurrence interval starting elevations; (4) Gaging station stage-discharge relations. Flood heights may be plotted versus distance above stream mouth and connected to construct flood profiles. They may also be used to indicate areas of inundation on detailed topographic maps.

Theoretical and experimental quantification of doubly and singly differential cross sections for electron-induced ionization of isolated tetrahydrofuran molecules

DOE PAGES

Champion, Christophe; Quinto, Michele A.; Bug, Marion U.; ...

2014-07-29

Electron-induced ionization of the commonly used surrogate of the DNA sugar-phosphate backbone, namely, the tetrahydrofuran molecule, is here theoretically described within the 1 st Born approximation by means of quantum-mechanical approach. Comparisons between theory and recent experiments are reported in terms of doubly and singly differential cross sections.

Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China.

PubMed

Wang, Li-Ping; Lei, Kun

2016-12-01

Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

Flooding and sedimentation in Wheeling Creek basin, Belmont County, Ohio

USGS Publications Warehouse

Kolva, J.R.; Koltun, G.F.

1987-01-01

The Wheeling Creek basin, which is located primarily in Belmont County, Ohio, experienced three damaging floods and four less severe floods during the 29-month period from February 1979 through June 1981. Residents of the basin became concerned about factors that could have affected the severity and frequency of out-of-bank floods. In response to those concerns, the U.S. Geological Survey, in cooperation with the Ohio Department of Natural Resources, undertook a study to estimate peak discharges and recurrence intervals for the seven floods of interest, provide information on current and historical mining-related stream-channel fill or scour, and examine storm-period subbasin contributions to the sediment load in Wheeling Creek. Streamflow data for adjacent basins, rainfall data, and, in two cases, flood-profile data were used in conjunction with streamflow data subsequently collected on Wheeling Creek to provide estimates of peak discharge for the seven floods that occurred from February 1979 through June 1981. Estimates of recurrence intervals were assigned to the Peak discharges on the basin of regional regression equations that relate selected basin characteristics to peak discharge with fixed recurrence intervals. These estimates indicate that a statistically unusual number of floods with recurrence intervals of 2 years or more occurred within that time period. Three cross sections located on Wheeling Creek and four located on tributaries were established and surveyed quarterly for approximately 2 years. No evidence of appreciable stream-channel fill or scour was observed at any of the cross sections, although minor profile changes were apparent at some locations. Attempts were made to obtain historical cross-section profile data for comparison with current cross-section profiles; however, no usable data were found. Excavations of stream-bottom materials were made near the three main-stem cross-section locations and near the mouth of Jug Run. The bottom materials were examined for evidence of recently deposited sediments of mining-related origin. The only evidence of appreciable mining-related sediment deposition was found at Jug Run, and, to a lesser extent, at one main-stem site.

Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis.

PubMed

Ding, Hang

2014-01-01

Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

Pre- and post-natal exposure to antibiotics and the development of eczema, recurrent wheezing and atopic sensitization in children up to the age of 4 years.

PubMed

Dom, S; Droste, J H J; Sariachvili, M A; Hagendorens, M M; Oostveen, E; Bridts, C H; Stevens, W J; Wieringa, M H; Weyler, J J

2010-09-01

Little data are available on the relationship between indirect antibiotic exposure of the child in utero or during lactation and allergic diseases. On the other hand, several studies have been conducted on the association with direct post-natal antibiotic exposure, but the results are conflicting. The aim of this study was to investigate pre- and post-natal antibiotic exposure and the subsequent development of eczema, recurrent wheeze and atopic sensitization in children up to the age of 4 years. We conducted an aetiologic study in 773 children based on a prospective birth cohort project in which environmental and health information were collected using questionnaires. Antibiotic exposure was assessed as maternal antibiotic intake during pregnancy and during lactation and as medication intake of the child. The chronology of exposures and outcomes was taken into account during the data processing. At the age of 1 and 4 years, a blood sample was taken for the quantification of specific IgE. Prenatal antibiotic exposure was significantly positively associated with eczema, whereas no association was found with recurrent wheeze and atopic sensitization. We found a positive, although statistically not significant, association between antibiotic exposure through breastfeeding and recurrent wheeze. Neither eczema nor atopic sensitization was significantly associated with antibiotic exposure through breastfeeding. Finally, we observed a negative association between the use of antibiotics in the first year of life and eczema and atopic sensitization, and also between antibiotic use after the first year of life and recurrent wheeze, eczema and atopic sensitization. Indirect exposure to antibiotics (in utero and during lactation) increases the risk for allergic symptoms in children, while direct exposure to antibiotics appears to be protective. The biological mechanisms underlying these findings still need to be elucidated.

Phase synchronization of instrumental music signals

NASA Astrophysics Data System (ADS)

Mukherjee, Sayan; Palit, Sanjay Kumar; Banerjee, Santo; Ariffin, M. R. K.; Bhattacharya, D. K.

2014-06-01

Signal analysis is one of the finest scientific techniques in communication theory. Some quantitative and qualitative measures describe the pattern of a music signal, vary from one to another. Same musical recital, when played by different instrumentalists, generates different types of music patterns. The reason behind various patterns is the psycho-acoustic measures - Dynamics, Timber, Tonality and Rhythm, varies in each time. However, the psycho-acoustic study of the music signals does not reveal any idea about the similarity between the signals. For such cases, study of synchronization of long-term nonlinear dynamics may provide effective results. In this context, phase synchronization (PS) is one of the measures to show synchronization between two non-identical signals. In fact, it is very critical to investigate any other kind of synchronization for experimental condition, because those are completely non identical signals. Also, there exists equivalence between the phases and the distances of the diagonal line in Recurrence plot (RP) of the signals, which is quantifiable by the recurrence quantification measure τ-recurrence rate. This paper considers two nonlinear music signals based on same raga played by two eminent sitar instrumentalists as two non-identical sources. The psycho-acoustic study shows how the Dynamics, Timber, Tonality and Rhythm vary for the two music signals. Then, long term analysis in the form of phase space reconstruction is performed, which reveals the chaotic phase spaces for both the signals. From the RP of both the phase spaces, τ-recurrence rate is calculated. Finally by the correlation of normalized tau-recurrence rate of their 3D phase spaces and the PS of the two music signals has been established. The numerical results well support the analysis.

Establishment and evaluation of a bead-based luminex assay allowing simultaneous quantification of equine IL-12 and IFN-γ.

PubMed

Duran, Maria Carolina; Willenbrock, Saskia; Müller, Jessika-M V; Nolte, Ingo; Feige, Karsten; Murua Escobar, Hugo

2013-04-01

Interleukin-12 (IL-12) and interferon gamma (IFN-γ) are key cytokines in immunemediated equine melanoma therapy. Currently, a method for accurate simultaneous quantification of these equine cytokines is lacking. Therefore, we sought to establish an assay that allows for accurate and simultaneous quantification of equine IL-12 (eIL-12) and IFN-γ (eIFN-γ). Several antibodies were evaluated for cross-reactivity to eIL-12 and eIFN-γ and were used to establish a bead-based Luminex assay, which was subsequently applied to quantify cytokine concentrations in biological samples. Cytokine detection ranged from 31.5-5,000 pg/ml and 15-10,000 pg/ml for eIL-12 and eIFN-γ, respectively. eIL-12 was detected in supernatants of stimulated peripheral blood mononuclear cells (PBMCs) and supernatants/cell lysates of eIL-12 expression plasmid-transfected cells. Low or undetectable cytokine concentrations were measured in negative controls. In equine serum samples, the mean measured eIL-12 concentration was 1,374 ± 8 pg/ml. The bead-based assay and ELISA for eIFN-γ used to measure eIFN-γ concentrations, showed similar concentrations. Results demonstrate, to our knowledge for the first time, that cross-reactive antibody pairs to eIL-12 and eIFN-γ and Luminex bead-based technology allow for accurate, simultaneous and multiplexed quantification of these key cytokines in biological samples.

Differentiation of Recurrent Glioblastoma from Delayed Radiation Necrosis by Using Voxel-based Multiparametric Analysis of MR Imaging Data.

PubMed

Yoon, Ra Gyoung; Kim, Ho Sung; Koh, Myeong Ju; Shim, Woo Hyun; Jung, Seung Chai; Kim, Sang Joon; Kim, Jeong Hoon

2017-10-01

Purpose To assess a volume-weighted voxel-based multiparametric (MP) clustering method as an imaging biomarker to differentiate recurrent glioblastoma from delayed radiation necrosis. Materials and Methods The institutional review board approved this retrospective study and waived the informed consent requirement. Seventy-five patients with pathologic analysis-confirmed recurrent glioblastoma (n = 42) or radiation necrosis (n = 33) who presented with enlarged contrast material-enhanced lesions at magnetic resonance (MR) imaging after they completed concurrent chemotherapy and radiation therapy were enrolled. The diagnostic performance of the total MP cluster score was determined by using the area under the receiver operating characteristic curve (AUC) with cross-validation and compared with those of single parameter measurements (10% histogram cutoffs of apparent diffusion coefficient [ADC10] or 90% histogram cutoffs of normalized cerebral blood volume and initial time-signal intensity AUC). Results Receiver operating characteristic curve analysis showed that an AUC for differentiating recurrent glioblastoma from delayed radiation necrosis was highest in the total MP cluster score and lowest for ADC10 for both readers. The total MP cluster score had significantly better diagnostic accuracy than any single parameter (corrected P = .001-.039 for reader 1; corrected P = .005-.041 for reader 2). The total MP cluster score was the best predictor of recurrent glioblastoma (cross-validated AUCs, 0.942-0.946 for both readers), with a sensitivity of 95.2% for reader 1 and 97.6% for reader 2. Conclusion Quantitative analysis with volume-weighted voxel-based MP clustering appears to be superior to the use of single imaging parameters to differentiate recurrent glioblastoma from delayed radiation necrosis. © RSNA, 2017 Online supplemental material is available for this article.

Women with breast cancer report substantially more disease- and treatment-related side or late effects than registered by clinical oncologists: a cross-sectional study of a standard follow-up program in an oncological department.

PubMed

Ellegaard, Mai-Britt Bjørklund; Grau, Cai; Zachariae, Robert; Jensen, Anders Bonde

2017-08-01

Follow-up after breast cancer treatment is standard due to the risk of development of new primary cancers and recurrent disease. The aim of the present study was to evaluate a standard follow-up program in an oncological department by assessing: (1) Symptoms or signs of new primary cancer or recurrent disease, (2) Disease- and treatment-related physical and psychosocial side or late effects, and (3) relevant actions by oncology staff. In a cross-sectional study, 194 women who came for follow-up visit after treatment for primary surgery were included. The clinical oncologists registered symptoms and signs of recurrent disease or new primary cancer. Side or late effects were both assessed by patient and the clinical oncologists. Loco-regional or distant signs of recurrent disease were suspected in eight (5%) patients. Further examinations revealed no disease recurrence. Most patients (93%) reported some degree of side or late effects. Statistically significant more side or late effects were reported by the women (average: 6.9) than registered by the clinical oncologists (average: 2.4), p < 0.001. The three most often patient-reported side or late effects were hot flushes (35%), fatigue (32%), and sleep disturbance (31%). None of the scheduled or additional visits resulted in detection of recurrent disease. Furthermore, the majority of patients reported side or late effects. Statistically significant more women reported side or late effects than registered by the clinical oncologists. This suggests the need for rethinking of the follow-up programs with more emphasis upon side or late effects of the treatment.

Are parents and adolescents in agreement on reporting of recurrent non-specific low back pain in adolescents? A cross-sectional descriptive study.

PubMed

Chiwaridzo, Matthew; Naidoo, Nirmala

2015-12-08

Non-specific low back pain is a prevalent symptom in adolescents and is recurrent in some instances. Recent studies have highlighted the marked impact the condition has on daily life of adolescents. However, it is unclear if parents of adolescents reporting recurrent non-specific low back pain know about their child's status. The purpose of the study was to determine the level of agreement between adolescents and their parents in reporting recurrent non-specific low back pain in Harare, Zimbabwe. This cross-sectional study formed part of a large study carried out to ascertain the prevalence of non-specific low back pain in Zimbabwean adolescents. Six hundred and twenty (n = 620) Medical Health Questionnaires were sent to parents. School-children with returned questionnaires and informed consents signed were subsequently eligible to participate. A reliable and validated low back pain study questionnaire was administered to 544 adolescents between the ages of 13 and 19 years randomly selected from government-administered schools. The questionnaire sought to determine adolescents with recurrent NSLBP. The Kappa statistic (k) was used to analyse agreement between adolescents and parental reports on recurrent NSLBP status. Parental and school-children response rates were acceptable (90.3 and 97.8 %, respectively). The prevalence of recurrent NSLBP was 28.8 % [95 % Confidence Interval, CI = 26.0-31.6]. Both sexes were equally affected [χ (2) (1) =0.19, p = 0.67]. The prevalence increased with age in both sexes [χ (2) trend =90.9, p < 0.001]. Parental reports agreed in 16.3 and 98.7 % for the adolescents with and without recurrent NSLBP respectively. The value of kappa (k) was 0.20 [SE = 0.04; 95 % CI, 0.13-0.27] with a prevalence index and bias index of -0.65 and 0.23, respectively. These results suggest poor strength of the agreement. Recurrent non-specific low back pain is relatively common among Zimbabwean adolescents. Most of the parents of school-children with recurrent non-specific low back pain are unaware of the low back pain status of their children. Although this does not dismiss the relevance of non-specific low back pain reported during adolescence, these findings create a need to involve parents in awareness or preventive initiatives against low back pain in schools.

Recurrent wheezing is associated with intestinal protozoan infections in Warao Amerindian children in Venezuela: a cross-sectional survey.

PubMed

Overeem, Marcella M A; Verhagen, Lilly M; Hermans, Peter W M; del Nogal, Berenice; Sánchez, Adriana Márquez; Acevedo, Natacha Martinez; Murga, Rosalicia Ramirez; Roelfsema, Jeroen; Pinelli, Elena; de Waard, Jacobus H

2014-05-29

While in developed countries the prevalence of allergic diseases is rising, inflammatory diseases are relatively uncommon in rural developing areas. High prevalence rates of helminth and protozoan infections are commonly found in children living in rural settings and several studies suggest an inverse association between helminth infections and allergies. No studies investigating the relationship between parasitic infections and atopic diseases in rural children of developing countries under the age of 2 years have been published so far. We performed a cross-sectional survey to investigate the association of helminth and protozoan infections and malnutrition with recurrent wheezing and atopic eczema in Warao Amerindian children in Venezuela. From August to November 2012, 229 children aged 0 to 2 years residing in the Orinoco Delta in Venezuela were enrolled. Data were collected through standardized questionnaires and physical examination, including inspection of the skin and anthropometric measurements. A stool sample was requested from all participants and detection of different parasites was performed using microscopy and real time polymerase chain reaction (PCR). We observed high prevalence rates of atopic eczema and recurrent wheezing, respectively 19% and 23%. The prevalence of helminth infections was 26% and the prevalence of protozoan infections was 59%. Atopic eczema and recurrent wheezing were more frequently observed in stunted compared with non-stunted children in multivariable analysis (OR 4.3, 95% CI 1.3 - 13.6, p = 0.015 and OR 4.5, 95% CI 0.97 - 21.2, p = 0.055). Furthermore, recurrent wheezing was significantly more often observed in children with protozoan infections than in children without protozoan infections (OR 6.7, 95% CI 1.5 - 30.5). High prevalence rates of atopic eczema and recurrent wheezing in Warao Amerindian children under 2 years of age were related to stunting and intestinal protozoan infections respectively. Helminth infections were not significantly associated with either atopic eczema or recurrent wheezing.

Recurrent wheezing is associated with intestinal protozoan infections in Warao Amerindian children in Venezuela: a cross-sectional survey

PubMed Central

2014-01-01

Background While in developed countries the prevalence of allergic diseases is rising, inflammatory diseases are relatively uncommon in rural developing areas. High prevalence rates of helminth and protozoan infections are commonly found in children living in rural settings and several studies suggest an inverse association between helminth infections and allergies. No studies investigating the relationship between parasitic infections and atopic diseases in rural children of developing countries under the age of 2 years have been published so far. We performed a cross-sectional survey to investigate the association of helminth and protozoan infections and malnutrition with recurrent wheezing and atopic eczema in Warao Amerindian children in Venezuela. Methods From August to November 2012, 229 children aged 0 to 2 years residing in the Orinoco Delta in Venezuela were enrolled. Data were collected through standardized questionnaires and physical examination, including inspection of the skin and anthropometric measurements. A stool sample was requested from all participants and detection of different parasites was performed using microscopy and real time polymerase chain reaction (PCR). Results We observed high prevalence rates of atopic eczema and recurrent wheezing, respectively 19% and 23%. The prevalence of helminth infections was 26% and the prevalence of protozoan infections was 59%. Atopic eczema and recurrent wheezing were more frequently observed in stunted compared with non-stunted children in multivariable analysis (OR 4.3, 95% CI 1.3 – 13.6, p = 0.015 and OR 4.5, 95% CI 0.97 – 21.2, p = 0.055). Furthermore, recurrent wheezing was significantly more often observed in children with protozoan infections than in children without protozoan infections (OR 6.7, 95% CI 1.5 – 30.5). Conclusions High prevalence rates of atopic eczema and recurrent wheezing in Warao Amerindian children under 2 years of age were related to stunting and intestinal protozoan infections respectively. Helminth infections were not significantly associated with either atopic eczema or recurrent wheezing. PMID:24885094

Uncovering the Role of BMP Signaling in Melanocyte Development and Melanoma Tumorigenesis

DTIC Science & Technology

2014-07-01

clear that these mutations are not sufficient for melanoma formation and other genes are involved. Using genomic studies and cross -species...studies and cross -species comparisons to identify several candidates. One of these candidates, GDF6, is a BMP factor that is recurrently amplified...having to cross cell membranes. Antibodies, such as the VEGF blocker bevacizumab, epitomize this type of therapy. We are currently investigating the

Dynamical transitions associated with turbulence in a helicon plasma

NASA Astrophysics Data System (ADS)

Light, Adam D.; Tian, Li; Chakraborty Thakur, Saikat; Tynan, George R.

2017-10-01

Diagnostic capabilities are often cited as a limiting factor in our understanding of transport in fusion devices. Increasingly advanced multichannel diagnostics are being applied to classify transport regimes and to search for ``trigger'' features that signal an oncoming dynamical event, such as an ELM or an L-H transition. In this work, we explore a technique that yields information about global properties of plasma dynamics from a single time series of a relevant plasma quantity. Electrostatic probe data from the Controlled Shear Decorrelation eXperiment (CSDX) is analyzed using recurrence quantification analysis (RQA) in the context of previous work on the transition to weak drift-wave turbulence. The recurrence characteristics of a phase space trajectory provide a quantitative means to classify dynamics and identify transitions in a complex system. We present and quantify dynamical variations in the plasma variables as a function of the background magnetic field strength. A dynamical transition corresponding to the emergence of broadband fluctuations is identified using RQA measures.

Artifacts Quantification of Metal Implants in MRI

NASA Astrophysics Data System (ADS)

Vrachnis, I. N.; Vlachopoulos, G. F.; Maris, T. G.; Costaridou, L. I.

2017-11-01

The presence of materials with different magnetic properties, such as metal implants, causes distortion of the magnetic field locally, resulting in signal voids and pile ups, i.e. susceptibility artifacts in MRI. Quantitative and unbiased measurement of the artifact is prerequisite for optimization of acquisition parameters. In this study an image gradient based segmentation method is proposed for susceptibility artifact quantification. The method captures abrupt signal alterations by calculation of the image gradient. Then the artifact is quantified in terms of its extent by an automated cross entropy thresholding method as image area percentage. The proposed method for artifact quantification was tested in phantoms containing two orthopedic implants with significantly different magnetic permeabilities. The method was compared against a method proposed in the literature, considered as a reference, demonstrating moderate to good correlation (Spearman’s rho = 0.62 and 0.802 in case of titanium and stainless steel implants). The automated character of the proposed quantification method seems promising towards MRI acquisition parameter optimization.

Nitric Oxide Analyzer Quantification of Plant S-Nitrosothiols.

PubMed

Hussain, Adil; Yun, Byung-Wook; Loake, Gary J

2018-01-01

Nitric oxide (NO) is a small diatomic molecule that regulates multiple physiological processes in animals, plants, and microorganisms. In animals, it is involved in vasodilation and neurotransmission and is present in exhaled breath. In plants, it regulates both plant immune function and numerous developmental programs. The high reactivity and short half-life of NO and cross-reactivity of its various derivatives make its quantification difficult. Different methods based on calorimetric, fluorometric, and chemiluminescent detection of NO and its derivatives are available, but all of them have significant limitations. Here we describe a method for the chemiluminescence-based quantification of NO using ozone-chemiluminescence technology in plants. This approach provides a sensitive, robust, and flexible approach for determining the levels of NO and its signaling products, protein S-nitrosothiols.

Recurrence quantification analysis of extremes of maximum and minimum temperature patterns for different climate scenarios in the Mesochora catchment in Central-Western Greece

NASA Astrophysics Data System (ADS)

Panagoulia, Dionysia; Vlahogianni, Eleni I.

2018-06-01

A methodological framework based on nonlinear recurrence analysis is proposed to examine the historical data evolution of extremes of maximum and minimum daily mean areal temperature patterns over time under different climate scenarios. The methodology is based on both historical data and atmospheric General Circulation Model (GCM) produced climate scenarios for the periods 1961-2000 and 2061-2100 which correspond to 1 × CO2 and 2 × CO2 scenarios. Historical data were derived from the actual daily observations coupled with atmospheric circulation patterns (CPs). The dynamics of the temperature was reconstructed in the phase-space from the time series of temperatures. The statistically comparing different temperature patterns were based on some discriminating statistics obtained by the Recurrence Quantification Analysis (RQA). Moreover, the bootstrap method of Schinkel et al. (2009) was adopted to calculate the confidence bounds of RQA parameters based on a structural preserving resampling. The overall methodology was implemented to the mountainous Mesochora catchment in Central-Western Greece. The results reveal substantial similarities between the historical maximum and minimum daily mean areal temperature statistical patterns and their confidence bounds, as well as the maximum and minimum temperature patterns in evolution under the 2 × CO2 scenario. A significant variability and non-stationary behaviour characterizes all climate series analyzed. Fundamental differences are produced from the historical and maximum 1 × CO2 scenarios, the maximum 1 × CO2 and minimum 1 × CO2 scenarios, as well as the confidence bounds for the two CO2 scenarios. The 2 × CO2 scenario reflects the strongest shifts in intensity, duration and frequency in temperature patterns. Such transitions can help the scientists and policy makers to understand the effects of extreme temperature changes on water resources, economic development, and health of ecosystems and hence to proceed to effective proactive management of extreme phenomena. The impacts of the findings on the predictability of the extreme daily mean areal temperature patterns are also commented.

Cigarette smoking status and recurrent subjective health complaints among US school-aged adolescents.

PubMed

Botello-Harbaum, M; Haynie, D L; Murray, K W; Iannotti, R J

2011-07-01

Subjective health complaints are common among adolescents. There is evidence that girls are more likely to register complaints than boys. This study examines gender differences in the relationship between daily smoking and recurrent subjective health complaints in school-aged adolescents in the USA. A cross-sectional design with a multistage probability sample was used to survey 13,339 middle and high school students (grades 6 through 10) with the US 2001-2002 Health Behavior in School-Aged Children Survey. Recurrent subjective health complaints were higher for adolescents who smoke daily and experiment with cigarettes than for those who never smoke. In logistic regression analyses, the odds of daily smoking increased twofold for both boys and girls who report recurrent irritability/bad temper. For girls, the odds of daily smoking were higher among those who reported recurrent headache, stomachache and backache compared with never smokers. For boys only recurrent backache and feeling dizzy were associated with increased odds of daily smoking. The relationship between recurrent subjective health complaints and daily smoking provides new insights into both conditions for school-aged adolescents. Findings from this study suggest different patterns of association between daily smoking and recurrent subjective health complaints occur for girls and boys. Further studies are needed to explore causes and treatment of daily smoking and recurrent health complaints among school-aged children. © 2010 Blackwell Publishing Ltd.

Early detection of lung cancer recurrence after stereotactic ablative radiation therapy: radiomics system design

NASA Astrophysics Data System (ADS)

Dammak, Salma; Palma, David; Mattonen, Sarah; Senan, Suresh; Ward, Aaron D.

2018-02-01

Stereotactic ablative radiotherapy (SABR) is the standard treatment recommendation for Stage I non-small cell lung cancer (NSCLC) patients who are inoperable or who refuse surgery. This option is well tolerated by even unfit patients and has a low recurrence risk post-treatment. However, SABR induces changes in the lung parenchyma that can appear similar to those of recurrence, and the difference between the two at an early follow-up time point is not easily distinguishable for an expert physician. We hypothesized that a radiomics signature derived from standard-of-care computed tomography (CT) imaging can detect cancer recurrence within six months of SABR treatment. This study reports on the design phase of our work, with external validation planned in future work. In this study, we performed cross-validation experiments with four feature selection approaches and seven classifiers on an 81-patient data set. We extracted 104 radiomics features from the consolidative and the peri-consolidative regions on the follow-up CT scans. The best results were achieved using the sum of estimated Mahalanobis distances (Maha) for supervised forward feature selection and a trainable automatic radial basis support vector classifier (RBSVC). This system produced an area under the receiver operating characteristic curve (AUC) of 0.84, an error rate of 16.4%, a false negative rate of 12.7%, and a false positive rate of 20.0% for leaveone patient out cross-validation. This suggests that once validated on an external data set, radiomics could reliably detect post-SABR recurrence and form the basis of a tool assisting physicians in making salvage treatment decisions.

Integrating public risk perception into formal natural hazard risk assessment

NASA Astrophysics Data System (ADS)

Plattner, Th.; Plapp, T.; Hebel, B.

2006-06-01

An urgent need to take perception into account for risk assessment has been pointed out by relevant literature, its impact in terms of risk-related behaviour by individuals is obvious. This study represents an effort to overcome the broadly discussed question of whether risk perception is quantifiable or not by proposing a still simple but applicable methodology. A novel approach is elaborated to obtain a more accurate and comprehensive quantification of risk in comparison to present formal risk evaluation practice. A consideration of relevant factors enables a explicit quantification of individual risk perception and evaluation. The model approach integrates the effective individual risk reff and a weighted mean of relevant perception affecting factors PAF. The relevant PAF cover voluntariness of risk-taking, individual reducibility of risk, knowledge and experience, endangerment, subjective damage rating and subjective recurrence frequency perception. The approach assigns an individual weight to each PAF to represent its impact magnitude. The quantification of these weights is target-group-dependent (e.g. experts, laypersons) and may be effected by psychometric methods. The novel approach is subject to a plausibility check using data from an expert-workshop. A first model application is conducted by means of data of an empirical risk perception study in Western Germany to deduce PAF and weight quantification as well as to confirm and evaluate model applicbility and flexibility. Main fields of application will be a quantification of risk perception by individual persons in a formal and technical way e.g. for the purpose of risk communication issues in illustrating differing perspectives of experts and non-experts. For decision making processes this model will have to be applied with caution, since it is by definition not designed to quantify risk acceptance or risk evaluation. The approach may well explain how risk perception differs, but not why it differs. The formal model generates only "snap shots" and considers neither the socio-cultural nor the historical context of risk perception, since it is a highly individualistic and non-contextual approach.

A computational model for three-dimensional incompressible wall jets with large cross flow

NASA Technical Reports Server (NTRS)

Murphy, W. D.; Shankar, V.; Malmuth, N. D.

1979-01-01

A computational model for the flow field of three dimensional incompressible wall jets prototypic of thrust augmenting ejectors with large cross flow is presented. The formulation employs boundary layer equations in an orthogonal curvilinear coordinate system. Simulation of laminar as well as turbulen wall jets is reported. Quantification of jet spreading, jet growth, nominal separation, and jet shrink effects due to corss flow are discussed.

Cost-effectiveness of the 21-gene recurrence score assay in the context of multifactorial decision making to guide chemotherapy for early-stage breast cancer.

PubMed

Reed, Shelby D; Dinan, Michaela A; Schulman, Kevin A; Lyman, Gary H

2013-03-01

New evidence is available regarding the utility of the 21-gene recurrence score assay in guiding chemotherapy use for node-negative, estrogen receptor-positive breast cancer. We applied this evidence in a decision-analytic model to re-evaluate the cost-effectiveness of the assay. We cross-classified patients by clinicopathologic characteristics from the Adjuvant! risk index and by recurrence score risk group. For non-recurrence score-guided treatment, we assumed patients receiving hormonal therapy alone had low-risk characteristics and patients receiving chemotherapy and hormonal therapy had higher-risk characteristics. For recurrence score-guided treatment, we assigned chemotherapy probabilities conditional on recurrence score risk group and clinicopathologic characteristics. An estimated 40.4% of patients in the recurrence score-guided strategy and 47.3% in the non-recurrence score-guided strategy were expected to receive chemotherapy. The incremental gain in quality-adjusted life-years was 0.16 (95% confidence interval, 0.08-0.28) with the recurrence score-guided strategy. Lifetime medical costs to the health system were $2,692 ($1,546-$3,821) higher with the recurrence score-guided strategy, for an incremental cost-effectiveness ratio of $16,677/quality-adjusted life-year ($7,613-$37,219). From a societal perspective, the incremental cost-effectiveness was $10,788/quality-adjusted life-year ($6,840-$30,265). The findings provide supportive evidence for the economic value of the 21-gene recurrence score assay in node-negative, estrogen receptor-positive breast cancer.

Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

PubMed Central

Michael, John; Bogart, Kathleen; Tylén, Kristian; Krueger, Joel; Bech, Morten; Østergaard, John Rosendahl; Fusaroli, Riccardo

2015-01-01

In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius syndrome (MS) to increase the use of alternative communication strategies (e.g., gestures) to compensate for their lack of facial expressivity. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual non-verbal behavior was assessed via behavioral coders, whereas verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed-effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, whereas overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact non-verbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment. PMID:26500605

YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research

PubMed Central

Cheng, Wei-Chung; Chung, I-Fang; Tsai, Cheng-Fong; Huang, Tse-Shun; Chen, Chen-Yang; Wang, Shao-Chuan; Chang, Ting-Yu; Sun, Hsing-Jen; Chao, Jeffrey Yung-Chuan; Cheng, Cheng-Chung; Wu, Cheng-Wen; Wang, Hsei-Wei

2015-01-01

We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function ‘Meta-analysis’ is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications. PMID:25398902

Infant Development in Fragile X Syndrome: Cross-Syndrome Comparisons

ERIC Educational Resources Information Center

Roberts, Jane E.; McCary, Lindsay M.; Shinkareva, Svetlana V.; Bailey, Donald B., Jr.

2016-01-01

This study examined the developmental profile of male infants with fragile X syndrome (FXS) and its divergence from typical development and development of infants at high risk for autism associated with familial recurrence (ASIBs). Participants included 174 boys ranging in age from 5 to 28 months. Cross-sectional profiles on the Mullen Scales of…

Woods Cross: Patterns and Profiles of a City.

ERIC Educational Resources Information Center

Eakle, Arlene H.; And Others

The pamphlet traces the social history of Woods Cross, Utah from pioneer arrival in 1847 through 1976. Each street of the town serves as the focal point for a discussion of the role of each family in the town's history. Content includes establishment of railway lines and a depot, growth of water companies and recurrent local water problems,…

Combined fluorescence and reflectance spectroscopy for in vivo quantification of cancer biomarkers in low- and high-grade glioma surgery

PubMed Central

Valdés, Pablo A.; Kim, Anthony; Leblond, Frederic; Conde, Olga M.; Harris, Brent T.; Paulsen, Keith D.; Wilson, Brian C.; Roberts, David W.

2011-01-01

Biomarkers are indicators of biological processes and hold promise for the diagnosis and treatment of disease. Gliomas represent a heterogeneous group of brain tumors with marked intra- and inter-tumor variability. The extent of surgical resection is a significant factor influencing post-surgical recurrence and prognosis. Here, we used fluorescence and reflectance spectral signatures for in vivo quantification of multiple biomarkers during glioma surgery, with fluorescence contrast provided by exogenously-induced protoporphyrin IX (PpIX) following administration of 5-aminolevulinic acid. We performed light-transport modeling to quantify multiple biomarkers indicative of tumor biological processes, including the local concentration of PpIX and associated photoproducts, total hemoglobin concentration, oxygen saturation, and optical scattering parameters. We developed a diagnostic algorithm for intra-operative tissue delineation that accounts for the combined tumor-specific predictive capabilities of these quantitative biomarkers. Tumor tissue delineation achieved accuracies of up to 94% (specificity = 94%, sensitivity = 94%) across a range of glioma histologies beyond current state-of-the-art optical approaches, including state-of-the-art fluorescence image guidance. This multiple biomarker strategy opens the door to optical methods for surgical guidance that use quantification of well-established neoplastic processes. Future work would seek to validate the predictive power of this proof-of-concept study in a separate larger cohort of patients. PMID:22112112

Combined fluorescence and reflectance spectroscopy for in vivo quantification of cancer biomarkers in low- and high-grade glioma surgery

NASA Astrophysics Data System (ADS)

Valdés, Pablo A.; Kim, Anthony; Leblond, Frederic; Conde, Olga M.; Harris, Brent T.; Paulsen, Keith D.; Wilson, Brian C.; Roberts, David W.

2011-11-01

Biomarkers are indicators of biological processes and hold promise for the diagnosis and treatment of disease. Gliomas represent a heterogeneous group of brain tumors with marked intra- and inter-tumor variability. The extent of surgical resection is a significant factor influencing post-surgical recurrence and prognosis. Here, we used fluorescence and reflectance spectral signatures for in vivo quantification of multiple biomarkers during glioma surgery, with fluorescence contrast provided by exogenously-induced protoporphyrin IX (PpIX) following administration of 5-aminolevulinic acid. We performed light-transport modeling to quantify multiple biomarkers indicative of tumor biological processes, including the local concentration of PpIX and associated photoproducts, total hemoglobin concentration, oxygen saturation, and optical scattering parameters. We developed a diagnostic algorithm for intra-operative tissue delineation that accounts for the combined tumor-specific predictive capabilities of these quantitative biomarkers. Tumor tissue delineation achieved accuracies of up to 94% (specificity = 94%, sensitivity = 94%) across a range of glioma histologies beyond current state-of-the-art optical approaches, including state-of-the-art fluorescence image guidance. This multiple biomarker strategy opens the door to optical methods for surgical guidance that use quantification of well-established neoplastic processes. Future work would seek to validate the predictive power of this proof-of-concept study in a separate larger cohort of patients.

The Slug and Churn Turbulence Characteristics of Oil-Gas-Water Flows in a Vertical Small Pipe

NASA Astrophysics Data System (ADS)

Liu, Weixin; Han, Yunfeng; Wang, Dayang; Zhao, An; Jin, Ningde

2017-08-01

The intention of the present study was to investigate the slug and churn turbulence characteristics of a vertical upward oil-gas-water three-phase flow. We firstly carried out a vertical upward oil-gas-water three-phase flow experiment in a 20-mm inner diameter (ID) pipe to measure the fluctuating signals of a rotating electric field conductance sensor under different flow patterns. Afterwards, typical flow patterns were identified with the aid of the texture structures in a cross recurrence plot. Recurrence quantitative analysis and multi-scale cross entropy (MSCE) algorithms were applied to investigate the turbulence characteristics of slug and churn flows with the varying flow parameters. The results suggest that with cross nonlinear analysis, the underlying dynamic characteristics in the evolution from slug to churn flow can be well understood. The present study provides a novel perspective for the analysis of the spatial-temporal evolution instability and complexity in oil-gas-water three-phase flow.

Are crossing dependencies really scarce?

NASA Astrophysics Data System (ADS)

Ferrer-i-Cancho, R.; Gómez-Rodríguez, C.; Esteban, J. L.

2018-03-01

The syntactic structure of a sentence can be modelled as a tree, where vertices correspond to words and edges indicate syntactic dependencies. It has been claimed recurrently that the number of edge crossings in real sentences is small. However, a baseline or null hypothesis has been lacking. Here we quantify the amount of crossings of real sentences and compare it to the predictions of a series of baselines. We conclude that crossings are really scarce in real sentences. Their scarcity is unexpected by the hubiness of the trees. Indeed, real sentences are close to linear trees, where the potential number of crossings is maximized.

Evaluation of the Coat-A-Count sup 125 I fentanyl RIA: Comparison of sup 12 5I RIA and GC/MS-SIM for quantification of fentanyl in case urine specimens

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

Watts, V.W.; Caplan, Y.H.

The Coat-A-Count solid phase {sup 125}I Fentanyl Radioimmunoassay was evaluated with respect to linearity and precision using equine urine fortified with fentanyl and then compared with a gas chromatographic/mass spectrometric method for quantification of fentanyl in urine. The RIA assay was found to be linear over the urine fentanyl concentration range of 0.25 to 7.5 ng/mL and precise with coefficients of variation (CV) ranging from 9.6 to 19.3%. The RIA calibrators, ranging in fentanyl concentrations from 0.25 to 7.5 ng/mL, and controls, at mean fentanyl concentrations of 0.46 and 1.32 ng/mL, were compared by both the RIA and GC/MS methods.more » The cross-reactivity with the {sup 125}I RIA test was determined for the fentanyl metabolites, norfentanyl and hydroxyfentanyl, and found to be 5% and 35%, respectively. The illicit fentanyl analogs were found to show significant cross-reactivity, ranging from 20 to 100%. The {sup 125}I RIA was compared to GC/MS quantifications of fentanyl in 35 positive and 20 negative case urine specimens.« less

Evaluation of muscle fatigue of wheelchair basketball players with spinal cord injury using recurrence quantification analysis of surface EMG.

PubMed

Uzun, S; Pourmoghaddam, A; Hieronymus, M; Thrasher, T A

2012-11-01

Wheelchair basketball is the most popular exercise activity among individuals with spinal cord injury (SCI). The purpose of this study was to investigate muscular endurance and fatigue in wheelchair basketball athletes with SCI using surface electromyography (SEMG) and maximal torque values. SEMG characteristics of 10 wheelchair basketball players (WBP) were compared to 13 able-bodied basketball players and 12 sedentary able-bodied subjects. Participants performed sustained isometric elbow flexion at 50% maximal voluntary contraction until exhaustion. Elbow flexion torque and SEMG signals were recorded from three elbow flexor muscles: biceps brachii longus, biceps brachii brevis and brachioradialis. SEMG signals were clustered into 0.5-s epochs with 50% overlap. Root mean square (RMS) and median frequency (MDF) of SEMG signals were calculated for each muscle and epoch as traditional fatigue monitoring. Recurrence quantification analysis was used to extract the percentage of determinism (%DET) of SEMG signals. The slope of the %DET for basketball players and WBP showed slower increase with time than the sedentary able-bodied control group for three different elbow flexor muscles, while no difference was observed for the slope of the %DET between basketball and WBP. This result indicated that the athletes are less fatigable during the task effort than the nonathletes. Normalized MDF slope decay exhibited similar results between the groups as %DET, while the slope of the normalized RMS failed to show any significant differences among the groups (p > 0.05). MDF and %DET could be useful for the evaluation of muscle fatigue in wheelchair basketball training. No conclusions about special training for WBP could be determined.

The effect of vision elimination during quiet stance tasks with different feet positions.

PubMed

Sarabon, Nejc; Rosker, Jernej; Loefler, Stefan; Kern, Helmut

2013-09-01

Literature confirms the effects of vision and stance on body sway and indicates possible interactions between the two. However, no attempts have been made to systematically compare the effect of vision on the different types of stance which are frequently used in clinical and research practice. The biomechanical changes that occur after changing shape and size of the support surface suggest possible sensory re-weighting might take place. The purpose of this study was to assess the effect of vision on body sway in relation to different stance configurations and width. Thirty-eight volunteers performed four quiet stance configurations (parallel, semi-tandem, tandem and single leg), repeating them with open and closed eyes. Traditional parameters, recurrence quantification analysis and sample entropy were analyzed from the CoP trajectory signal. Traditional and recurrence quantification analysis parameters were affected by vision removal and stance type. Exceptions were frequency of oscillation, entropy and trapping time. The most prominent effect of vision elimination on traditional parameters was observed for narrower stances. A significant interaction effect between vision removal and stance type was present for most of the parameters observed (p<0.05). The interaction effect between medio-lateral and antero-posterior traditional parameters differed in linearity between stances. The results confirm the effect of vision removal on the body sway. However, for the medio-lateral traditional parameters, the effects did not increase linearly with the change in width and stance type. This suggests that removal of vision could be more effectively compensated by other sensory systems in semi-tandem stance, tandem and single legged stance. Copyright © 2013 Elsevier B.V. All rights reserved.

Prognostic implications of epicardial fat volume quantification in acute pericarditis.

PubMed

Lazaros, George; Antonopoulos, Alexios S; Oikonomou, Evangelos K; Vasileiou, Panagiotis; Oikonomou, Evangelos; Stroumpouli, Evangelia; Karavidas, Apostolos; Antoniades, Charalambos; Tousoulis, Dimitris

2017-02-01

The pathophysiology of acute pericarditis remains largely unknown, and biomarkers are needed to identify patients susceptible to complications. As adipose tissue has a pivotal role in cardiovascular disease pathogenesis, we hypothesized that quantification of epicardial fat volume (EFV) provides prognostic information in patients with acute pericarditis. Fifty (n = 50) patients with first diagnosis of acute pericarditis were enrolled in this study. Patients underwent a cardiac computerized tomography (CT) scan to quantify EFV on a dedicated workstation. Patients were followed up in hospital for atrial fibrillation (AF) development and up to 18 months for the composite clinical endpoint of development of constrictive, recurrent or incessant pericarditis or poor response to nonsteroidal anti-inflammatory drugs. Patients presenting with chest pain had lower EFV vs. patients without chest pain (167·2 ± 21·7 vs. 105·1 ± 11·1 cm 3 , respectively, P < 0·01); EFV (but not body mass index) was strongly positively correlated with pericardial effusion size (r = 0·395, P = 0·007) and associated with in-hospital AF. At follow-up, patients that reached the composite clinical endpoint had lower EFV (P < 0·05). After adjustment for age, EFV was associated with lower odds ratio for the composite clinical endpoint point of poor response to NSAIDs or the development of constrictive, recurrent or incessant pericarditis during follow-up (per 20 cm 3 increase in EFV: OR = 0·802 [0·656-0·981], P < 0·05). We report for the first time a significant association of EFV with the clinical features and the outcome of patients with acute pericarditis. Measurement of EFV by CT may have important prognostic implications in these patients. © 2016 Stichting European Society for Clinical Investigation Journal Foundation.

Validation of a DIXON-based fat quantification technique for the measurement of visceral fat using a CT-based reference standard.

PubMed

Heckman, Katherine M; Otemuyiwa, Bamidele; Chenevert, Thomas L; Malyarenko, Dariya; Derstine, Brian A; Wang, Stewart C; Davenport, Matthew S

2018-06-27

The purpose of the study is to determine whether a novel semi-automated DIXON-based fat quantification algorithm can reliably quantify visceral fat using a CT-based reference standard. This was an IRB-approved retrospective cohort study of 27 subjects who underwent abdominopelvic CT within 7 days of proton density fat fraction (PDFF) mapping on a 1.5T MRI. Cross-sectional visceral fat area per slice (cm 2 ) was measured in blinded fashion in each modality at intervertebral disc levels from T12 to L4. CT estimates were obtained using a previously published semi-automated computational image processing system that sums pixels with attenuation - 205 to - 51 HU. MR estimates were obtained using two novel semi-automated DIXON-based fat quantification algorithms that measure visceral fat area by spatially regularizing non-uniform fat-only signal intensity or de-speckling PDFF 2D images and summing pixels with PDFF ≥ 50%. Pearson's correlations and Bland-Altman analyses were performed. Visceral fat area per slice ranged from 9.2 to 429.8 cm 2 for MR and from 1.6 to 405.5 cm 2 for CT. There was a strong correlation between CT and MR methods in measured visceral fat area across all studied vertebral body levels (r = 0.97; n = 101 observations); the least (r = 0.93) correlation was at T12. Bland-Altman analysis revealed a bias of 31.7 cm 2 (95% CI [- 27.1]-90.4 cm 2 ), indicating modestly higher visceral fat assessed by MR. MR- and CT-based visceral fat quantification are highly correlated and have good cross-modality reliability, indicating that visceral fat quantification by either method can yield a stable and reliable biomarker.

The effect of midline crossing of lateral supraglottic cancer on contralateral cervical lymph node metastasis.

PubMed

Yılmaz, Taner; Süslü, Nilda; Atay, Gamze; Günaydın, Rıza Önder; Bajin, Münir Demir; Özer, Serdar

2015-05-01

The degree of midline crossing of lateral supraglottic cancer does not significantly change its rate of contralateral cervical metastasis. The rate of occult metastasis is too high to take the risk of contralateral regional recurrence. We support routine bilateral neck dissection even in lateral supraglottic cancers with no or minimal midline crossing. Data on the rate of contralateral cervical metastasis of laterally located supraglottic cancer, the effect of its degree of midline crossing on contralateral cervical metastasis, and its treatment are still controversial. This was a retrospective cohort, chart review involving 305 surgically treated patients with T1-3 squamous cell carcinoma of the supraglottic larynx. In all, 184 patients had bilateral neck dissection; 86 N0 contralateral necks were followed up. Thirty-five patients who needed postoperative radiation therapy because of the primary tumor or ipsilateral neck dissection specimen also received radiation therapy to the contralateral neck. The degree of midline crossing at the epiglottis was measured on a laryngectomy specimen with a ruler and expressed as 'no,' '<5 mm' or '≥5 mm.' The rates of occult and overall contralateral metastasis in our series were 16% and 28%, respectively. There was no statistically significant difference between contralateral neck metastasis and recurrence rates in the neck dissection, follow-up, and irradiation groups according to the degree of midline crossing.

EasyLCMS: an asynchronous web application for the automated quantification of LC-MS data

PubMed Central

2012-01-01

Background Downstream applications in metabolomics, as well as mathematical modelling, require data in a quantitative format, which may also necessitate the automated and simultaneous quantification of numerous metabolites. Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of μmol have not been carried out. Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account in these applications. Moreover, only a few are web-based applications, which could improve stand-alone software in terms of compatibility, sharing capabilities and hardware requirements, even though a strong bandwidth is required. Furthermore, none of these incorporate asynchronous communication to allow real-time interaction with pre-processed results. Findings Here, we present EasyLCMS (http://www.easylcms.es/), a new application for automated quantification which was validated using more than 1000 concentration comparisons in real samples with manual operation. The results showed that only 1% of the quantifications presented a relative error higher than 15%. Using clustering analysis, the metabolites with the highest relative error distributions were identified and studied to solve recurrent mistakes. Conclusions EasyLCMS is a new web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field. PMID:22884039

[Can cross-allergic reactions to food antigens be the cause of recurrent pancreatitis in children with food allergies?].

PubMed

Subbotina, O A; Geppe, N A; Primak, E A; Surikova, O A; Orekhova, V P

2014-01-01

Drug and food allergy in 80% of cases are the cause of duodenal inflammation disrupting the function of the pancreatic ducts. However, in some cases, elimination diet in patients with food allergy does not provide a sufficient effect. The article shows the effect of cross-allergic reactions on recurrent pancreatitis in 28 children with food allergy (mean age 11.7 +/- 2.9 years). As an additional diagnostic criterion the coefficient of degranulation of mast cell in the intestinal mucosa (the ratio of degranulated forms to granulated) was determined, through which the effect of cross-allergic reactions (between food antigens and drugs of animal origin) on the duration and frequency of exacerbations of chronic pancreatitis in children with food sensitization has been shown. The exception of enzyme preparations for children with sensitization to pork and exception of eubiotics prepared using sucrose-gelatin-milk medium for children with sensitization to cow's milk and beef led to feel better in a shorter time (2-3 days) and to reduce the frequency of relapses. Catamnesis observation for 3 years showed that the incidence of recurrent exacerbations of the disease in 11 children with excepted cross-allergic reactions in the first year of follow-up was 9.1%, in the second year--9.1% and in the third year--0%, while in control group (17 children) the frequency of exacerbations was respectively 23.5; 35.3; 35.3%. In patients of the main group there was a slight overall increase of mast cells in the intestinal mucosa from 211.7 to 230.2 mm2 (p > 0.05) with decreasing of degranulated forms from 163.6 to 138.71 mm2 (p > 0.05) and significant increase of granulated forms from 47.41 to 91.51 mm2 (p < 0.05), resulting in a significant decrease in mast cells degranulation coefficient from 3.2 +/- 0.62/mm2 to 1.24 +/- 0.26/mm2 (p < 0.0001). Thus, duodenal etiology of recurrent pancreatitis caused by exposure to food antigens or cross-allergic reactions can be diagnosed with an additional diagnostic criterion--the coefficient of mast cell degranulation, whose exponents greater than 1.5 indicate evidence of antigenic exposure to the mucosa of the duodenum and allergic inflammation.

Assessing the Prevalence of Recurrent Neck and Shoulder Pain in Korean High School Male Students: A Cross-sectional Observational Study.

PubMed

Koh, Min Jung; Park, Sun Young; Woo, Young Sun; Kang, Sung Hyun; Park, Sang Hoon; Chun, Hye Jung; Park, Eun Jung

2012-07-01

Neck and shoulder pain (NSP) is fairly common in adolescents, which is associated with a high prevalence of NSP found during adulthood as well; therefore, its significance during adolescence should not be underestimated. We surveyed the prevalence of recurrent NSP, lifestyle, and risk factors in Korean high school students, and examined the influence of recurrent NSP on the quality of life. Nine hundred thirty one male students (16-19 years old) from two academic high schools in Seoul were included in this study. The survey consisted of a questionnaire to assess the prevalence of recurrent NSP, with questions regarding having an occurrence more than once a week, characteristics of NSP, activity and lifestyle of the students, and the risk factors for recurrent NSP. A 36-item Short Form questionnaire was also examined. We found that 44.3% of the high school students surveyed had recurrent NSP (more than once a week) and the overall prevalence of NSP was 79.1%. The average sitting time was 10.2 ± 2.7 h/day. 59.0% did not sit straight, 14.7% used assisting devices during reading, and 11.9% answered that they stretched regularly. Found from their self assessed health, frequent fatigue and frequent depressed mood presented significant associations with the higher prevalence of recurrent NSP. Korean high school students had a high prevalence of recurrent NSP. Clinical attention is needed for the prevention and resolution of recurrent NSP found in high school students.

MIXING QUANTIFICATION BY VISUAL IMAGING ANALYSIS

EPA Science Inventory

This paper reports on development of a method for quantifying two measures of mixing, the scale and intensity of segregation, through flow visualization, video recording, and software analysis. This non-intrusive method analyzes a planar cross section of a flowing system from an ...

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

PubMed

Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

2010-12-01

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Serum and vitreous humor antibody titers in and isolation of Leptospira interrogans from horses with recurrent uveitis.

PubMed

Wollanke, B; Rohrbach, B W; Gerhards, H

2001-09-15

To measure antibody titers against Leptospira interrogans in serum and vitreous humor and determine the prevalence of L interrogans in vitreous humor of horses with recurrent uveitis. Cross-sectional study. 242 horses (270 eyes) with recurrent uveitis undergoing vitrectomy and 39 control horses (54 eyes) without any history or clinical signs of recurrent uveitis undergoing euthanasia or enucleation for unrelated reasons. Serum and vitreous humor were tested for antibodies against 13 serovars of L interrogans. Vitreous humor was submitted for leptospiral culture; isolates were typed to the serogroup level. Leptospira interrogans was isolated from vitreous humor from 120/229 (52%) horses (126/252 [50%] eyes) with recurrent uveitis but was not isolated from vitreous humor from 36 eyes of 21 control horses. Duration of recurrent uveitis was > or = 1 year for 45 of the 120 (38%) horses from which the organism was isolated. Geometric mean antibody titers against L interrogans in the vitreous humor and serum of horses with recurrent uveitis were 1:1,332 and 1:186, respectively. Only 91 of 120 (76%) horses from which the organism was isolated had a 4-fold or greater difference between serum and vitreous humor antibody titers. Results suggest that persistent ocular infection with L interrogans is common in horses with recurrent uveitis. A 4-fold increase in vitreous humor versus serum antibody titers may not be a sensitive test for the diagnosis of L interrogans-induced recurrent uveitis. We hypothesize that the immune component of recurrent uveitis can be directly induced and maintained by persistent infection of the eye with L interrogans.

MicroRNA Profile Predicts Recurrence after Resection in Patients with Hepatocellular Carcinoma within the Milan Criteria

PubMed Central

Sato, Fumiaki; Hatano, Etsuro; Kitamura, Koji; Myomoto, Akira; Fujiwara, Takeshi; Takizawa, Satoko; Tsuchiya, Soken; Tsujimoto, Gozoh; Uemoto, Shinji; Shimizu, Kazuharu

2011-01-01

Objective Hepatocellular carcinoma (HCC) is difficult to manage due to the high frequency of post-surgical recurrence. Early detection of the HCC recurrence after liver resection is important in making further therapeutic options, such as salvage liver transplantation. In this study, we utilized microRNA expression profiling to assess the risk of HCC recurrence after liver resection. Methods We examined microRNA expression profiling in paired tumor and non-tumor liver tissues from 73 HCC patients who satisfied the Milan Criteria. We constructed prediction models of recurrence-free survival using the Cox proportional hazard model and principal component analysis. The prediction efficiency was assessed by the leave-one-out cross-validation method, and the time-averaged area under the ROC curve (ta-AUROC). Results The univariate Cox analysis identified 13 and 56 recurrence-related microRNAs in the tumor and non-tumor tissues, such as miR-96. The number of recurrence-related microRNAs was significantly larger in the non-tumor-derived microRNAs (N-miRs) than in the tumor-derived microRNAs (T-miRs, P<0.0001). The best ta-AUROC using the whole dataset, T-miRs, N-miRs, and clinicopathological dataset were 0.8281, 0.7530, 0.7152, and 0.6835, respectively. The recurrence-free survival curve of the low-risk group stratified by the best model was significantly better than that of the high-risk group (Log-rank: P = 0.00029). The T-miRs tend to predict early recurrence better than late recurrence, whereas N-miRs tend to predict late recurrence better (P<0.0001). This finding supports the concept of early recurrence by the dissemination of primary tumor cells and multicentric late recurrence by the ‘field effect’. Conclusion microRNA profiling can predict HCC recurrence in Milan criteria cases. PMID:21298008

Chaos of radiative heat-loss-induced flame front instability.

PubMed

Kinugawa, Hikaru; Ueda, Kazuhiro; Gotoda, Hiroshi

2016-03-01

We are intensively studying the chaos via the period-doubling bifurcation cascade in radiative heat-loss-induced flame front instability by analytical methods based on dynamical systems theory and complex networks. Significant changes in flame front dynamics in the chaotic region, which cannot be seen in the bifurcation diagrams, were successfully extracted from recurrence quantification analysis and nonlinear forecasting and from the network entropy. The temporal dynamics of the fuel concentration in the well-developed chaotic region is much more complicated than that of the flame front temperature. It exhibits self-affinity as a result of the scale-free structure in the constructed visibility graph.

Mistreatment in an academic setting and medical students' perceptions about their course in São Paulo, Brazil: a cross-sectional study.

PubMed

Peres, Maria Fernanda Tourinho; Babler, Fernanda; Arakaki, Juliana Naomy Lacerda; Quaresma, Irene Yamamoto do Vale; Barreto, Abraão Deyvid Alves de Lima; Silva, Andréa Tenório Correia da; Eluf-Neto, José

2016-04-01

High prevalence of mistreatment among medical students has been described in the worldwide literature since the 1980s. However, studies addressing the severity and recurrence of victimization and its effects on students' perceptions of their medical course are scarce. This study had the aim of estimating the prevalence of exposure to mistreatment that was considered to be severe and recurrent and its association with medical students' perceptions about their medical course. A cross-sectional study was conducted in a medical school in São Paulo, Brazil. Three hundred and seventeen students from the first to the sixth year answered the online questionnaire. High prevalence of mistreatment during the course was found. Two thirds of the students considered the episodes to be severe, and around one third reported experiencing recurrent victimization. Occurences of mistreatment that the students considered to be severe were correlated with feeling overloaded and wanting to abandon the medical course. Occurrences of mistreatment within the academic environment are frequent in Brazil. The results suggest that mistreatment that was considered to be severe might negatively affect students' perceptions about their course.

Analysis of laser fluorosensor systems for remote algae detection and quantification

NASA Technical Reports Server (NTRS)

Browell, E. V.

1977-01-01

The development and performance of single- and multiple-wavelength laser fluorosensor systems for use in the remote detection and quantification of algae are discussed. The appropriate equation for the fluorescence power received by a laser fluorosensor system is derived in detail. Experimental development of a single wavelength system and a four wavelength system, which selectively excites the algae contained in the four primary algal color groups, is reviewed, and test results are presented. A comprehensive error analysis is reported which evaluates the uncertainty in the remote determination of the chlorophyll a concentration contained in algae by single- and multiple-wavelength laser fluorosensor systems. Results of the error analysis indicate that the remote quantification of chlorophyll a by a laser fluorosensor system requires optimum excitation wavelength(s), remote measurement of marine attenuation coefficients, and supplemental instrumentation to reduce uncertainties in the algal fluorescence cross sections.

A benchmarking procedure for PIGE related differential cross-sections

NASA Astrophysics Data System (ADS)

Axiotis, M.; Lagoyannis, A.; Fazinić, S.; Harissopulos, S.; Kokkoris, M.; Preketes-Sigalas, K.; Provatas, G.

2018-05-01

The application of standard-less PIGE requires the a priori knowledge of the differential cross section of the reaction used for the quantification of each detected light element. Towards this end, a lot of datasets have been published the last few years from several laboratories around the world. The discrepancies often found between different measured cross sections can be resolved by applying a rigorous benchmarking procedure through the measurement of thick target yields. Such a procedure is proposed in the present paper and is applied in the case of the 19F(p,p‧ γ)19F reaction.

Presence of intrahepatic (total and ccc) HBV DNA is not predictive of HBV recurrence after liver transplantation.

PubMed

Hussain, Munira; Soldevila-Pico, Consuelo; Emre, Sukru; Luketic, Velimir; Lok, Anna S F

2007-08-01

Previous studies reported that hepatitis B virus (HBV) deoxyribonucleic acid (DNA) can be detected in livers of patients who received transplants for hepatitis B despite the absence of serological markers of HBV recurrence. Quantification of HBV DNA was not performed and presence of covalently closed circular (ccc) DNA was not analyzed in most studies. We aimed to quantify total and ccc HBV DNA in explant liver and post-orthotopic liver transplantation (OLT) biopsies and to correlate the values with HBV recurrence post-OLT. Frozen liver tissue from 34 patients (9 with explant liver only, 9 with explant liver and post-OLT liver biopsies, and 16 with post-OLT biopsies only) in the National Institutes of Health HBV-OLT study was examined using real-time polymerase chain reaction (PCR). Among the 18 patients with explant liver, 7 were hepatitis B e antigen (HBeAg)-positive, 8 had detectable serum HBV DNA, and 10 received antiviral therapy prior to OLT. Total and ccc HBV DNA was detected in explant livers of 17 and 16 patients, respectively. Of the 10 patients who received antiviral therapy pre-OLT, serum HBV DNA was undetectable in 8 at transplantation but 7 had detectable total and ccc HBV DNA in their explant liver. Of the 25 patients with post-OLT biopsies, total HBV DNA was detected in 83% and ccc DNA in 17% of 47 biopsies, although only 2 patients had HBV recurrence. In conclusion, total and ccc HBV DNA could be detected in explant livers of most patients despite antiviral therapy pre-OLT. Total but not ccc HBV DNA could be detected in post-OLT liver biopsies of most patients despite undetectable serum HBV DNA and hepatitis B surface antigen (HBsAg). Our findings suggest that occult HBV reinfection occurs in most HBV patients after OLT and continued administration of appropriate prophylactic therapy is important in preventing overt HBV recurrence. Copyright (c) 2007 AASLD.

Investigation of associations between recurrence of major depressive disorder and spinal posture alignment: A quantitative cross-sectional study.

PubMed

Canales, Janette Z; Fiquer, Juliana T; Campos, Rodolfo N; Soeiro-de-Souza, Márcio Gerhardt; Moreno, Ricardo Alberto

2017-02-01

The aim of this study was to investigate associations between poor spinal posture and the recurrence of major depressive episodes and severity of symptoms in patients with major depressive disorder (MDD). This was a cross-sectional quantitative study of MDD patients. Outpatients were recruited from consecutive admissions at a mood disorders unit of a tertiary psychiatric hospital. Of 136 MDD patients, 72 (53 women, 19 men; mean age, 42.4±9.1years) met all the criteria and completed the study. Forty-one patients were classified with a recurrent episode (RE) of MDD and 31 with a single episode (SE). Quantitative assessments of postural deviations were made using photogrammetry, including kyphosis, shoulder protraction, and head inclination. The severity of depressive episodes was assessed using the Hamilton Depression Rating Scale. The diagnosis and classification of patients were performed according to DSM-IV-TR and SCID criteria. Multivariate analysis of variance indicated that the RE group had greater anterior head inclination (35.39; SD: 1.57), greater scapular abduction (1.69; SD: 0.93), and worse thoracic kyphosis (139.38; SD: 1.19) than the SE group (p<0.001 for all). Multivariate analysis of covariance showed an interaction between the severity of depressive symptoms and the degree of thoracic kyphosis (p=0.002). Recurrence of depressive episodes is associated with measures of postural misalignment. Copyright © 2016 Elsevier B.V. All rights reserved.

Closing the Feedback Loop: A Productive Interplay between Practice-Based Research and School Development through Cross-Professional Collaboration in Secondary Education

ERIC Educational Resources Information Center

Schenke, Wouter; van Driel, Jan H.; Geijsel, Femke P.; Volman, Monique L. L.

2017-01-01

A recurrent discussion in the field of education is how to build linkages between educational research and school practice. Cross-professional collaboration between researchers and school practitioners can contribute to the interplay between practice-based research and school development. The aim of our study is to obtain a better understanding of…

Thrombophilic disorders and fetal loss: a meta-analysis.

PubMed

Rey, Evelyne; Kahn, Susan R; David, Michèle; Shrier, Ian

2003-03-15

Our aim was to assess the strength of the controversial association between thrombophilia and fetal loss, and to examine whether it varies according to the timing or definition of fetal loss. We searched Medline and Current Contents for articles published between 1975 and 2002 and their references with terms denoting recurrent fetal and non-recurrent fetal loss combined with various thrombophilic disorders. We included in our meta-analysis case-control, cohort, and cross-sectional studies published in English, the methodological quality of which was rated as moderate or strong. Pooled odds ratios (OR) with 95% CI were generated by random effects models with Cochrane Review Manager software. We included 31 studies. Factor V Leiden was associated with early (OR 2.01, 95% CI 1.13-3.58) and late (7.83, 2.83-21.67) recurrent fetal loss, and late non-recurrent fetal loss (3.26, 1.82-5.83). Exclusion of women with other pathologies that could explain fetal loss strengthened the association between Factor V Leiden and recurrent fetal loss. Activated protein C resistance was associated with early recurrent fetal loss (3.48, 1.58-7.69), and prothrombin G20210A mutation with early recurrent (2.56, 1.04-.29) and late non-recurrent (2.30, 1.09-4.87) fetal loss. Protein S deficiency was associated with recurrent fetal loss (14.72, 0.99-218.01) and late non-recurrent fetal loss (7.39, 1.28-42.63). Methylenetetrahydrofolate mutation, protein C, and antithrombin deficiencies were not significantly associated with fetal loss. The magnitude of the association between thrombophilia and fetal loss varies, according to type of fetal loss and type of thrombophilia.

The ARTICO study: identification of patients at high risk of vascular recurrence after a first non-cardioembolic stroke.

PubMed

Serena, Joaquín; Segura, Tomás; Roquer, Jaume; García-Gil, María; Castillo, José

2015-03-11

About 20% of patients with a first ischaemic stroke will experience a new vascular event within the first year. The atherosclerotic burden, an indicator of the extension of atherosclerosis in a patient, has been associated with the risk of new cardiovascular events in the general population. However, no predictive models reliably identify groups at a high risk of recurrence. The ARTICO study prospectively analysed the predictive value for the risk of recurrence of specific atherosclerotic markers. The multicentre ARTICO study included 620 consecutive independent patients older than 60 years suffering from a first non-cardioembolic stroke. We analysed classical stroke risk factors; duplex study of supraaortic trunk including intima-media thickness (IMT) measurement; quantification of internal carotid (ICA) stenosis; number, morphology and surface characteristics of carotid plaques; ankle brachial index (ABI); and the presence of microalbuminuria. Patients were followed up at 6 and 12 months after inclusion. The primary end-point was death or major cardiovascular events. Any vascular event or death at 12 months occurred in 78 (13.8%) patients. In 40 (7.1%) of these the vascular event was a stroke recurrence. Weight, history of diabetes mellitus, history of symptomatic PAD, ABI <0.9 and significant ICA stenosis (>50%) were associated with a higher risk of vascular events on follow-up in the bivariate analysis. In the final Cox regression analysis, body mass index (BMI), systolic blood pressure, history of diabetes mellitus, symptomatic PAD (HR, 2.76; 95% CI, 1.10-6.95; p=0.03), and particularly patients with both ICA stenosis >50% and PAD (HR 4.52; 95% CI, 2.14-9.53; p<0.001) were independently associated with an increased risk of vascular events. Neither isolated ICA stenosis >50% nor isolated abnormal ABI remained associated with an increased risk of recurrence in comparison with the whole population. Symptomatic PAD identifies a high risk group of vascular recurrence after a first non-cardioembolic stroke. The associated increased risk was particularly high in patients with both ICA stenosis and either symptomatic or asymptomatic PAD. Neither asymptomatic PAD alone nor isolated ICA stenosis >50% were associated with an increased risk of recurrence in this particularly high-risk group of non-cardioembolic stroke.

Prediction of paroxysmal atrial fibrillation using recurrence plot-based features of the RR-interval signal.

PubMed

Mohebbi, Maryam; Ghassemian, Hassan

2011-08-01

Atrial fibrillation (AF) is the most common cardiac arrhythmia and increases the risk of stroke. Predicting the onset of paroxysmal AF (PAF), based on noninvasive techniques, is clinically important and can be invaluable in order to avoid useless therapeutic intervention and to minimize risks for the patients. In this paper, we propose an effective PAF predictor which is based on the analysis of the RR-interval signal. This method consists of three steps: preprocessing, feature extraction and classification. In the first step, the QRS complexes are detected from the electrocardiogram (ECG) signal and then the RR-interval signal is extracted. In the next step, the recurrence plot (RP) of the RR-interval signal is obtained and five statistically significant features are extracted to characterize the basic patterns of the RP. These features consist of the recurrence rate, length of longest diagonal segments (L(max )), average length of the diagonal lines (L(mean)), entropy, and trapping time. Recurrence quantification analysis can reveal subtle aspects of dynamics not easily appreciated by other methods and exhibits characteristic patterns which are caused by the typical dynamical behavior. In the final step, a support vector machine (SVM)-based classifier is used for PAF prediction. The performance of the proposed method in prediction of PAF episodes was evaluated using the Atrial Fibrillation Prediction Database (AFPDB) which consists of both 30 min ECG recordings that end just prior to the onset of PAF and segments at least 45 min distant from any PAF events. The obtained sensitivity, specificity, positive predictivity and negative predictivity were 97%, 100%, 100%, and 96%, respectively. The proposed methodology presents better results than other existing approaches.

Extraction of tamoxifen and its metabolites from formalin-fixed, paraffin-embedded tissues: an innovative quantitation method using liquid chromatography and tandem mass spectrometry.

PubMed

Ng, Ella S M; Kangarloo, S Bill; Konno, Mie; Paterson, Alexander; Magliocco, Anthony M

2014-03-01

Tamoxifen is a key therapeutic option for breast cancer treatment. Understanding its complex metabolism and pharmacokinetics is important for dose optimization. We examined the possibility of utilizing archival formalin-fixed paraffin-embedded (FFPE) tissue as an alternative sample source for quantification since well-annotated retrospective samples were always limited. Six 15 μm sections of FFPE tissues were deparaffinized with xylene and purified using solid-phase extraction. Tamoxifen and its metabolites were separated and detected by liquid chromatography-tandem mass spectrometry using multiple-reaction monitoring. This method was linear between 0.4 and 200 ng/g for 4-hydroxy-tamoxifen and endoxifen, and 4-2,000 ng/g for tamoxifen and N-desmethyl-tamoxifen. Inter- and intra-assay precisions were <9 %, and mean accuracies ranged from 81 to 106 %. Extraction recoveries were between 83 and 88 %. The validated method was applied to FFPE tissues from two groups of patients, who received 20 mg/day of tamoxifen for >6 months, and were classified into breast tumor recurrence and non-recurrence. Our preliminary data show that levels of tamoxifen metabolites were significantly lower in patients with recurrent cancer, suggesting that inter-individual variability in tamoxifen metabolism might partly account for the development of cancer recurrence. Nevertheless, other causes such as non-compliance or stopping therapy of tamoxifen could possibly lead to the concentration differences. The ability to successfully study tamoxifen metabolism in such tissue samples will rapidly increase our knowledge of how tamoxifen's action, metabolism and tissue distribution contribute to breast cancer control. However, larger population studies are required to understand the underlying mechanism of tamoxifen metabolism for optimization of its treatment.

Rank-based testing of equal survivorship based on cross-sectional survival data with or without prospective follow-up.

PubMed

Chan, Kwun Chuen Gary; Qin, Jing

2015-10-01

Existing linear rank statistics cannot be applied to cross-sectional survival data without follow-up since all subjects are essentially censored. However, partial survival information are available from backward recurrence times and are frequently collected from health surveys without prospective follow-up. Under length-biased sampling, a class of linear rank statistics is proposed based only on backward recurrence times without any prospective follow-up. When follow-up data are available, the proposed rank statistic and a conventional rank statistic that utilizes follow-up information from the same sample are shown to be asymptotically independent. We discuss four ways to combine these two statistics when follow-up is present. Simulations show that all combined statistics have substantially improved power compared with conventional rank statistics, and a Mantel-Haenszel test performed the best among the proposal statistics. The method is applied to a cross-sectional health survey without follow-up and a study of Alzheimer's disease with prospective follow-up. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Patterns of Intraosseous Recurrence After Stereotactic Body Radiation Therapy for Coxal Bone Metastasis.

PubMed

Ito, Kei; Shimizuguchi, Takuya; Nihei, Keiji; Furuya, Tomohisa; Ogawa, Hiroaki; Tanaka, Hiroshi; Sasai, Keisuke; Karasawa, Katsuyuki

2018-01-01

To analyze the detailed pattern of intraosseous failure after stereotactic body radiation therapy (SBRT) for coxal bone metastasis. Patients treated with SBRT to coxal bone metastasis were identified by retrospective chart review. The SBRT doses were 30 Gy or 35 Gy in 5 fractions. A margin of 5 to 10 mm was added to the gross tumor volume to create the clinical target volume. We evaluated the presence or absence of intraosseous recurrence using magnetic resonance imaging. Intraosseous recurrences were assessed as "in-field" or "marginal/out-of-field." In addition, we measured the distance between the center of the recurrent tumor and the nearest edge of the initial bone metastasis in cases of marginal/out-of-field recurrence. Seventeen patients treated for 17 coxal bone metastases were included. Median age was 64 years (range, 48-79 years). Coxal lesions involved the ilium in 14 cases, pubis in 3, and ischium in 4 (3 lesions crossed over multiple regions). Patients most commonly had renal cell carcinoma (29.4%), followed by lung, hepatic cell, and colorectal cancers (23.5%, 11.8%, and 11.8%, respectively). Median follow-up after SBRT was 13 months (range, 2-44 months). Among all 17 cases, 7 cases developed 8 intraosseous recurrences, including in-field recurrence in 1 case and marginal/out-of-field recurrences in 7 cases. Median time to intraosseous recurrence was 10 months (range, 2-35 months). Among 7 cases with marginal/out-of-field recurrence, mean distance to the center of the recurrent tumor from the nearest edge of the initial bone metastasis was 34 mm (range, 15-55 mm). Most recurrences were observed out-of-field in the same coxal bone. These results suggest that defining the optimal clinical target volume in SBRT for coxal bone metastasis to obtain sufficient local tumor control is difficult. Copyright © 2017 Elsevier Inc. All rights reserved.

In-vitro Equilibrium Phosphate Binding Study of Sevelamer Carbonate by UV-Vis Spectrophotometry.

PubMed

Prasaja, Budi; Syabani, M Maulana; Sari, Endah; Chilmi, Uci; Cahyaningsih, Prawitasari; Kosasih, Theresia Weliana

2018-06-12

Sevelamer carbonate is a cross-linked polymeric amine; it is the active ingredient in Renvela ® tablets. US FDA provides recommendation for demonstrating bioequivalence for the development of a generic product of sevelamer carbonte using in-vitro equilibrium binding study. A simple UV-vis spectrophotometry method was developed and validated for quantification of free phosphate to determine the binding parameter constant of sevelamer. The method validation demonstrated the specificity, limit of quantification, accuracy and precision of measurements. The validated method has been successfully used to analyze samples in in-vitro equilibrium binding study for demonstrating bioequivalence. © Georg Thieme Verlag KG Stuttgart · New York.

Comparative quantification of dietary supplemented neural creatine concentrations with (1)H-MRS peak fitting and basis spectrum methods.

PubMed

Turner, Clare E; Russell, Bruce R; Gant, Nicholas

2015-11-01

Magnetic resonance spectroscopy (MRS) is an analytical procedure that can be used to non-invasively measure the concentration of a range of neural metabolites. Creatine is an important neurometabolite with dietary supplementation offering therapeutic potential for neurological disorders with dysfunctional energetic processes. Neural creatine concentrations can be probed using proton MRS and quantified using a range of software packages based on different analytical methods. This experiment examines the differences in quantification performance of two commonly used analysis packages following a creatine supplementation strategy with potential therapeutic application. Human participants followed a seven day dietary supplementation regime in a placebo-controlled, cross-over design interspersed with a five week wash-out period. Spectroscopy data were acquired the day immediately following supplementation and analyzed with two commonly-used software packages which employ vastly different quantification methods. Results demonstrate that neural creatine concentration was augmented following creatine supplementation when analyzed using the peak fitting method of quantification (105.9%±10.1). In contrast, no change in neural creatine levels were detected with supplementation when analysis was conducted using the basis spectrum method of quantification (102.6%±8.6). Results suggest that software packages that employ the peak fitting procedure for spectral quantification are possibly more sensitive to subtle changes in neural creatine concentrations. The relative simplicity of the spectroscopy sequence and the data analysis procedure suggest that peak fitting procedures may be the most effective means of metabolite quantification when detection of subtle alterations in neural metabolites is necessary. The straightforward technique can be used on a clinical magnetic resonance imaging system. Copyright © 2015 Elsevier Inc. All rights reserved.

Factors associated with occasional and recurrent falls in Mexican community-dwelling older people.

PubMed

Agudelo-Botero, Marcela; Giraldo-Rodríguez, Liliana; Murillo-González, Juana Catalina; Mino-León, Dolores; Cruz-Arenas, Esteban

2018-01-01

Falls are a frequent event among older adults that can cause wounds, disability, psychological disorders, and premature death. Although the large number of existing studies on the issue, few have been conducted in middle- and low-income countries. The objective of the present study is to identify the sociodemographic, medical, and functional performance factors associated with occasional and recurrent falls in Mexican older adults dwelling in community. Cross-sectional analysis of 9 598 adults ≥60 years old who participated in the fourth round (2015) of the Mexican Health and Aging Study. Bivariate tests were performed to evaluate the differences between covariates by distinct fall groups (no falls, occasional falls, and recurrent falls). Multiple logistic regressions with unadjusted and adjusted models were estimated. Approximately 46% of older adults had had at least one fall during the previous two years (one fall 16% and recurrent falls 30%). Occasional falls were only associated with being a woman; in addition to the sex, recurrent falls were strongly associated with advanced age, rural residence, bad and very bad self-perception of health status, activity-limiting pain, urinary incontinence, depression, arthritis, limitations in basic activities of daily living, and limitations in advanced activities of daily living. Falls, primarily recurrent falls, deserve to be addressed through multifactorial strategies that include different areas of intervention.

Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma. | Office of Cancer Genomics

Cancer.gov

High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream of genomic alterations, including recurrent chromosomal alterations. Our analysis identified three molecular subtypes of high-risk neuroblastomas, consistent with chromosomal alterations, and identified subtype-specific master regulator (MR) proteins that were conserved across independent cohorts.

Determining team cognition from delay analysis using cross recurrence plot.

PubMed

Hajari, Nasim; Cheng, Irene; Bin Zheng; Basu, Anup

2016-08-01

Team cognition is an important factor in evaluating and determining team performance. Forming a team with good shared cognition is even more crucial for laparoscopic surgery applications. In this study, we analyzed the eye tracking data of two surgeons during a laparoscopic simulation operation, then performed Cross Recurrence Analysis (CRA) on the recorded data to study the delay behaviour for good performer and poor performer teams. Dual eye tracking data for twenty two dyad teams were recorded during a laparoscopic task and then the teams were divided into good performer and poor performer teams based on the task times. Eventually we studied the delay between two team members for good and poor performer teams. The results indicated that the good performer teams show a smaller delay comparing to poor performer teams. This study is compatible with gaze overlap analysis between team members and therefore it is a good evidence of shared cognition between team members.

Single cell genomic quantification by non-fluorescence nonlinear microscopy

NASA Astrophysics Data System (ADS)

Kota, Divya; Liu, Jing

2017-02-01

Human epidermal growth receptor 2 (Her2) is a gene which plays a major role in breast cancer development. The quantification of Her2 expression in single cells is limited by several drawbacks in existing fluorescence-based single molecule techniques, such as low signal-to-noise ratio (SNR), strong autofluorescence and background signals from biological components. For rigorous genomic quantification, a robust method of orthogonal detection is highly desirable and we demonstrated it by two non-fluorescent imaging techniques -transient absorption microscopy (TAM) and second harmonic generation (SHG). In TAM, gold nanoparticles (AuNPs) are chosen as an orthogonal probes for detection of single molecules which gives background-free quantifications of single mRNA transcript. In SHG, emission from barium titanium oxide (BTO) nanoprobes was demonstrated which allows stable signal beyond the autofluorescence window. Her2 mRNA was specifically labeled with nanoprobes which are conjugated with antibodies or oligonucleotides and quantified at single copy sensitivity in the cancer cells and tissues. Furthermore, a non-fluorescent super-resolution concept, named as second harmonic super-resolution microscopy (SHaSM), was proposed to quantify individual Her2 transcripts in cancer cells beyond the diffraction limit. These non-fluorescent imaging modalities will provide new dimensions in biomarker quantification at single molecule sensitivity in turbid biological samples, offering a strong cross-platform strategy for clinical monitoring at single cell resolution.

YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.

PubMed

Cheng, Wei-Chung; Chung, I-Fang; Tsai, Cheng-Fong; Huang, Tse-Shun; Chen, Chen-Yang; Wang, Shao-Chuan; Chang, Ting-Yu; Sun, Hsing-Jen; Chao, Jeffrey Yung-Chuan; Cheng, Cheng-Chung; Wu, Cheng-Wen; Wang, Hsei-Wei

2015-01-01

We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Change in Pattern of Relapse After Antiangiogenic Therapy in High-Grade Glioma

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

Narayana, Ashwatha, E-mail: ashwatha.narayana@nyumc.org; Department of Neurosurgery, New York University Langone Medical Center, New York, NY; Kunnakkat, Saroj D.

2012-01-01

Purpose: Local recurrence is the dominant pattern of relapse in high-grade glioma (HGG) after conventional therapy. The recent use of antiangiogenic therapy has shown impressive radiologic and clinical responses in adult HGG. The preclinical data suggesting increased invasiveness after angiogenic blockade have necessitated a detailed analysis of the pattern of recurrence after therapy. Methods and Materials: A total of 162 consecutive patients with HGG, either newly diagnosed (n = 58) or with recurrent disease (n = 104) underwent therapy with bevacizumab at 10 mg/kg every 2 weeks and conventional chemotherapy with or without involved field radiotherapy until disease progression. Themore » pattern of recurrence and interval to progression were the primary aims of the present study. Diffuse invasive recurrence (DIR) was defined as the involvement of multiple lobes with or without crossing the midline. Results: At a median follow-up of 7 months (range, 1-37), 105 patients had recurrence, and 79 patients ultimately developed DIR. The interval to progression was similar in the DIR and local recurrence groups (6.5 and 6.3 months, p = .296). The hazard risk of DIR increased exponentially with time and was similar in those with newly diagnosed and recurrent HGG (R{sup 2} = 0.957). The duration of bevacizumab therapy increased the interval to recurrence (p < .0001) and improved overall survival (p < .0001). However, the pattern of relapse did not affect overall survival (p = .253). Conclusion: Along with an increase in median progression-free survival, bevacizumab therapy increased the risk of DIR in HGG patients. The risk of increased invasion with prolonged angiogenic blockade should be addressed in future clinical trials.« less

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms: Cross-platform Transferable Chemical Signatures

PubMed Central

Telu, Kelly H.; Yan, Xinjian; Wallace, William E.; Stein, Stephen E.; Simón-Manso, Yamil

2016-01-01

RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different LC-MS platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC-MS platforms using reversed phase chromatography and different chromatographic scales (nano, conventional and UHPLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (RSD < 2%); however, substantial differences were found in the LC-MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. PMID:26842580

Optically transmitted and inductively coupled electric reference to access in vivo concentrations for quantitative proton-decoupled ¹³C magnetic resonance spectroscopy.

PubMed

Chen, Xing; Pavan, Matteo; Heinzer-Schweizer, Susanne; Boesiger, Peter; Henning, Anke

2012-01-01

This report describes our efforts on quantification of tissue metabolite concentrations in mM by nuclear Overhauser enhanced and proton decoupled (13) C magnetic resonance spectroscopy and the Electric Reference To access In vivo Concentrations (ERETIC) method. Previous work showed that a calibrated synthetic magnetic resonance spectroscopy-like signal transmitted through an optical fiber and inductively coupled into a transmit/receive coil represents a reliable reference standard for in vivo (1) H magnetic resonance spectroscopy quantification on a clinical platform. In this work, we introduce a related implementation that enables simultaneous proton decoupling and ERETIC-based metabolite quantification and hence extends the applicability of the ERETIC method to nuclear Overhauser enhanced and proton decoupled in vivo (13) C magnetic resonance spectroscopy. In addition, ERETIC signal stability under the influence of simultaneous proton decoupling is investigated. The proposed quantification method was cross-validated against internal and external reference standards on human skeletal muscle. The ERETIC signal intensity stability was 100.65 ± 4.18% over 3 months including measurements with and without proton decoupling. Glycogen and unsaturated fatty acid concentrations measured with the ERETIC method were in excellent agreement with internal creatine and external phantom reference methods, showing a difference of 1.85 ± 1.21% for glycogen and 1.84 ± 1.00% for unsaturated fatty acid between ERETIC and creatine-based quantification, whereas the deviations between external reference and creatine-based quantification are 6.95 ± 9.52% and 3.19 ± 2.60%, respectively. Copyright © 2011 Wiley Periodicals, Inc.

Quantification of Material Fluorescence and Light Scattering Cross Sections Using Ratiometric Bandwidth-Varied Polarized Resonance Synchronous Spectroscopy.

PubMed

Xu, Joanna Xiuzhu; Hu, Juan; Zhang, Dongmao

2018-05-25

Presented herein is the ratiometric bandwidth-varied polarized resonance synchronous spectroscopy (BVPRS2) method for quantification of material optical activity spectra. These include the sample light absorption and scattering cross-section spectrum, the scattering depolarization spectrum, and the fluorescence emission cross-section and depolarization spectrum in the wavelength region where the sample both absorbs and emits. This ratiometric BVPRS2 spectroscopic method is a self-contained technique capable of quantitatively decoupling material fluorescence and light scattering signal contribution to its ratiometric BVPRS2 spectra through the linear curve-fitting of the ratiometric BVPRS2 signal as a function of the wavelength bandwidth used in the PRS2 measurements. Example applications of this new spectroscopic method are demonstrated with materials that can be approximated as pure scatterers, simultaneous photon absorbers/emitters, simultaneous photon absorbers/scatterers, and finally simultaneous photon absorbers/scatterers/emitters. Because the only instruments needed for this ratiometric BVPRS2 technique are the conventional UV-vis spectrophotometer and spectrofluorometer, this work should open doors for routine decomposition of material UV-vis extinction spectrum into its absorption and scattering component spectra. The methodology and insights provided in this work should be of broad significance to all chemical research that involves photon/matter interactions.

[Experience in the surgical treatment of paranasal sinus mucoceles in a university hospital].

PubMed

Waizel-Haiat, Salomón; Díaz-Lara, Ivette Margarita; Vargas-Aguayo, Alejandro Martin; Santiago-Cordova, Jorge Luis

Mucoceles are benign cystic lesions of the paranasal sinuses. Endoscopic marsupialisation is considered the first choice of treatment, due to its low morbidity and recurrence rates. To establish the number of patients with recurrence, who were diagnosed clinically or by computed tomography, and who were submitted to surgery in the Ear, Nose and Throat Unit in a tertiary university hospital. A clinical, cross-sectional, descriptive, observational and retrospective study was conducted on patients with a mucocele diagnosis operated on in the period from January 2006 to December 2013. A descriptive statistical analysis was performed to obtain the frequencies, ratios and proportions. Measures of central tendency and dispersion were obtained. The recurrence rates of each surgical technique were compared using the Chi-squared test. Of the 59 patients included in the study, 39 were female and 20 were men. The most common location was in the maxillary sinus (22 patients) followed by frontoethmoidal (20 patients). There was a recurrence of 9% in those submitted to a surgical procedure. The endoscopic approach was used in 51 patients, 8 cases were combined (open plus endoscopic), and there was no open approach. There was a recurrence in 7 of 51 of patients with endoscopic surgery, and one out of 8 patients had a recurrence with a combined technique. No statistically significant relationship was found between the type of surgery and recurrence, or between the presence or absence of a predisposing factor and recurrence. Copyright © 2016 Academia Mexicana de Cirugía A.C. Publicado por Masson Doyma México S.A. All rights reserved.

Differences in personal and lifestyle characteristics among Zimbabwean high school adolescents with and without recurrent non-specific low back pain: a two part cross-sectional study.

PubMed

Chiwaridzo, Matthew; Naidoo, Nirmala

2015-01-01

Recurrent non-specific low back pain (NSLBP) is increasingly becoming common among adolescents worldwide. A recent study in Zimbabwe showed a relatively high prevalence (28.8 %) among high school students. Influential associated factors, however, remain unclear. This is a significant shortcoming. The aim was to determine personal or lifestyle-related factors associated with recurrent NSLBP among high school adolescents in Harare, Zimbabwe. This study was part of a large epidemiological study conducted in two continuous parts. Part one sought to determine self-reported associated factors among 532 participants (mean age =16 ± 1.72 years) drawn randomly from selected government schools using a reliable and content-validated questionnaire (Kappa coefficient, k = 0.32-1). Part two purposively identified adolescents ( N  = 64, median age =17 years, interquartile range, IQR = 15-18 years) with a history of 'severe' recurrent NSLBP from part one based on a specific eligibility criteria and compared body mass index, relative school bag weight and hamstring flexibility with matched adolescents without NSLBP. Data was analysed using Statistica version 11. Independent t -tests or χ 2 tests of association were used for continuous and categorical data, respectively. The statistical significance was set at p  < .05. Recurrent NSLBP was associated with self-reported factors such as perceptions of a heavy school bag [χ 2 (1) = 85.9, p  < 0.001]. A significant proportion of adolescents with recurrent NSLBP spent over 30 min carrying the school bag to and from school [χ 2 (1) =32.2, p  < 0.001]. It was also associated with prolonged sitting ( p  < 0.001), not playing sports [χ 2 (1) =5.85, p  = 0.02] and tight hamstrings [χ 2 (1) =7.6, p  = 0.006]. Although conclusions from this study are hesitant because of the cross-sectional nature of the study and the relatively small sample size in follow-up study, recurrent NSLBP is associated with perceptions of a heavy school bag, duration of school bag carriage, no sports participation, prolonged sitting on entertainment activities, and tight hamstrings. These findings add to the importance of promoting physical activity at school or home especially aimed at improving muscle flexibility.

Anxiety, depression and behavioral problems among adolescents with recurrent headache: the Young-HUNT study

PubMed Central

2014-01-01

Background It is well documented that both anxiety and depression are associated with headache, but there is limited knowledge regarding the relation between recurrent primary headaches and symptoms of anxiety and depression as well as behavioral problems among adolescents. Assessment of co-morbid disorders is important in order to improve the management of adolescents with recurrent headaches. Thus the main purpose of the present study was to assess the relationship of recurrent headache with anxiety and depressive symptoms and behavioral problems in a large population based cross-sectional survey among adolescents in Norway. Methods A cross-sectional, population-based study was conducted in Norway from 1995 to 1997 (Young-HUNT1). In Young-HUNT1, 4872 adolescents aged 12 to 17 years were interviewed about their headache complaints and completed a comprehensive questionnaire that included assessment of symptoms of anxiety and depression and behavioral problems, i.e. conduct and attention difficulties. Results In adjusted multivariate analyses among adolescents aged 12–14 years, recurrent headache was associated with symptoms of anxiety and depression (OR: 2.05, 95% CI: 1.61-2.61, p < 0.001), but not with behavioral problems. A significant association with anxiety and depressive symptoms was evident for all headache categories; i.e. migraine, tension-type headache and non-classifiable headache. Among adolescents aged 15–17 years there was a significant association between recurrent headache and symptoms of anxiety and depression (OR: 1.64, 95% CI: 1.39-1.93, p < 0,001) and attention difficulties (OR: 1.25, 95% CI: 1.09-1.44, p =0.001). For migraine there was a significant association with both anxiety and depressive symptoms and attention difficulties, while tension-type headache was significantly associated only with symptoms of anxiety and depression. Non-classifiable headache was associated with attention difficulties and conduct difficulties, but not with anxiety and depressive symptoms. Headache frequency was significantly associated with increasing symptoms scores for anxiety and depressive symptoms as well as attention difficulties, evident for both age groups. Conclusions The results from the present study indicate that both anxiety and depressive symptoms and behavioral problems are associated with recurrent headache, and should accordingly be considered a part of the clinical assessment of children and adolescents with headache. Identification of these associated factors and addressing them in interventions may improve headache management. PMID:24925252

Systemic risk score evaluation in ischemic stroke patients (SCALA): a prospective cross sectional study in 85 German stroke units.

PubMed

Weimar, Christian; Goertler, Michael; Röther, Joachim; Ringelstein, E Bernd; Darius, Harald; Nabavi, Darius Günther; Kim, In-Ha; Theobald, Karlheinz; Diener, Han-Christoph

2007-11-01

Stratification of patients with transient ischemic attack (TIA) or ischemic stroke (IS) by risk of recurrent stroke can contribute to optimized secondary prevention. We therefore aimed to assess cardiovascular risk factor profiles of consecutive patients hospitalized with TIA/IS to stratify the risk of recurrent stroke according to the Essen Stroke Risk Score (ESRS) and of future cardiovascular events according to the ankle brachial index (ABI) as a marker of generalized atherosclerosis In this cross-sectional observational study, 85 neurological stroke units throughout Germany documented cardiovascular risk factor profiles of 10 consecutive TIA/IS patients on standardized questionnaires. Screening for PAD was done with Doppler ultrasonography to calculate the ABI. A total of 852 patients (57% men) with a mean age of 67+/-12.4 years were included of whom 82.9 % had IS. The median National Institutes of Health stroke sum score was 4 (TIA: 1). Arterial hypertension was reported in 71%, diabetes mellitus in 26%, clinical PAD in 10%, and an ABI < or = 0.9 in 51%. An ESRS > or = 3 was observed in 58%, which in two previous retrospective analyses corresponded to a recurrent stroke risk of > or = 4%/year. The correlation between the ESRS and the ABI was low (r = 0.21). A high proportion of patients had asymptomatic atherosclerotic disease and a considerable risk of recurrent stroke according to the ABI and ESRS category. The prognostic accuracy as well as the potential benefit of various risk stratification scores in secondary stroke prevention require validation in a larger prospective study.

Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer.

PubMed

Tamez-Peña, Jose-Gerardo; Rodriguez-Rojas, Juan-Andrés; Gomez-Rueda, Hugo; Celaya-Padilla, Jose-Maria; Rivera-Prieto, Roxana-Alicia; Palacios-Corona, Rebeca; Garza-Montemayor, Margarita; Cardona-Huerta, Servando; Treviño, Victor

2018-01-01

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures.

Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer

PubMed Central

Tamez-Peña, Jose-Gerardo; Rodriguez-Rojas, Juan-Andrés; Gomez-Rueda, Hugo; Celaya-Padilla, Jose-Maria; Rivera-Prieto, Roxana-Alicia; Palacios-Corona, Rebeca; Garza-Montemayor, Margarita; Cardona-Huerta, Servando

2018-01-01

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures. PMID:29596496

Predictors of adjustment and growth in women with recurrent ovarian cancer.

PubMed

Ponto, Julie Ann; Ellington, Lee; Mellon, Suzanne; Beck, Susan L

2010-05-01

To analyze predictors of adjustment and growth in women who had experienced recurrent ovarian cancer using components of the Resiliency Model of Family Stress, Adjustment, and Adaptation as a conceptual framework. Cross-sectional. Participants were recruited from national cancer advocacy groups. 60 married or partnered women with recurrent ovarian cancer. Participants completed an online or paper survey. Independent variables included demographic and illness variables and meaning of illness. Outcome variables were psychological adjustment and post-traumatic growth. A model of five predictor variables (younger age, fewer years in the relationship, poorer performance status, greater symptom distress, and more negative meaning) accounted for 64% of the variance in adjustment but did not predict post-traumatic growth. This study supports the use of a model of adjustment that includes demographic, illness, and appraisal variables for women with recurrent ovarian cancer. Symptom distress and poorer performance status were the most significant predictors of adjustment. Younger age and fewer years in the relationship also predicted poorer adjustment. Nurses have the knowledge and skills to influence the predictors of adjustment to recurrent ovarian cancer, particularly symptom distress and poor performance status. Nurses who recognize the predictors of poorer adjustment can anticipate problems and intervene to improve adjustment for women.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

2016-04-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Computational Approach to Musical Consonance and Dissonance

PubMed Central

Trulla, Lluis L.; Di Stefano, Nicola; Giuliani, Alessandro

2018-01-01

In sixth century BC, Pythagoras discovered the mathematical foundation of musical consonance and dissonance. When auditory frequencies in small-integer ratios are combined, the result is a harmonious perception. In contrast, most frequency combinations result in audible, off-centered by-products labeled “beating” or “roughness;” these are reported by most listeners to sound dissonant. In this paper, we consider second-order beats, a kind of beating recognized as a product of neural processing, and demonstrate that the data-driven approach of Recurrence Quantification Analysis (RQA) allows for the reconstruction of the order in which interval ratios are ranked in music theory and harmony. We take advantage of computer-generated sounds containing all intervals over the span of an octave. To visualize second-order beats, we use a glissando from the unison to the octave. This procedure produces a profile of recurrence values that correspond to subsequent epochs along the original signal. We find that the higher recurrence peaks exactly match the epochs corresponding to just intonation frequency ratios. This result indicates a link between consonance and the dynamical features of the signal. Our findings integrate a new element into the existing theoretical models of consonance, thus providing a computational account of consonance in terms of dynamical systems theory. Finally, as it considers general features of acoustic signals, the present approach demonstrates a universal aspect of consonance and dissonance perception and provides a simple mathematical tool that could serve as a common framework for further neuro-psychological and music theory research. PMID:29670552

Polarization-sensitive optical coherence tomography-based imaging, parameterization, and quantification of human cartilage degeneration

NASA Astrophysics Data System (ADS)

Brill, Nicolai; Wirtz, Mathias; Merhof, Dorit; Tingart, Markus; Jahr, Holger; Truhn, Daniel; Schmitt, Robert; Nebelung, Sven

2016-07-01

Polarization-sensitive optical coherence tomography (PS-OCT) is a light-based, high-resolution, real-time, noninvasive, and nondestructive imaging modality yielding quasimicroscopic cross-sectional images of cartilage. As yet, comprehensive parameterization and quantification of birefringence and tissue properties have not been performed on human cartilage. PS-OCT and algorithm-based image analysis were used to objectively grade human cartilage degeneration in terms of surface irregularity, tissue homogeneity, signal attenuation, as well as birefringence coefficient and band width, height, depth, and number. Degeneration-dependent changes were noted for the former three parameters exclusively, thereby questioning the diagnostic value of PS-OCT in the assessment of human cartilage degeneration.

Demonstration of a rapidly-swept external cavity quantum cascade laser for rapid and sensitive quantification of chemical mixtures

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

Brumfield, Brian E.; Taubman, Matthew S.; Phillips, Mark C.

2016-02-13

A rapidly-swept external cavity quantum cascade laser (ECQCL) system for fast open-path quantification of multiple chemicals and mixtures is presented. The ECQCL system is swept over its entire tuning range (>100 cm-1) at frequencies up to 200 Hz. At 200 Hz the wavelength tuning rate and spectral resolution are 2x104 cm-1/sec and < 0.2 cm-1, respectively. The capability of the current system to quantify changes in chemical concentrations on millesecond timescales is demonstrated at atmospheric pressure using an open-path multi-pass cell. The detection limits for chemicals ranged from ppb to ppm levels depending on the absorption cross-section.

CROSS and beyond: a clinical perspective on the results of the randomized ChemoRadiotherapy for Oesophageal cancer followed by Surgery Study.

PubMed

van der Woude, Stephanie O; Hulshof, Maarten C C M; van Laarhoven, Hanneke W M

2016-02-01

Despite extensive research efforts oesophageal cancer remains a malignancy with a poor prognosis. Improvement of treatment is urgently needed. Although multimodality treatment for resectable oesophageal cancer has established it place in standard practice, there are still many differences worldwide in the preferred treatment. The Dutch ChemoRadiotherapy for Oesophageal cancer followed by Surgery Study (CROSS) trial has contributed significantly to the current use of neoadjuvant chemoradiation. This study compared neoadjuvant chemoradiotherapy (CRT) using a moderate radiation dose weekly combined with carboplatin and paclitaxel followed by surgery versus surgery alone. Median overall survival in the CRT group is 49.4 months compared to 24.0 months in the surgery alone group, resulting in an overall survival benefit of 13% in favor of the CRT group (HR, 0.81; 95% CI: 0.70-0.93; P=0.002). Recently the results after long-term follow-up (median 60 months) have been published and confirm the benefit of neoadjuvant CRT to surgery alone. Perioperative mortality rates are low and did not increase by adding CRT (4%) and the CROSS scheme has a favorable toxicity profile. Recurrence patterns in patients treated according to the CROSS protocol report significantly reduced loco regional recurrence in the CRT group (34% to 14%; P<0.001) and less peritoneal carcinomatosis (14% to 4%; P<0.001). With the contemporary focus of research on tumor tailored therapy, the effective and safe CROSS protocol serves as a backbone in many ongoing trials.

Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

PubMed

Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

2016-01-01

Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic selection in autogamous crops, especially bringing long-term improvement.

Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops

PubMed Central

Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

2016-01-01

Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an “island model” inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic selection in autogamous crops, especially bringing long-term improvement. PMID:27115872

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

PubMed

Röst, Hannes L; Liu, Yansheng; D'Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-09-01

Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.

Semiparametric Thurstonian Models for Recurrent Choices: A Bayesian Analysis

ERIC Educational Resources Information Center

Ansari, Asim; Iyengar, Raghuram

2006-01-01

We develop semiparametric Bayesian Thurstonian models for analyzing repeated choice decisions involving multinomial, multivariate binary or multivariate ordinal data. Our modeling framework has multiple components that together yield considerable flexibility in modeling preference utilities, cross-sectional heterogeneity and parameter-driven…

The measurement of creep in ultrahigh molecular weight polyethylene: a comparison of conventional versus highly cross-linked polyethylene.

PubMed

Estok, Daniel M; Bragdon, Charles R; Plank, Gordon R; Huang, Anna; Muratoglu, Orhun K; Harris, William H

2005-02-01

Quantification of creep of highly cross-linked polyethylene would enable separation of creep from wear when evaluating femoral head penetration into polyethylene. We compared creep magnitude of a highly cross-linked versus conventional polyethylene in the laboratory. Twelve acetabular liners of each material were tested, 6 of which had a 32-mm inner diameter (ID) and 6 had 28-mm ID. Creep was measured using coordinate measuring machines during loading at 2 Hz without motion to 4 million cycles. Penetration into 32-mm ID conventional liners reached 97 microm versus 107 microm for highly cross-linked material, not significant. Penetration into 28-mm conventional liners was 132 microm versus 155 microm for highly cross-linked material (P = .017). Ninety percent of the creep had occurred by 2.5 million cycles.

Understanding Chronically Reported Families

PubMed Central

Jonson-Reid, Melissa; Emery, Clifton R.; Drake, Brett; Stahlschmidt, Mary Jo

2013-01-01

Although a strong literature on child maltreatment re-reporting exists, much of that literature stops at the first re-report. The literature on chronic re-reporting, meaning reports beyond the second report, is scant. The authors follow Loman’s lead in focusing on reports beyond the first two to determine what factors predict these “downstream” report stages. Cross-sector, longitudinal administrative data are used. The authors analyze predictors at each of the first four recurrences (first to second report, second to third report, third to fourth report, and fourth to fifth report). Findings demonstrate that some factors (e.g., tract poverty) which predict initial recurrence lose their predictive value at later stages, whereas others (e.g., aid to families with dependent children history) remain predictive across stages. In-home child welfare services and mental health treatment emerged as consistent predictors of reduced recurrence. PMID:20941889

The role of the actinomyces in obstructive tonsillar hypertrophy and recurrent tonsillitis in pediatric population.

PubMed

Kutluhan, Ahmet; Salvız, Mehti; Yalçıner, Gökhan; Kandemir, Olcay; Yeşil, Cemile

2011-03-01

To determine the prevalence of tonsillar Actinomyces in subjects with recurrent tonsillitis and those with obstructive tonsillar hypertrophy, and to determine the association between the presence of Actinomyces and tonsillar volume, and crypt abscess. A prospective designed cross-sectional study consisted of 90 children subjects who underwent tonsillectomy or adenotonsillectomy for recurrent tonsillitis and obstructive tonsillar hypertrophy. The subjects of recurrent tonsillitis (Group A) and obstructive tonsillar hypertrophy (Group B) were compared to the presence of Actinomyces. The relationship between the presence of Actinomyces and the presence of crypt abscess, and tonsillar volume were also compared. Actinomyces was found to be significantly more prominent in obstructive tonsillar hypertrophy group (61.5%) compared to recurrent tonsillitis group (26.6%) (p<0.001). Additionally, the mean tonsillar volume was significantly higher in tonsils with Actinomyces than those without (p<0.001). The histopathological study revealed that there was no significant inflammatory response to the existence of Actinomyces. According to the presented study, Actinomyces was seen more prominent in subjects with obstructive tonsillar hypertrophy compared those with recurrent tonsillitis. Furthermore Actinomyces had a pathological influence on tonsil size. This study showed there was a significant relation between Actinomyces and enlargement of tonsillar tissue. However, how causes tonsillar hypertrophy is not understood yet in tonsillar disease. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Factors associated with occasional and recurrent falls in Mexican community-dwelling older people

PubMed Central

Mino-León, Dolores; Cruz-Arenas, Esteban

2018-01-01

Falls are a frequent event among older adults that can cause wounds, disability, psychological disorders, and premature death. Although the large number of existing studies on the issue, few have been conducted in middle- and low-income countries. The objective of the present study is to identify the sociodemographic, medical, and functional performance factors associated with occasional and recurrent falls in Mexican older adults dwelling in community. Cross-sectional analysis of 9 598 adults ≥60 years old who participated in the fourth round (2015) of the Mexican Health and Aging Study. Bivariate tests were performed to evaluate the differences between covariates by distinct fall groups (no falls, occasional falls, and recurrent falls). Multiple logistic regressions with unadjusted and adjusted models were estimated. Approximately 46% of older adults had had at least one fall during the previous two years (one fall 16% and recurrent falls 30%). Occasional falls were only associated with being a woman; in addition to the sex, recurrent falls were strongly associated with advanced age, rural residence, bad and very bad self-perception of health status, activity-limiting pain, urinary incontinence, depression, arthritis, limitations in basic activities of daily living, and limitations in advanced activities of daily living. Falls, primarily recurrent falls, deserve to be addressed through multifactorial strategies that include different areas of intervention. PMID:29462159

Knowledge of Stroke Risk Factors and Warning Signs in Patients with Recurrent Stroke or Recurrent Transient Ischaemic Attack in Thailand.

PubMed

Saengsuwan, Jittima; Suangpho, Pathitta; Tiamkao, Somsak

2017-01-01

Stroke is a global burden. It is not known whether patients who are most at risk of stroke (recurrent stroke or recurrent transient ischaemic attack) have enough knowledge of stroke risk factors and warning signs. The aim of this study was to assess the knowledge of stroke risk factors and warning signs in this high-risk population. We performed a cross-sectional questionnaire-based study of patients with recurrent stroke or recurrent TIA admitted to Srinagarind Hospital and Khon Kaen Hospital, Thailand. A total of 140 patients were included in the study (age 65.6 ± 11.3 years [mean ± SD], 62 females). Using an open-ended questionnaire, nearly one-third of patients (31.4%) could not name any risk factors for stroke. The most commonly recognized risk factors were hypertension (35%), dyslipidemia (28.6%), and diabetes (22.9%). Regarding stroke warning signs, the most commonly recognized warning signs were sudden unilateral weakness (61.4%), sudden trouble with speaking (25.7%), and sudden trouble with walking, loss of balance, or dizziness (21.4%). Nineteen patients (13.6%) could not identify any warning signs. The results showed that knowledge of stroke obtained from open-ended questionnaires is still unsatisfactory. The healthcare provider should provide structured interventions to increase knowledge and awareness of stroke in these patients.

Aspirin for the prevention of recurrent venous thromboembolism: the INSPIRE collaboration.

PubMed

Simes, John; Becattini, Cecilia; Agnelli, Giancarlo; Eikelboom, John W; Kirby, Adrienne C; Mister, Rebecca; Prandoni, Paolo; Brighton, Timothy A

2014-09-23

In patients with a first unprovoked venous thromboembolism (VTE) the risk of recurrent VTE remains high after anticoagulant treatment is discontinued. The Aspirin for the Prevention of Recurrent Venous Thromboembolism (the Warfarin and Aspirin [WARFASA]) and the Aspirin to Prevent Recurrent Venous Thromboembolism (ASPIRE) trials showed that aspirin reduces this risk, but they were not individually powered to detect treatment effects for particular outcomes or subgroups. An individual patient data analysis of these trials was planned, before their results were known, to assess the effect of aspirin versus placebo on recurrent VTE, major vascular events (recurrent VTE, myocardial infarction, stroke, and cardiovascular disease death) and bleeding, overall and within predefined subgroups. The primary analysis, for VTE, was by intention to treat using time-to-event data. Of 1224 patients, 193 had recurrent VTE over 30.4 months' median follow-up. Aspirin reduced recurrent VTE (7.5%/yr versus 5.1%/yr; hazard ratio [HR], 0.68; 95% confidence interval [CI], 0.51-0.90; P=0.008), including both deep-vein thrombosis (HR, 0.66; 95% CI, 0.47-0.92; P=0.01) and pulmonary embolism (HR, 0.66; 95% CI, 0.41-1.06; P=0.08). Aspirin reduced major vascular events (8.7%/yr versus 5.7%/yr; HR, 0.66; 95% CI, 0.50-0.86; P=0.002). The major bleeding rate was low (0.4%/yr for placebo and 0.5%/yr for aspirin). After adjustment for treatment adherence, recurrent VTE was reduced by 42% (HR, 0.58; 95% CI, 0.40-0.85; P=0.005). Prespecified subgroup analyses indicate similar relative, but larger absolute, risk reductions in men and older patients. Aspirin after anticoagulant treatment reduces the overall risk of recurrence by more than a third in a broad cross-section of patients with a first unprovoked VTE, without significantly increasing the risk of bleeding. www.anzctr.org.au. Unique identifier: ACTRN12611000684921. © 2014 American Heart Association, Inc.

Examining Whether Offspring Psychopathology Influences Illness Course in Mothers With Recurrent Depression Using a High-Risk Longitudinal Sample

PubMed Central

2016-01-01

Depression is known to be influenced by psychosocial stressors. For mothers with recurrent depressive illness, the presence of psychopathology in their children may have important effects on their own mental health. Although the impact of maternal depression on child mental health is well-established, no study to date, as far as we are aware, has examined the extent to which offspring psychopathology influences the course of depression in mothers with a history of recurrent depressive illness, what types of child psychopathology impact maternal mental health, or whether risks vary by child gender. Aims were to (a) Use a longitudinal design to examine whether adolescent psychopathology (depression, disruptive behavior disorder; DBD) predicts recurrence of a depressive episode and depression symptom course in women with a history of recurrent depression; and (b) To test if observed effects vary by child gender. 299 mothers with recurrent major depressive disorder and their adolescent offspring were assessed on 2 occasions, 29 months apart. Maternal depression and offspring psychopathology were assessed using semistructured interview measures. Cross-generational links across time were assessed using structural equation modeling. Analyses were adjusted for past severity of maternal depression. Offspring depression symptoms but not DBD symptoms at baseline predicted future episode recurrence in mothers. Depression symptoms in daughters (β = .16, p = .039) but not sons (β = −.07, p = .461), predicted an increase in maternal depression symptoms across time. Psychopathology in daughters is associated with long-term depressive symptoms in women (mothers) with a history of recurrent depression. Findings highlight the importance of careful assessment and management of mental health problems in adolescents for more effective management of maternal depression. This study suggests that offspring symptoms of depression may be important for the recurrence of maternal depression episodes. Girls’ symptoms of depression may be a particularly important psychosocial stressor for the development of depressive symptoms in mothers with a history of recurrent depression. PMID:26854510

Examining whether offspring psychopathology influences illness course in mothers with recurrent depression using a high-risk longitudinal sample.

PubMed

Sellers, Ruth; Hammerton, Gemma; Harold, Gordon T; Mahedy, Liam; Potter, Robert; Langley, Kate; Thapar, Ajay; Rice, Frances; Thapar, Anita; Collishaw, Stephan

2016-02-01

Depression is known to be influenced by psychosocial stressors. For mothers with recurrent depressive illness, the presence of psychopathology in their children may have important effects on their own mental health. Although the impact of maternal depression on child mental health is well-established, no study to date, as far as we are aware, has examined the extent to which offspring psychopathology influences the course of depression in mothers with a history of recurrent depressive illness, what types of child psychopathology impact maternal mental health, or whether risks vary by child gender. Aims were to (a) Use a longitudinal design to examine whether adolescent psychopathology (depression, disruptive behavior disorder; DBD) predicts recurrence of a depressive episode and depression symptom course in women with a history of recurrent depression; and (b) To test if observed effects vary by child gender. 299 mothers with recurrent major depressive disorder and their adolescent offspring were assessed on 2 occasions, 29 months apart. Maternal depression and offspring psychopathology were assessed using semistructured interview measures. Cross-generational links across time were assessed using structural equation modeling. Analyses were adjusted for past severity of maternal depression. Offspring depression symptoms but not DBD symptoms at baseline predicted future episode recurrence in mothers. Depression symptoms in daughters (β = .16, p = .039) but not sons (β = -.07, p = .461), predicted an increase in maternal depression symptoms across time. Psychopathology in daughters is associated with long-term depressive symptoms in women (mothers) with a history of recurrent depression. Findings highlight the importance of careful assessment and management of mental health problems in adolescents for more effective management of maternal depression. This study suggests that offspring symptoms of depression may be important for the recurrence of maternal depression episodes. Girls' symptoms of depression may be a particularly important psychosocial stressor for the development of depressive symptoms in mothers with a history of recurrent depression. (c) 2016 APA, all rights reserved).

Vulnerability for new episodes in recurrent major depressive disorder: protocol for the longitudinal DELTA-neuroimaging cohort study

PubMed Central

Mocking, Roel J T; Figueroa, Caroline A; Rive, Maria M; Geugies, Hanneke; Servaas, Michelle N; Assies, Johanna; Koeter, Maarten W J; Vaz, Frédéric M; Wichers, Marieke; van Straalen, Jan P; de Raedt, Rudi; Bockting, Claudi L H; Harmer, Catherine J; Schene, Aart H; Ruhé, Henricus G

2016-01-01

Introduction Major depressive disorder (MDD) is widely prevalent and severely disabling, mainly due to its recurrent nature. A better understanding of the mechanisms underlying MDD-recurrence may help to identify high-risk patients and to improve the preventive treatment they need. MDD-recurrence has been considered from various levels of perspective including symptomatology, affective neuropsychology, brain circuitry and endocrinology/metabolism. However, MDD-recurrence understanding is limited, because these perspectives have been studied mainly in isolation, cross-sectionally in depressed patients. Therefore, we aim at improving MDD-recurrence understanding by studying these four selected perspectives in combination and prospectively during remission. Methods and analysis In a cohort design, we will include 60 remitted, unipolar, unmedicated, recurrent MDD-participants (35–65 years) with ≥2 MDD-episodes. At baseline, we will compare the MDD-participants with 40 matched controls. Subsequently, we will follow-up the MDD-participants for 2.5 years while monitoring recurrences. We will invite participants with a recurrence to repeat baseline measurements, together with matched remitted MDD-participants. Measurements include questionnaires, sad mood-induction, lifestyle/diet, 3 T structural (T1-weighted and diffusion tensor imaging) and blood-oxygen-level-dependent functional MRI (fMRI) and MR-spectroscopy. fMRI focusses on resting state, reward/aversive-related learning and emotion regulation. With affective neuropsychological tasks we will test emotional processing. Moreover, we will assess endocrinology (salivary hypothalamic-pituitary-adrenal-axis cortisol and dehydroepiandrosterone-sulfate) and metabolism (metabolomics including polyunsaturated fatty acids), and store blood for, for example, inflammation analyses, genomics and proteomics. Finally, we will perform repeated momentary daily assessments using experience sampling methods at baseline. We will integrate measures to test: (1) differences between MDD-participants and controls; (2) associations of baseline measures with retro/prospective recurrence-rates; and (3) repeated measures changes during follow-up recurrence. This data set will allow us to study different predictors of recurrence in combination. Ethics and dissemination The local ethics committee approved this study (AMC-METC-Nr.:11/050). We will submit results for publication in peer-reviewed journals and presentation at (inter)national scientific meetings. Trial registration number NTR3768. PMID:26932139

A single-sampling hair trap for mesocarnivores

Treesearch

Jonathan N. Pauli; Matthew B. Hamilton; Edward B. Crain; Steven W. Buskirk

2007-01-01

Although techniques to analyze and quantifY DNA-based data have progressed, methods to noninvasively collect samples lag behind. Samples are generally collected from devices that permit coincident sampling of multiple individuals. Because of cross-contamination, substantive genotyping errors can arise. We developed a cost-effective (US$4.60/trap) single-capture hair...

A Proposal for Research on Complex Media, Imagining and Uncertainty Quantification

DTIC Science & Technology

2013-11-26

demonstration that the Green’s function for wave propagation in an ergodic cavity can be recovered exactly by cross correlation of signals at two points...the continuation of a project in which we have developed autofocus methods based on a phase space formulation ( Wigner transform) of the array data and

Differences in leukocyte differentiation molecule abundances on domestic sheep (Ovis aries) and bighorn sheep (Ovis canadensis) neutrophils identified by flow cytometry

USDA-ARS?s Scientific Manuscript database

Abundance was assessed by utilizing a panel of cross-reactive monoclonal antibodies (mAbs) tested in this study. Characterization of multichannel autofluorescence of eosinophils permitted cell-type specific gating of granulocytes for quantification of LDMs on neutrophils and eosinophils by indirect,...

Quantification of human upper extremity nerves and fascicular anatomy.

PubMed

Brill, Natalie A; Tyler, Dustin J

2017-09-01

In this study we provide detailed quantification of upper extremity nerve and fascicular anatomy. The purpose is to provide values and trends in neural features useful for clinical applications and neural interface device design. Nerve cross-sections were taken from 4 ulnar, 4 median, and 3 radial nerves from 5 arms of 3 human cadavers. Quantified nerve features included cross-sectional area, minor diameter, and major diameter. Fascicular features analyzed included count, perimeter, area, and position. Mean fascicular diameters were 0.57 ± 0.39, 0.6 ± 0.3, 0.5 ± 0.26 mm in the upper arm and 0.38 ± 0.18, 0.47 ± 0.18, 0.4 ± 0.27 mm in the forearm of ulnar, median, and radial nerves, respectively. Mean fascicular diameters were inversely proportional to fascicle count. Detailed quantitative anatomy of upper extremity nerves is a resource for design of neural electrodes, guidance in extraneural procedures, and improved neurosurgical planning. Muscle Nerve 56: 463-471, 2017. © 2016 Wiley Periodicals, Inc.

In vivo evaluation of antiviral efficacy against genital herpes using mouse and guinea pig models.

PubMed

Valencia, Frances; Veselenak, Ronald L; Bourne, Nigel

2013-01-01

Both the guinea pig and mouse are important animal models for the study of genital herpes. The murine model has been used extensively to evaluate vaccines and antiviral agents by measuring the incidence of infection and the magnitude of viral replication; however, this model is limited with regard to distinguishing between candidate vaccines or treatments. In contrast, the guinea pig closely mimics human infection and provides an excellent model of both primary and recurrent genital herpes disease. This animal model is especially important in the study of viral transmission through the evaluation of latent viral reactivation and virus shedding into the genital tract. Here, we describe methodologies to determine viral infection, severity of primary disease, and quantification of primary viral replication in the genital tract for both the guinea pig and murine models of genital herpes. Additionally, we detail the evaluation of the onset of primary disease and progression to the day of death in the mouse model. Further, we summarize methods to assess the frequency of recurrences, frequency and magnitude of virus shedding, and latent viral load in the sensory nerve ganglia of the guinea pig.

Epidemiology of Recurrent Acute and Chronic Pancreatitis: Similarities and Differences.

PubMed

Machicado, Jorge D; Yadav, Dhiraj

2017-07-01

Emerging data in the past few years suggest that acute, recurrent acute (RAP), and chronic pancreatitis (CP) represent a disease continuum. This review discusses the similarities and differences in the epidemiology of RAP and CP. RAP is a high-risk group, comprised of individuals at varying risk of progression. The premise is that RAP is an intermediary stage in the pathogenesis of CP, and a subset of RAP patients during their natural course transition to CP. Although many clinical factors have been identified, accurately predicting the probability of disease course in individual patients remains difficult. Future studies should focus on providing more precise estimates of the risk of disease transition in a cohort of patients, quantification of clinical events during the natural course of disease, and discovery of biomarkers of the different stages of the disease continuum. Availability of clinically relevant endpoints and linked biomarkers will allow more accurate prediction of the natural course of disease over intermediate- or long-term-based characteristics of an individual patient. These endpoints will also provide objective measures for use in clinical trials of interventions that aim to alter the natural course of disease.

Automated quantification of the synchrogram by recurrence plot analysis.

PubMed

Nguyen, Chinh Duc; Wilson, Stephen James; Crozier, Stuart

2012-04-01

Recently, the concept of phase synchronization of two weakly coupled oscillators has raised a great research interest and has been applied to characterize synchronization phenomenon in physiological data. Phase synchronization of cardiorespiratory coupling is often studied by a synchrogram analysis, a graphical tool investigating the relationship between instantaneous phases of two signals. Although several techniques have been proposed to automatically quantify the synchrogram, most of them require a preselection of a phase-locking ratio by trial and error. One technique does not require this information; however, it is based on the power spectrum of phase's distribution in the synchrogram, which is vulnerable to noise. This study aims to introduce a new technique to automatically quantify the synchrogram by studying its dynamic structure. Our technique exploits recurrence plot analysis, which is a well-established tool for characterizing recurring patterns and nonstationarities in experiments. We applied our technique to detect synchronization in simulated and measured infants' cardiorespiratory data. Our results suggest that the proposed technique is able to systematically detect synchronization in noisy and chaotic data without preselecting the phase-locking ratio. By embedding phase information of the synchrogram into phase space, the phase-locking ratio is automatically unveiled as the number of attractors.

Imaging Surrogates of Infiltration Obtained Via Multiparametric Imaging Pattern Analysis Predict Subsequent Location of Recurrence of Glioblastoma

PubMed Central

Akbari, Hamed; Macyszyn, Luke; Da, Xiao; Bilello, Michel; Wolf, Ronald L.; Martinez-Lage, Maria; Biros, George; Alonso-Basanta, Michelle; O’Rourke, Donald M.; Davatzikos, Christos

2016-01-01

Background Glioblastoma is an aggressive and highly infiltrative brain cancer. Standard surgical resection is guided by enhancement on postcontrast T1-weighted (T1) magnetic resonance imaging (MRI), which is insufficient for delineating surrounding infiltrating tumor. Objective To develop imaging biomarkers that delineate areas of tumor infiltration and predict early recurrence in peritumoral tissue. Such markers would enable intensive, yet targeted, surgery and radiotherapy, thereby potentially delaying recurrence and prolonging survival. Methods Preoperative multiparametric MRIs (T1, T1-Gad, T2-weighted [T2], T2-fluid-attenuated inversion recovery [FLAIR], diffusion tensor imaging (DTI), and dynamic susceptibility contrast-enhanced [DSC]-MRI) from 31 patients were combined using machine learning methods, thereby creating predictive spatial maps of infiltrated peritumoral tissue. Cross validation was used in the retrospective cohort to achieve generalizable biomarkers. Subsequently, the imaging signatures learned from the retrospective study were used in a replication cohort of 34 new patients. Spatial maps representing likelihood of tumor infiltration and future early recurrence were compared to regions of recurrence on postresection follow-up studies with pathology confirmation. Results This technique produced predictions of early recurrence with a mean area under the curve (AUC) of 0.84, sensitivity of 91%, specificity of 93%, and odds ratio estimates of 9.29 (99% CI, 8.95–9.65) for tissue predicted to be heavily infiltrated in the replication study. Regions of tumor recurrence were found to have subtle, yet fairly distinctive multiparametric imaging signatures when analyzed quantitatively by pattern analysis and machine learning. Conclusion Visually imperceptible imaging patterns discovered via multiparametric pattern analysis methods were found to estimate the extent of infiltration and location of future tumor recurrence, paving the way for improved targeted treatment. PMID:26813856

Impact of sex and traditional cardiovascular risk factors on the risk of recurrent venous thromboembolism: results from the German MAISTHRO Registry.

PubMed

Linnemann, Birgit; Zgouras, Dimitrios; Schindewolf, Marc; Schwonberg, Jan; Jarosch-Preusche, Marie; Lindhoff-Last, Edelgard

2008-03-01

As arterial and venous thrombosis share common risk factors, a link between arterial and venous thrombosis has been suggested recently. Therefore, we aimed to investigate the impact of established cardiovascular risk factors on the risk of recurrent venous thromboembolism (VTE). With a cross-sectional study design, we analyzed the data of 1006 patients (582 F, 424 M) consecutively treated in our outpatient department for VTE (i.e. lower extremity deep vein thrombosis and/or pulmonary embolism) and registered in the MAISTHRO (MAin-ISar-THROmbosis) database. Of the total cohort, 324 (32.2%) patients suffered a recurrent VTE. Compared with the patients with a single thromboembolic event, patients with recurrent VTE were more frequently male (39.4 vs. 27.0%, P < 0.001). In univariate analysis, the relative risk of recurrent VTE was 1.9 [95% confidence interval (CI) 1.53-2.39] for male sex and 1.6 (1.25-1.95) for age over 50 years (PAOD). After adjustments for age, sex, thrombophilia and other common VTE risk factors, male sex [hazard ratio (HR) = 1.7 (1.38-21.9)] and arterial hypertension [HR = 1.4 (1.05-1.78)] were independent risk factors of recurrent VTE. The higher risk in men than in women persisted even after the exclusion of women with transient hormonal risk factors [HR = 1.57 (1.19-2.07)]. In contrast, no association between the presence of diabetes, obesity, hypercholesterolemia or smoking and the risk of VTE recurrence was observed. Male sex and arterial hypertension are independently associated with an increased risk of recurrent VTE after termination of anticoagulant therapy for the first VTE event.

Use of Artificial Intelligence and Machine Learning Algorithms with Gene Expression Profiling to Predict Recurrent Nonmuscle Invasive Urothelial Carcinoma of the Bladder.

PubMed

Bartsch, Georg; Mitra, Anirban P; Mitra, Sheetal A; Almal, Arpit A; Steven, Kenneth E; Skinner, Donald G; Fry, David W; Lenehan, Peter F; Worzel, William P; Cote, Richard J

2016-02-01

Due to the high recurrence risk of nonmuscle invasive urothelial carcinoma it is crucial to distinguish patients at high risk from those with indolent disease. In this study we used a machine learning algorithm to identify the genes in patients with nonmuscle invasive urothelial carcinoma at initial presentation that were most predictive of recurrence. We used the genes in a molecular signature to predict recurrence risk within 5 years after transurethral resection of bladder tumor. Whole genome profiling was performed on 112 frozen nonmuscle invasive urothelial carcinoma specimens obtained at first presentation on Human WG-6 BeadChips (Illumina®). A genetic programming algorithm was applied to evolve classifier mathematical models for outcome prediction. Cross-validation based resampling and gene use frequencies were used to identify the most prognostic genes, which were combined into rules used in a voting algorithm to predict the sample target class. Key genes were validated by quantitative polymerase chain reaction. The classifier set included 21 genes that predicted recurrence. Quantitative polymerase chain reaction was done for these genes in a subset of 100 patients. A 5-gene combined rule incorporating a voting algorithm yielded 77% sensitivity and 85% specificity to predict recurrence in the training set, and 69% and 62%, respectively, in the test set. A singular 3-gene rule was constructed that predicted recurrence with 80% sensitivity and 90% specificity in the training set, and 71% and 67%, respectively, in the test set. Using primary nonmuscle invasive urothelial carcinoma from initial occurrences genetic programming identified transcripts in reproducible fashion, which were predictive of recurrence. These findings could potentially impact nonmuscle invasive urothelial carcinoma management. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

The genomic impacts of drift and selection for hybrid performance in maize

USDA-ARS?s Scientific Manuscript database

Modern maize breeding relies upon selection in inbreeding populations to improve performance in cross-population hybrids. The United States Department of Agriculture - Agricultural Research Service (USDA-ARS) reciprocal recurrent selection experiment between the BSSS and BSCB1 populations represent...

Quantification of pelvic floor muscle strength in female urinary incontinence: A systematic review and comparison of contemporary methodologies.

PubMed

Deegan, Emily G; Stothers, Lynn; Kavanagh, Alex; Macnab, Andrew J

2018-01-01

There remains no gold standard for quantification of voluntary pelvic floor muscle (PFM) strength, despite international guidelines that recommend PFM assessment in females with urinary incontinence (UI). Methods currently reported for quantification of skeletal muscle strength across disciplines are systematically reviewed and their relevance for clinical and academic use related to the pelvic floor are described. A systematic review via Medline, PubMed, CINHAL, and the Cochrane database using key terms for pelvic floor anatomy and function were cross referenced with skeletal muscle strength quantification from 1946 to 2016. Full text peer-reviewed articles in English having female subjects with incontinence were identified. Each study was analyzed for use of controls, type of methodology as direct or indirect measures, benefits, and limitations of the technique. A total of 1586 articles were identified of which 50 met the inclusion criteria. Nine methodologies of determining PFM strength were described including: digital palpation, perineometer, dynamometry, EMG, vaginal cones, ultrasonography, magnetic resonance imaging, urine stream interruption test, and the Colpexin pull test. Thirty-two percent lacked a control group. Technical refinements in both direct and indirect instrumentation for PFM strength measurement are allowing for sensitivity. However, the most common methods of quantification remain digital palpation and perineometry; techniques that pose limitations and yield subjective or indirect measures of muscular strength. Dynamometry has potential as an accurate and sensitive tool, but is limited by inability to assess PFM strength during dynamic movements. © 2017 Wiley Periodicals, Inc.

Quantification of FDG-PET/CT with delayed imaging in patients with newly diagnosed recurrent breast cancer.

PubMed

Baun, Christina; Falch, Kirsten; Gerke, Oke; Hansen, Jeanette; Nguyen, Tram; Alavi, Abass; Høilund-Carlsen, Poul-Flemming; Hildebrandt, Malene G

2018-05-09

Several studies have shown the advantage of delayed-time-point imaging with 18F-FDG-PET/CT to distinguish malignant from benign uptake. This may be relevant in cancer diseases with low metabolism, such as breast cancer. We aimed at examining the change in SUV from 1 h (1h) to 3 h (3h) time-point imaging in local and distant lesions in patients with recurrent breast cancer. Furthermore, we investigated the effect of partial volume correction in the different types of metastases, using semi-automatic quantitative software (ROVER™). One-hundred and two patients with suspected breast cancer recurrence underwent whole-body PET/CT scans 1h and 3h after FDG injection. Semi-quantitative standardised uptake values (SUVmax, SUVmean) and partial volume corrected SUVmean (cSUVmean), were estimated in malignant lesions, and as reference in healthy liver tissue. The change in quantitative measures from 1h to 3h was calculated, and SUVmean was compared to cSUVmean. Metastases were verified by biopsy. Of the 102 included patients, 41 had verified recurrent disease with in median 15 lesions (range 1-70) amounting to a total of 337 malignant lesions included in the analysis. SUVmax of malignant lesions increased from 6.4 ± 3.4 [0.9-19.7] (mean ± SD, min and max) at 1h to 8.1 ± 4.4 [0.7-29.7] at 3h. SUVmax in breast, lung, lymph node and bone lesions increased significantly (p < 0.0001) between 1h and 3h by on average 25, 40, 33, and 27%, respectively. A similar pattern was observed with (uncorrected) SUVmean. Partial volume correction increased SUVmean significantly, by 63 and 71% at 1h and 3h imaging, respectively. The highest impact was in breast lesions at 3h, where cSUVmean increased by 87% compared to SUVmean. SUVs increased from 1h to 3h in malignant lesions, SUVs of distant recurrence were in general about twice as high as those of local recurrence. Partial volume correction caused significant increases in these values. However, it is questionable, if these relatively modest quantitative advances of 3h imaging are sufficient to warrant delayed imaging in this patient group. ClinicalTrails.gov NCT01552655 . Registered 28 February 2012, partly retrospectively registered.

Computer-aided Assessment of Regional Abdominal Fat with Food Residue Removal in CT

PubMed Central

Makrogiannis, Sokratis; Caturegli, Giorgio; Davatzikos, Christos; Ferrucci, Luigi

2014-01-01

Rationale and Objectives Separate quantification of abdominal subcutaneous and visceral fat regions is essential to understand the role of regional adiposity as risk factor in epidemiological studies. Fat quantification is often based on computed tomography (CT) because fat density is distinct from other tissue densities in the abdomen. However, the presence of intestinal food residues with densities similar to fat may reduce fat quantification accuracy. We introduce an abdominal fat quantification method in CT with interest in food residue removal. Materials and Methods Total fat was identified in the feature space of Hounsfield units and divided into subcutaneous and visceral components using model-based segmentation. Regions of food residues were identified and removed from visceral fat using a machine learning method integrating intensity, texture, and spatial information. Cost-weighting and bagging techniques were investigated to address class imbalance. Results We validated our automated food residue removal technique against semimanual quantifications. Our feature selection experiments indicated that joint intensity and texture features produce the highest classification accuracy at 95%. We explored generalization capability using k-fold cross-validation and receiver operating characteristic (ROC) analysis with variable k. Losses in accuracy and area under ROC curve between maximum and minimum k were limited to 0.1% and 0.3%. We validated tissue segmentation against reference semimanual delineations. The Dice similarity scores were as high as 93.1 for subcutaneous fat and 85.6 for visceral fat. Conclusions Computer-aided regional abdominal fat quantification is a reliable computational tool for large-scale epidemiological studies. Our proposed intestinal food residue reduction scheme is an original contribution of this work. Validation experiments indicate very good accuracy and generalization capability. PMID:24119354

Computer-aided assessment of regional abdominal fat with food residue removal in CT.

PubMed

Makrogiannis, Sokratis; Caturegli, Giorgio; Davatzikos, Christos; Ferrucci, Luigi

2013-11-01

Separate quantification of abdominal subcutaneous and visceral fat regions is essential to understand the role of regional adiposity as risk factor in epidemiological studies. Fat quantification is often based on computed tomography (CT) because fat density is distinct from other tissue densities in the abdomen. However, the presence of intestinal food residues with densities similar to fat may reduce fat quantification accuracy. We introduce an abdominal fat quantification method in CT with interest in food residue removal. Total fat was identified in the feature space of Hounsfield units and divided into subcutaneous and visceral components using model-based segmentation. Regions of food residues were identified and removed from visceral fat using a machine learning method integrating intensity, texture, and spatial information. Cost-weighting and bagging techniques were investigated to address class imbalance. We validated our automated food residue removal technique against semimanual quantifications. Our feature selection experiments indicated that joint intensity and texture features produce the highest classification accuracy at 95%. We explored generalization capability using k-fold cross-validation and receiver operating characteristic (ROC) analysis with variable k. Losses in accuracy and area under ROC curve between maximum and minimum k were limited to 0.1% and 0.3%. We validated tissue segmentation against reference semimanual delineations. The Dice similarity scores were as high as 93.1 for subcutaneous fat and 85.6 for visceral fat. Computer-aided regional abdominal fat quantification is a reliable computational tool for large-scale epidemiological studies. Our proposed intestinal food residue reduction scheme is an original contribution of this work. Validation experiments indicate very good accuracy and generalization capability. Published by Elsevier Inc.

Absolute photoionization cross sections of two cyclic ketones: cyclopentanone and cyclohexanone.

PubMed

Price, Chelsea; Fathi, Yasmin; Meloni, Giovanni

2017-05-01

Absolute photoionization cross sections for cyclopentanone and cyclohexanone, as well as partial ionization cross sections for the dissociative ionized fragments, are presented in this investigation. Experiments are performed via a multiplexed photoionization mass spectrometer utilizing vacuum ultraviolet (VUV) synchrotron radiation supplied by the Advanced Light Source of Lawrence Berkeley National Laboratory. These results allow the quantification of these species that is relevant to investigate the kinetics and combustion reactions of potential biofuels. The CBS-QB3 calculated values for the adiabatic ionization energies agree well with the experimental values, and the identification of possible dissociative fragments is discussed for both systems. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

PubMed

Telu, Kelly H; Yan, Xinjian; Wallace, William E; Stein, Stephen E; Simón-Manso, Yamil

2016-03-15

The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

Evidence of Paternal N5, N10 - Methylenetetrahydrofolate Reductase (MTHFR) C677T Gene Polymorphism in Couples with Recurrent Spontaneous Abortions (RSAs) in Kolar District- A South West of India

PubMed Central

Vanilla, Shiny; Kotur, Pushpa F; Kutty, Moideen A; Vegi, Pradeep Kumar

2015-01-01

Introduction: Recurrent spontaneous abortion (RSA) is a multifactorial clinical obstetrics complication commonly occurring in pregnancy. Many research studies have noted the mutations such as C677T in N5, N10 - Methylenetetrahydrofolate reductase (MTHFR)gene which is regarded as RSA risk factor. This study was carried out to determine the occurrence of frequency of C677T of the MTHFR gene mutations with RSA. Aim: The purpose of present study is to determine the frequency of MTHFR C677T polymorphisms in couples with recurrent pregnancy loss and the impact of paternal polymorphisms of MTHFR C677T in recurrent pregnancy loss in population of couples living in Kolar district of Karnataka with RSA. Design: A total of 15 couples with a history of two or more unexplained RSA were enrolled as subjects in the study and a total of 15 couples with normal reproductive history, having two or more children and no history of miscarriages were enrolled as controls. Materials and Methods: DNA extraction from samples case and control group couples and its quantification by Agarose gel electrophoresis, assessment of DNA purity, MTHFR C 677T gene mutation detection by PCR-RFLP method. Statistical analysis: Carried out by web based online SPSS tool. Results: The frequency of C677T genotype showed homozygous wild type CC (80%), heterozygous CT type (13.3%) and homozygous mutation TT type (6.67%) observed in males. Similarly from female’s homozygous wild type CC (86.6%), heterozygous type (13.3%), and homozygous type mutations TT (0%) was recorded. In couple control groups, we observed homozygous wild type CC (86.6%), heterozygous CT type (13.3%) and homozygous type mutations TT type (0%). Conclusion: We noticed a high frequency of MTHFR specifically T allele associated with paternal side.Therefore, the present study indicated the impact of paternal gene polymorphism of MTHFR C677T on screening in couples with recurrent pregnancy loss. PMID:25859445

Assessment of SCAR markers to design real-time PCR primers for rhizosphere quantification of Azospirillum brasilense phytostimulatory inoculants of maize.

PubMed

Couillerot, O; Poirier, M-A; Prigent-Combaret, C; Mavingui, P; Caballero-Mellado, J; Moënne-Loccoz, Y

2010-08-01

To assess the applicability of sequence characterized amplified region (SCAR) markers obtained from BOX, ERIC and RAPD fragments to design primers for real-time PCR quantification of the phytostimulatory maize inoculants Azospirillum brasilense UAP-154 and CFN-535 in the rhizosphere. Primers were designed based on strain-specific SCAR markers and were screened for successful amplification of target strain and absence of cross-reaction with other Azospirillum strains. The specificity of primers thus selected was verified under real-time PCR conditions using genomic DNA from strain collection and DNA from rhizosphere samples. The detection limit was 60 fg DNA with pure cultures and 4 x 10(3) (for UAP-154) and 4 x 10(4) CFU g(-1) (for CFN-535) in the maize rhizosphere. Inoculant quantification was effective from 10(4) to 10(8) CFU g(-1) soil. BOX-based SCAR markers were useful to find primers for strain-specific real-time PCR quantification of each A. brasilense inoculant in the maize rhizosphere. Effective root colonization is a prerequisite for successful Azospirillum phytostimulation, but cultivation-independent monitoring methods were lacking. The real-time PCR methods developed here will help understand the effect of environmental conditions on root colonization and phytostimulation by A. brasilense UAP-154 and CFN-535.

ICPP: Identification and Quantification of Elementary Plasma Surface Processes during thin Film Growth

NASA Astrophysics Data System (ADS)

Keudell, A. V.

2000-10-01

The quantification of elementary plasma surface processes in glow discharges used for thin film deposition, is mandatory for a complete description of these low temperature plasmas. Since the surface to volume ratio in these discharge systems is often large, all particle densities in the discharge can be strongly influenced by any surface reactions. The identification and quantification of these surface processes will be illustrated for the plasma deposition of amorphous hydrogenated carbon films. A variety of experiments will be discussed ranging from plasma experiments using the cavity technique or ionization threshold mass spectrometry as well as a new class of experiments using quantified radical beams to quantify surface reactions in terms of sticking coefficients directly. It is shown that the reactivity of the hydrocarbon radicals depends strongly on the state of hybridization of the hydrocarbon growth precursor, and that the sticking coefficients for various hydrocarbon radicals are strongly influenced by the simultaneous interaction of several reactive species with the film surface. With the knowledge of these interaction mechanisms and the quantification of the corresponding cross sections, a better understanding of growth processes has become possible, ranging from the deposition of polycrystalline diamond in microwave discharges to the formation of re-deposited layers in fusion experiments.

Ansa pancreatica as a predisposing factor for recurrent acute pancreatitis.

PubMed

Hayashi, Takana Yamakawa; Gonoi, Wataru; Yoshikawa, Takeharu; Hayashi, Naoto; Ohtomo, Kuni

2016-10-28

To determine the non-biased prevalence and clinical significance of ansa pancreatica in patients with acute pancreatitis using magnetic resonance imaging (MRI). Our institutional review board approved this cross-sectional study, which consisted of a community-based cohort of 587 consecutive participants in a whole-body health-check program, and 73 subjects with episode of acute pancreatitis (55 patients with a single episode of acute pancreatitis, and 18 patients with recurrent acute pancreatitis). All of the subjects underwent abdominal MRI including magnetic resonance cholangiopancreatography, medical examinations, and blood tests. Two board-certified, diagnostic, abdominal radiologists evaluated the images, and ansa pancreatica was diagnosed based on its characteristic anatomy on MRI. Compared with the community group [5/587 (0.85%)], patients with recurrent acute pancreatitis had a significantly higher frequency of ansa pancreatica [2/18 (11.1%)] ( P = 0.016; OR = 14.3; 95%CI: 1.27-96.1), but not compared with patients with single-episode acute pancreatitis [1/55 (1.8%)] ( P = 0.42; OR = 2.1; 95%CI: 0.44-19.7). Multiple logistic regression analysis using age, alcohol intake, presence of ansa pancreatica, and presence of autoimmune disease as independent covariates, revealed a significant relationship between the presence of ansa pancreatica and recurrent acute pancreatitis. The presence of autoimmune disease was also significantly associated with the onset of recurrent acute pancreatitis. On the other hand, neither age nor alcohol intake were significantly related to the onset of recurrent acute pancreatitis. The present study is the first to provide robust evidence that the presence of ansa pancreatica is significantly associated with recurrent acute pancreatitis.

Early prediction of lung cancer recurrence after stereotactic radiotherapy using second order texture statistics

NASA Astrophysics Data System (ADS)

Mattonen, Sarah A.; Palma, David A.; Haasbeek, Cornelis J. A.; Senan, Suresh; Ward, Aaron D.

2014-03-01

Benign radiation-induced lung injury is a common finding following stereotactic ablative radiotherapy (SABR) for lung cancer, and is often difficult to differentiate from a recurring tumour due to the ablative doses and highly conformal treatment with SABR. Current approaches to treatment response assessment have shown limited ability to predict recurrence within 6 months of treatment. The purpose of our study was to evaluate the accuracy of second order texture statistics for prediction of eventual recurrence based on computed tomography (CT) images acquired within 6 months of treatment, and compare with the performance of first order appearance and lesion size measures. Consolidative and ground-glass opacity (GGO) regions were manually delineated on post-SABR CT images. Automatic consolidation expansion was also investigated to act as a surrogate for GGO position. The top features for prediction of recurrence were all texture features within the GGO and included energy, entropy, correlation, inertia, and first order texture (standard deviation of density). These predicted recurrence with 2-fold cross validation (CV) accuracies of 70-77% at 2- 5 months post-SABR, with energy, entropy, and first order texture having leave-one-out CV accuracies greater than 80%. Our results also suggest that automatic expansion of the consolidation region could eliminate the need for manual delineation, and produced reproducible results when compared to manually delineated GGO. If validated on a larger data set, this could lead to a clinically useful computer-aided diagnosis system for prediction of recurrence within 6 months of SABR and allow for early salvage therapy for patients with recurrence.

Unraveling the secrets of rice wild species

USDA-ARS?s Scientific Manuscript database

The rice wild species (Oryza spp.) genepool is a relatively untapped source of novel alleles for crop improvement. Several different accessions of rice wild species have been crossed as donor parents with several different Asian rice (O. sativa) cultivars, as the recurrent parent to develop mappi...

Reduction of salmonella on valencia oranges by cold plasma treatment

USDA-ARS?s Scientific Manuscript database

Orange juice has been the source of recurrent food borne illness outbreaks, primarily associated with Salmonella. There is a need for antimicrobial interventions which can effectively eliminate pathogens from fruit surfaces and reduce the risk of cross-contamination during peeling and processing. To...

BIPOLAR DISORDER AND SUBSTANCE ABUSE: PATHOLOGICAL AND THERAPEUTIC IMPLICATIONS OF THEIR COMORBIDITY AND CROSS SENSITIZATION

PubMed Central

Post, Robert M.; Kalivas, Peter

2015-01-01

Background Bipolar disorder has a high co-occurrence with substance abuse disorders, but the pathophysiological mechanisms have not been adequately explored. Aims Review the role of stress in the onset and recurrence of affective episodes and substance abuse. Method We review the mechanisms involved in sensitization (increased responsivity) to recurrence of stressors, mood episodes, and cocaine use. Results Evidence suggests that intermittent stressors, mood episodes, and bouts of cocaine use not only show sensitization to themselves, but cross sensitization to the others contributing to illness progression. However, common mechanisms of sensitization, (such as regionally selective alterations in brain derived neurotrophic factor (BDNF) and hyperactivity of striatally-based habit memories), could also result in single therapies (such as N-acetylcysteine) having positive effects in all 3 domains. Conclusions These interacting sensitization processes suggest the importance of early intervention in attempting to prevent increasingly severe manifestations of bipolar illness and substance abuse progression. PMID:23457180

Retained guidewire penetrating through the aorta into the thorax: an unusual cause of recurrent bilateral pneumothorax.

PubMed

Kim, YongHun; Yu, JunSik; Kim, YoHan; Lee, WooSurng

2016-01-01

Although numerous complications of the Seldinger technique have been reported in the literature, only a few complications are related to guidewires. We here report a case of a patient with a guidewire lost and retained in the aorta during vertebral artery stenting. Unfortunately, the guidewire in the aorta was not detected for 5 years, and it penetrated through the aorta into the left thorax, leading to recurrent left pneumothorax. No physician identified the wandering guidewire in the left thorax, and the recurrent left pneumothorax was only managed with closed thoracostomy drainage several times. After 4 months, the patient presented to our hospital with repeated severe chest pain, and newly developed right pneumothorax was diagnosed on chest X-rays. We meticulously evaluated the radiological findings of the other hospitals to identify the cause of the recurrent pneumothorax and discovered that the lost and wandering guidewire had crossed over from the left to the right thorax through the anterior mediastinum. The guidewire was identified as the cause of the recurrent bilateral pneumothorax, and the patient was successfully treated with video-assisted thoracoscopic surgery without any events. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Strong Recurrent Networks Compute the Orientation-Tuning of Surround Modulation in Primate V1

PubMed Central

Shushruth, S.; Mangapathy, Pradeep; Ichida, Jennifer M.; Bressloff, Paul C.; Schwabe, Lars; Angelucci, Alessandra

2012-01-01

In macaque primary visual cortex (V1) neuronal responses to stimuli inside the receptive field (RF) are modulated by stimuli in the RF surround. This modulation is orientation-specific. Previous studies suggested that for some cells this specificity may not be fixed, but changes with the stimulus orientation presented to the RF. We demonstrate, in recording studies, that this tuning behavior is instead highly prevalent in V1 and, in theoretical work, that it arises only if V1 operates in a regime of strong local recurrence. Strongest surround suppression occurs when the stimuli in the RF and the surround are iso-oriented, and strongest facilitation when the stimuli are cross-oriented. This is the case even when the RF is sub-optimally activated by a stimulus of non-preferred orientation, but only if this stimulus can activate the cell when presented alone. This tuning behavior emerges from the interaction of lateral inhibition (via the surround pathways), which is tuned to the RF’s preferred orientation, with weakly-tuned, but strong, local recurrent connections, causing maximal withdrawal of recurrent excitation at the feedforward input orientation. Thus, horizontal and feedback modulation of strong recurrent circuits allows the tuning of contextual effects to change with changing feedforward inputs. PMID:22219292

Falls and fear of falling in vertigo and balance disorders: A controlled cross-sectional study.

PubMed

Schlick, Cornelia; Schniepp, Roman; Loidl, Verena; Wuehr, Max; Hesselbarth, Kristin; Jahn, Klaus

2016-01-01

Vertigo and dizziness are among the most prevalent symptoms in neurologic disorders. Although many of these patients suffer from postural instability and gait disturbances, there is only limited data on their risk of falling. We conducted a controlled cross-sectional study at the tertiary care outpatient clinic of the German Center for Vertigo and Balance Disorders using a self-administered questionnaire to assess falls, fall-related injuries, and fear of falling. The recruitment period was 6 months. A total of 569 patients (mean age 59.6 ± 17.1 years, 55% females) and 100 healthy participants were included (response rate > 90%). Dizzy patients with central balance disorders (Parkinsonian, cerebellar, and brainstem oculomotor syndromes) had the highest fall rates (> 50% recurrent fallers, odds ratio > 10). The rate of recurrent fallers was 30% in bilateral vestibular failure and peripheral neuropathy (odds ratio > 5). Patients with functional dizziness (somatoform or phobic vertigo) were concerned about falling but did not fall more often than healthy controls (odds ratio 0.87). Falls are common in patients presenting to a dizziness unit. Those with central syndromes are at risk of recurrent and injurious falling. Fall rates and fear of falling should be assessed in balance disorders and used to guide the regimen of rehabilitation therapy. The identification of risk factors would help provide protective measures to these groups of patients.

Quantification of shear stress in a meandering native topographic channel using a physical hydraulic model

Treesearch

Michael E. Ursic

2011-01-01

Current guidelines for predicting increases in shear stress in open-channel bends were developed from investigations that were primarily prismatic in cross section. This study provides possible increases in shear stress relative to approach flow conditions resulting from planimetric and topographic geometric features. Boundary shear stress estimates were determined by...

A Standardized System of Training Intensity Guidelines for the Sports of Track and Field and Cross Country

ERIC Educational Resources Information Center

Belcher, Christopher P.; Pemberton, Cynthia Lee A.

2012-01-01

Accurate quantification of training intensity is an essential component of a training program (Rowbottom, 2000). A training program designed to optimize athlete performance abilities cannot be practically planned or implemented without a valid and reliable indication of training intensity and its effect on the physiological mechanisms of the human…

Dynamics of intracranial electroencephalographic recordings from epilepsy patients using univariate and bivariate recurrence networks

NASA Astrophysics Data System (ADS)

Subramaniyam, Narayan Puthanmadam; Hyttinen, Jari

2015-02-01

Recently Andrezejak et al. combined the randomness and nonlinear independence test with iterative amplitude adjusted Fourier transform (iAAFT) surrogates to distinguish between the dynamics of seizure-free intracranial electroencephalographic (EEG) signals recorded from epileptogenic (focal) and nonepileptogenic (nonfocal) brain areas of epileptic patients. However, stationarity is a part of the null hypothesis for iAAFT surrogates and thus nonstationarity can violate the null hypothesis. In this work we first propose the application of the randomness and nonlinear independence test based on recurrence network measures to distinguish between the dynamics of focal and nonfocal EEG signals. Furthermore, we combine these tests with both iAAFT and truncated Fourier transform (TFT) surrogate methods, which also preserves the nonstationarity of the original data in the surrogates along with its linear structure. Our results indicate that focal EEG signals exhibit an increased degree of structural complexity and interdependency compared to nonfocal EEG signals. In general, we find higher rejections for randomness and nonlinear independence tests for focal EEG signals compared to nonfocal EEG signals. In particular, the univariate recurrence network measures, the average clustering coefficient C and assortativity R , and the bivariate recurrence network measure, the average cross-clustering coefficient Ccross, can successfully distinguish between the focal and nonfocal EEG signals, even when the analysis is restricted to nonstationary signals, irrespective of the type of surrogates used. On the other hand, we find that the univariate recurrence network measures, the average path length L , and the average betweenness centrality BC fail to distinguish between the focal and nonfocal EEG signals when iAAFT surrogates are used. However, these two measures can distinguish between focal and nonfocal EEG signals when TFT surrogates are used for nonstationary signals. We also report an improvement in the performance of nonlinear prediction error N and nonlinear interdependence measure L used by Andrezejak et al., when TFT surrogates are used for nonstationary EEG signals. We also find that the outcome of the nonlinear independence test based on the average cross-clustering coefficient Ccross is independent of the outcome of the randomness test based on the average clustering coefficient C . Thus, the univariate and bivariate recurrence network measures provide independent information regarding the dynamics of the focal and nonfocal EEG signals. In conclusion, recurrence network analysis combined with nonstationary surrogates can be applied to derive reliable biomarkers to distinguish between epileptogenic and nonepileptogenic brain areas using EEG signals.

Quantification of vocal fold motion using echography: application to recurrent nerve paralysis detection

NASA Astrophysics Data System (ADS)

Cohen, Mike-Ely; Lefort, Muriel; Bergeret-Cassagne, Héloïse; Hachi, Siham; Li, Ang; Russ, Gilles; Lazard, Diane; Menegaux, Fabrice; Leenhardt, Laurence; Trésallet, Christophe; Frouin, Frédérique

2015-03-01

Recurrent nerve paralysis (RP) is one of the most frequent complications of thyroid surgery. It reduces vocal fold mobility. Nasal endoscopy, a mini-invasive procedure, is the conventional way to detect RP. We suggest a new approach based on laryngeal ultrasound and a specific data analysis was designed to help with the automated detection of RP. Ten subjects were enrolled for this feasibility study: four controls, three patients with RP and three patients without RP according to nasal endoscopy. The ultrasound protocol was based on a ten seconds B-mode acquisition in a coronal plane during normal breathing. Image processing included three steps: 1) automated detection of two consecutive closing and opening images, corresponding to extreme positions of vocal folds in the sequence of B-mode images, using principal component analysis of the image sequence; 2) positioning of three landmarks and robust tracking of these points using a multi-pyramidal refined optical flow approach; 3) estimation of quantitative parameters indicating left and right fractions of mobility, and motion symmetry. Results provided by automated image processing were compared to those obtained by an expert. Detection of extreme images was accurate; tracking of landmarks was reliable in 80% of cases. Motion symmetry indices showed similar values for controls and patients without RP. Fraction of mobility was reduced in cases of RP. Thus, our CAD system helped in the detection of RP. Laryngeal ultrasound combined with appropriate image processing helped in the diagnosis of recurrent nerve paralysis and could be proposed as a first-line method.

Global relative quantification with liquid chromatography-matrix-assisted laser desorption ionization time-of-flight (LC-MALDI-TOF)--cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences.

PubMed

Hessling, Bernd; Büttner, Knut; Hecker, Michael; Becher, Dörte

2013-10-01

Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC-electrospray ionization workflows. Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis. Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments.

A resilience-oriented approach for quantitatively assessing recurrent spatial-temporal congestion on urban roads.

PubMed

Tang, Junqing; Heinimann, Hans Rudolf

2018-01-01

Traffic congestion brings not only delay and inconvenience, but other associated national concerns, such as greenhouse gases, air pollutants, road safety issues and risks. Identification, measurement, tracking, and control of urban recurrent congestion are vital for building a livable and smart community. A considerable amount of works has made contributions to tackle the problem. Several methods, such as time-based approaches and level of service, can be effective for characterizing congestion on urban streets. However, studies with systemic perspectives have been minor in congestion quantification. Resilience, on the other hand, is an emerging concept that focuses on comprehensive systemic performance and characterizes the ability of a system to cope with disturbance and to recover its functionality. In this paper, we symbolized recurrent congestion as internal disturbance and proposed a modified metric inspired by the well-applied "R4" resilience-triangle framework. We constructed the metric with generic dimensions from both resilience engineering and transport science to quantify recurrent congestion based on spatial-temporal traffic patterns and made the comparison with other two approaches in freeway and signal-controlled arterial cases. Results showed that the metric can effectively capture congestion patterns in the study area and provides a quantitative benchmark for comparison. Also, it suggested not only a good comparative performance in measuring strength of proposed metric, but also its capability of considering the discharging process in congestion. The sensitivity tests showed that proposed metric possesses robustness against parameter perturbation in Robustness Range (RR), but the number of identified congestion patterns can be influenced by the existence of ϵ. In addition, the Elasticity Threshold (ET) and the spatial dimension of cell-based platform differ the congestion results significantly on both the detected number and intensity. By tackling this conventional problem with emerging concept, our metric provides a systemic alternative approach and enriches the toolbox for congestion assessment. Future work will be conducted on a larger scale with multiplex scenarios in various traffic conditions.

When Routines Are Not so Routine: Exploring Coordination Work in Hospitals

ERIC Educational Resources Information Center

Haque, Saira Naim

2010-01-01

Many work processes take place through routines, or recurrent patterns of action. These activities involve individuals from several occupations working across spatial, temporal, and organizational boundaries. Crossing these professional, temporal and spatial boundaries has unique challenges which can lead to coordination failures. In these…

Development Of Interspecific Cssls In Rice Using SNP-Based Selection

USDA-ARS?s Scientific Manuscript database

Six libraries of chromosome segment substitution lines (CSSLs) are being developed based on crosses between three diverse accessions of O. rufipogon (from China, Laos and Indonesia) and two O. sativa recurrent parents, IR64, an indica variety (from the Philippines), and Cybonnet, a tropical japonica...

Association between benzodiazepines and recurrent falls: a cross-sectional elderly population-based study.

PubMed

Rossat, A; Fantino, B; Bongue, B; Colvez, A; Nitenberg, C; Annweiler, C; Beauchet, O

2011-01-01

While the association between benzodiazepines (BZD) and single fall is long-known, the association between BZD and recurrent falls has been few studied. The aims of this study were 1) to examine whether BZD were associated with recurrent falls while taking into account the effect of potential confounders, and 2) to determine whether there was an interaction in terms of risk of falls between BZD and balance impairment in a community-dwelling population-based adults aged 65 and older. Cross-sectional. Three health centers in North-East of France. 7643 community-dwelling volunteers aged 65 and older. The use of BZD, the Mini Mental State Examination (MMSE) score, the Clock Drawing Test (CDT), the One Leg Balance (OLB) test, the Five Times Sit-To-Stand test (FTSS), and a history of falls were recorded. Subjects were separated into 4 groups based on the number of falls: 0, 1, 2 and ≥ 3 falls. Among the 1456 (19.2%) fallers, 994 (13.0%) were single fallers and 462 (6.1%) were recurrent fallers (i.e., > 2 falls). The number of falls increased significantly with age (Incident Rate Ratio (IRR)=1.04, P < 0.001), female gender (IRR=2.24, P < 0.001), the use of benzodiazepine (IRR=1.65 P < 0.001) and especially while subjects used bromazepam (IRR=1.44, P=0.006), clobazam (IRR=3.01, P=0.014) and prazepam (IRR=2.29, P < 0.001). A low MMSE score (IRR=0.96, P < 0.001), an impaired CDT (IRR=0.91, P < 0.001), and a bad performance at OLB and FTSS (respectively IRR=1.85, P < 0.001 and IRR=1.26, P < 0.001) were related to the recurrence of falls. After adjustment only the advance in age (IRR=1.02, P < 0.001), female gender (IRR=2.15, P < 0.001), clobazam (IRR=2.54, P=0.04), prazepam (IRR=1.63, P=0.03) and OLB (IRR=1.55, P < 0.001) were still significantly related to the number of falls. The current study shows that the age, the female gender, the use of clobazam or prazepam and a low score at OLB are related to the recurrence of falls.

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

NASA Astrophysics Data System (ADS)

Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

The role of oxidative stress in spontaneous abortion and recurrent pregnancy loss: a systematic review.

PubMed

Gupta, Sajal; Agarwal, Ashok; Banerjee, Jashoman; Alvarez, Juan G

2007-05-01

Human reproduction is not considered a highly efficient biological process. Before the end of the first trimester, 30%-50% of conceptions end in spontaneous abortion. Most losses occur at the time of implantation. 15%-20% of clinical pregnancies end in spontaneous abortions. Recurrent pregnancy loss is a frustrating clinical problem both for clinicians and patients. Recurrent pregnancy loss affects 0.5%-3% of women in the reproductive age group, and between 50%-60% of recurrent pregnancy losses are idiopathic. Oxidative stress-induced damage has been hypothesized to play a role in spontaneous abortion, idiopathic recurrent pregnancy loss, hydatidiform mole, defective embryogenesis, and drug-induced teratogenicity. Some studies implicate systemic and placental oxidative stress in the pathophysiology of abortion and recurrent pregnancy loss. Oxidant-induced endothelial damage, impaired placental vascularization and immune malfunction have all been proposed to play a role in the pathophysiology of idiopathic recurrent pregnancy loss. Oxidative stress-induced placental dysfunction may be a common cause of the multifactorial and polygenic etiologies of abortion, recurrent pregnancy loss, defective embryogenesis, hydatidiform mole, and drug-induced teratogenic effects. Oxidative stress-induced modification of phospholipids has been linked to the formation of antiphospholipid antibodies in the antiphospholipid syndrome. The objective of this review was to examine the association between oxidative stress, spontaneous abortion and recurrent pregnancy loss, based on the published literature. We conducted an extensive literature search utilizing the databases of Medline, CINAHL, and Cochrane from 1986 to 2005. The following keywords were used: oxidative stress, abortion, recurrent pregnancy loss, reactive oxygen species, antioxidants, fetal development, and embryopathies. We conducted an electronic search, as well as a manual search of cross-references. We have included all studies in the English language found in the literature focusing on oxidative stress and its association with abortions, recurrent pregnancy loss and drug-induced teratogenicity. The role of antioxidant vitamins for primary prevention of oxidative stress-induced pathologies needs to be investigated further. Obstetricians & Gynecologists, Family Physicians. After completion of this article, the reader should be able to state that the causes of spontaneous and recurrent abortion are multifaceted, however, some of the causes may be preventable and also explain that the role of oxidative stress during pregnancy and adverse pregnancy outcomes has a basis in pathophysiology, although the role of oxidative stress and the treatment of oxidative stress during or before pregnancy remains speculative.

Quantification of electrical field-induced flow reversal in a microchannel.

PubMed

Pirat, C; Naso, A; van der Wouden, E J; Gardeniers, J G E; Lohse, D; van den Berg, A

2008-06-01

We characterize the electroosmotic flow in a microchannel with field effect flow control. High resolution measurements of the flow velocity, performed by micro particle image velocimetry, evidence the flow reversal induced by a local modification of the surface charge due to the presence of the gate. The shape of the microchannel cross-section is accurately extracted from these measurements. Experimental velocity profiles show a quantitative agreement with numerical results accounting for this exact shape. Analytical predictions assuming a rectangular cross-section are found to give a reasonable estimate of the velocity far enough from the walls.

Absolute photoionization cross sections of furanic fuels: 2-ethylfuran, 2-acetylfuran and furfural.

PubMed

Smith, Audrey R; Meloni, Giovanni

2015-11-01

Absolute photoionization cross sections of the molecules 2-ethylfuran, 2-acetylfuran and furfural, including partial ionization cross sections for the dissociative ionized fragments, are measured for the first time. These measurements are important because they allow fuel quantification via photoionization mass spectrometry and the development of quantitative kinetic modeling for the complex combustion of potential fuels. The experiments are carried out using synchrotron photoionization mass spectrometry with an orthogonal time-of-flight spectrometer used for mass analysis at the Advanced Light Source of Lawrence Berkeley National Laboratory. The CBS-QB3 calculations of adiabatic ionization energies and appearance energies agree well with the experimental results. Several bond dissociation energies are also derived and presented. Copyright © 2015 John Wiley & Sons, Ltd.

Functional consequences and health-care seeking behaviour for recurrent non-specific low back pain in Zimbabwean adolescents: a cross-sectional study.

PubMed

Chiwaridzo, Matthew; Naidoo, Nirmala

2016-02-01

The purpose of the study was to investigate the consequences of recurrent non-specific low back pain in Zimbabwean adolescents. Recurrent non-specific low back pain is a common cause of adult disability in low-income countries. However, its impact in adolescents has been a matter of debate in the literature. A survey was conducted using a cluster sample of 544 school children between the ages of 13 and 19 years. The school children were randomly selected from government-administered secondary schools in Harare, Zimbabwe. Parental and students' response rate were 90.3 and 97.8 %, respectively. Almost a third (28.8 %) of school children reported recurrent symptoms (CI 27.8-31.6). However, the majority (84 %) of these cases were unknown to parents. Twenty-seven percent reported having sought medical treatment. On the nine-item Hanover Low Back Pain Disability Questionnaire, 71.2 % of school children had at least one activity of daily living compromised by recurrent NSLBP, especially sports participation. However, severe disability was reported in 28 % of the adolescents. Health-care seeking behaviour was not associated with the level of disability [χ (2)(1) = 0.36, p = 0.55]. Although most parents are unaware, recurrent NSLBP is common in Zimbabwean school children. However, treatment is rarely sought for the symptoms. A preponderance of adolescents with recurrent NSLBP experiences some degree of functional consequences, although severe disability is rare. There is need to raise awareness of the condition in schools and to parents. Spinal health educational programmes may need to be implemented to avert the functional consequences. Further studies are needed in the future to investigate the coping strategies for pain in adolescents.

Quantification of scaling exponents and dynamical complexity of microwave refractivity in a tropical climate

NASA Astrophysics Data System (ADS)

Fuwape, Ibiyinka A.; Ogunjo, Samuel T.

2016-12-01

Radio refractivity index is used to quantify the effect of atmospheric parameters in communication systems. Scaling and dynamical complexities of radio refractivity across different climatic zones of Nigeria have been studied. Scaling property of the radio refractivity across Nigeria was estimated from the Hurst Exponent obtained using two different scaling methods namely: The Rescaled Range (R/S) and the detrended fluctuation analysis(DFA). The delay vector variance (DVV), Largest Lyapunov Exponent (λ1) and Correlation Dimension (D2) methods were used to investigate nonlinearity and the results confirm the presence of deterministic nonlinear profile in the radio refractivity time series. The recurrence quantification analysis (RQA) was used to quantify the degree of chaoticity in the radio refractivity across the different climatic zones. RQA was found to be a good measure for identifying unique fingerprint and signature of chaotic time series data. Microwave radio refractivity was found to be persistent and chaotic in all the study locations. The dynamics of radio refractivity increases in complexity and chaoticity from the Coastal region towards the Sahelian climate. The design, development and deployment of robust and reliable microwave communication link in the region will be greatly affected by the chaotic nature of radio refractivity in the region.

Suppression of anomalous synchronization and nonstationary behavior of neural network under small-world topology

NASA Astrophysics Data System (ADS)

Boaretto, B. R. R.; Budzinski, R. C.; Prado, T. L.; Kurths, J.; Lopes, S. R.

2018-05-01

It is known that neural networks under small-world topology can present anomalous synchronization and nonstationary behavior for weak coupling regimes. Here, we propose methods to suppress the anomalous synchronization and also to diminish the nonstationary behavior occurring in weakly coupled neural network under small-world topology. We consider a network of 2000 thermally sensitive identical neurons, based on the model of Hodgkin-Huxley in a small-world topology, with the probability of adding non local connection equal to p = 0 . 001. Based on experimental protocols to suppress anomalous synchronization, as well as nonstationary behavior of the neural network dynamics, we make use of (i) external stimulus (pulsed current); (ii) biologic parameters changing (neuron membrane conductance changes); and (iii) body temperature changes. Quantification analysis to evaluate phase synchronization makes use of the Kuramoto's order parameter, while recurrence quantification analysis, particularly the determinism, computed over the easily accessible mean field of network, the local field potential (LFP), is used to evaluate nonstationary states. We show that the methods proposed can control the anomalous synchronization and nonstationarity occurring for weak coupling parameter without any effect on the individual neuron dynamics, neither in the expected asymptotic synchronized states occurring for large values of the coupling parameter.

Cross-Reactivity of Antibodies against Leptospiral Recurrent Uveitis-Associated Proteins A and B (LruA and LruB) with Eye Proteins

PubMed Central

Verma, Ashutosh; Kumar, Pawan; Babb, Kelly; Timoney, John F.; Stevenson, Brian

2010-01-01

Infection by Leptospira interrogans has been causally associated with human and equine uveitis. Studies in our laboratories have demonstrated that leptospiral lipoprotein LruA and LruB are expressed in the eyes of uveitic horses, and that antibodies directed against LruA and LruB react with equine lenticular and retinal extracts, respectively. These reactivities were investigated further by performing immunofluorescent assays on lenticular and retinal tissue sections. Incubation of lens tissue sections with LruA-antiserum and retinal sections with LruB-antiserum resulted in positive fluorescence. By employing two-dimensional gel analyses followed by immunoblotting and mass spectrometry, lens proteins cross-reacting with LruA antiserum were identified to be α-crystallin B and vimentin. Similarly, mass spectrometric analyses identified β-crystallin B2 as the retinal protein cross-reacting with LruB-antiserum. Purified recombinant human α-crystallin B and vimentin were recognized by LruA-directed antiserum, but not by control pre-immune serum. Recombinant β-crystallin B2 was likewise recognized by LruB-directed antiserum, but not by pre-immune serum. Moreover, uveitic eye fluids contained significantly higher levels of antiibodies that recognized α-crystallin B, β-crystallin B2 and vimentin than did normal eye fluids. Our results indicate that LruA and LruB share immuno-relevant epitopes with eye proteins, suggesting that cross-reactive antibody interactions with eye antigens may contribute to immunopathogenesis of Leptospira-associated recurrent uveitis. PMID:20689825

Cross-reactivity of antibodies against leptospiral recurrent uveitis-associated proteins A and B (LruA and LruB) with eye proteins.

PubMed

Verma, Ashutosh; Kumar, Pawan; Babb, Kelly; Timoney, John F; Stevenson, Brian

2010-08-03

Infection by Leptospira interrogans has been causally associated with human and equine uveitis. Studies in our laboratories have demonstrated that leptospiral lipoprotein LruA and LruB are expressed in the eyes of uveitic horses, and that antibodies directed against LruA and LruB react with equine lenticular and retinal extracts, respectively. These reactivities were investigated further by performing immunofluorescent assays on lenticular and retinal tissue sections. Incubation of lens tissue sections with LruA-antiserum and retinal sections with LruB-antiserum resulted in positive fluorescence. By employing two-dimensional gel analyses followed by immunoblotting and mass spectrometry, lens proteins cross-reacting with LruA antiserum were identified to be alpha-crystallin B and vimentin. Similarly, mass spectrometric analyses identified beta-crystallin B2 as the retinal protein cross-reacting with LruB-antiserum. Purified recombinant human alpha-crystallin B and vimentin were recognized by LruA-directed antiserum, but not by control pre-immune serum. Recombinant beta-crystallin B2 was likewise recognized by LruB-directed antiserum, but not by pre-immune serum. Moreover, uveitic eye fluids contained significantly higher levels of antiibodies that recognized alpha-crystallin B, beta-crystallin B2 and vimentin than did normal eye fluids. Our results indicate that LruA and LruB share immuno-relevant epitopes with eye proteins, suggesting that cross-reactive antibody interactions with eye antigens may contribute to immunopathogenesis of Leptospira-associated recurrent uveitis.

Direct Visual and Radar Methods for the Detection, Quantification, and Prediction of Bird Migration.

DTIC Science & Technology

1980-04-30

domesticus), 12 cm2 ; and Rock Dove ( Columba livia ), 80 cm’. Eastwood (1967) has given the radar cross sections of a number of European birds as mea...in Table 4 and Table 5 it is apparent that a single pigeon ( Columba livia ) flying toward the radar should theoretically produce an echo on the ASR-4

StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images.

PubMed

De Backer, A; van den Bos, K H W; Van den Broek, W; Sijbers, J; Van Aert, S

2016-12-01

An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of crossability between triticale (X Triticosecale Wittmack) and common wheat, durum wheat and rye.

PubMed

Hills, Melissa J; Hall, Linda M; Messenger, Doug F; Graf, Robert J; Beres, Brian L; Eudes, François

2007-01-01

Development of transgenic triticale as a platform for novel bio-industrial products is predicated on an environmental biosafety assessment that quantifies the potential risks associated with its release. Pollen-mediated gene flow to related species and conventional triticale varieties is one pathway for transgene movement. A tier 1 quantification of triticale hybridization was conducted by emasculating and hand pollinating flowers under greenhouse conditions. Approximately 2000 manual pollinations were conducted for each cross and its reciprocal between two triticale genotypes: a modern triticale cultivar (AC Alta) and primary triticale (89TT108), and common wheat, durum wheat and rye. The frequency of outcrossing, hybrid seed appearance and weight, and F(1) emergence and fertility were recorded. Outcrossing, F(1) emergence and fertility rates were high from crosses between triticale genotypes. Outcrossing in inter-specific crosses was influenced by the species, and the genotype and gender of the triticale parent. In crosses to common and durum wheat where triticale was the male parent, outcrossing was > or =73.0% and > or =69.5%, respectively, but < or =23.9% and < or =3.0% when triticale was the female parent. Overall, outcrossing with rye was lower than with common and durum wheat. F(1) hybrid emergence was greater when triticale was the female parent. With the exception of a single seed, all wheat-triticale F(1) hybrid seeds were non-viable when triticale was the male parent in the cross. Only seven durum wheat-triticale F(1) hybrids emerged from 163 seeds sown, and all were produced with triticale 89TT108 as female parent. With rye, 8 F(1) hybrids emerged from 38 seeds sown, and all were produced from crosses to AC Alta; five with AC Alta as the female parent and three as the male. Interspecific F(1) hybrids were self-sterile, with the exception of those produced in crosses between common wheat and triticale where triticale was the female parent. Tier 2 hybridization quantification will be conducted under field conditions.

OR14-V-Uncertainty-PD2La Uncertainty Quantification for Nuclear Safeguards and Nondestructive Assay Final Report

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

Nicholson, Andrew D.; Croft, Stephen; McElroy, Robert Dennis

2017-08-01

The various methods of nondestructive assay (NDA) of special nuclear material (SNM) have applications in nuclear nonproliferation, including detection and identification of illicit SNM at border crossings and quantifying SNM at nuclear facilities for safeguards. No assay method is complete without “error bars,” which provide one way of expressing confidence in the assay result. Consequently, NDA specialists typically provide error bars and also partition total uncertainty into “random” and “systematic” components so that, for example, an error bar can be developed for the total mass estimate in multiple items. Uncertainty Quantification (UQ) for NDA has always been important, but itmore » is recognized that greater rigor is needed and achievable using modern statistical methods.« less

Development of a Specific Monoclonal Antibody for the Quantification of Artemisinin in Artemisia annua and Rat Serum.

PubMed

Guo, Suqin; Cui, Yongliang; Wang, Kunbi; Zhang, Wei; Tan, Guiyu; Wang, Baomin; Cui, Liwang

2016-03-01

Artemisinin, extracted from Artemisia annua, and its derivatives are important frontline antimalarials. To produce specific antibodies for the detection and quantification of artemisinin, artemisinin was transformed to 9-hydroxyartemisinin by microbial fermentation, which was used to prepare a 9-succinate artemisinin hapten for conjugation with ovalbumin. A monoclonal antibody (mAb), designated as 3H7A10, was selected from hybridoma cell lines which showed high specificity to artemisinin. No competitive inhibition was observed with artesunate, dihydroartemisinin, and artemether for up to 20,000 ng mL(-1). An indirect competitive enzyme-linked immunosorbent assay (icELISA) was developed, which showed a concentration causing 50% of inhibition (IC50) for artemisinin as 2.6 ng mL(-1) and a working range of 0.6-11.5 ng mL(-1). The icELISA was applied for the quantification of artemisinin in crude extracts of wild A. annua and the study of pharmacokinetics of artemisinin in rat serum after intraperitoneal injection. The results were highly correlated with those determined by HPLC-UV analysis (R(2) = 0.9919). In comparison with reported antiartemisinin mAbs which have broad cross-reactivity with other artemisinin derivatives, the high specificity of 3H7A10 for artemisinin will enable development of methods for quantification of artemisinin in Artemisia plants and antimalarial drugs such as Arco and for pharmacokinetic studies.

miR-MaGiC improves quantification accuracy for small RNA-seq.

PubMed

Russell, Pamela H; Vestal, Brian; Shi, Wen; Rudra, Pratyaydipta D; Dowell, Robin; Radcliffe, Richard; Saba, Laura; Kechris, Katerina

2018-05-15

Many tools have been developed to profile microRNA (miRNA) expression from small RNA-seq data. These tools must contend with several issues: the small size of miRNAs, the small number of unique miRNAs, the fact that similar miRNAs can be transcribed from multiple loci, and the presence of miRNA isoforms known as isomiRs. Methods failing to address these issues can return misleading information. We propose a novel quantification method designed to address these concerns. We present miR-MaGiC, a novel miRNA quantification method, implemented as a cross-platform tool in Java. miR-MaGiC performs stringent mapping to a core region of each miRNA and defines a meaningful set of target miRNA sequences by collapsing the miRNA space to "functional groups". We hypothesize that these two features, mapping stringency and collapsing, provide more optimal quantification to a more meaningful unit (i.e., miRNA family). We test miR-MaGiC and several published methods on 210 small RNA-seq libraries, evaluating each method's ability to accurately reflect global miRNA expression profiles. We define accuracy as total counts close to the total number of input reads originating from miRNAs. We find that miR-MaGiC, which incorporates both stringency and collapsing, provides the most accurate counts.

Statistical downscaling of precipitation using long short-term memory recurrent neural networks

NASA Astrophysics Data System (ADS)

Misra, Saptarshi; Sarkar, Sudeshna; Mitra, Pabitra

2017-11-01

Hydrological impacts of global climate change on regional scale are generally assessed by downscaling large-scale climatic variables, simulated by General Circulation Models (GCMs), to regional, small-scale hydrometeorological variables like precipitation, temperature, etc. In this study, we propose a new statistical downscaling model based on Recurrent Neural Network with Long Short-Term Memory which captures the spatio-temporal dependencies in local rainfall. The previous studies have used several other methods such as linear regression, quantile regression, kernel regression, beta regression, and artificial neural networks. Deep neural networks and recurrent neural networks have been shown to be highly promising in modeling complex and highly non-linear relationships between input and output variables in different domains and hence we investigated their performance in the task of statistical downscaling. We have tested this model on two datasets—one on precipitation in Mahanadi basin in India and the second on precipitation in Campbell River basin in Canada. Our autoencoder coupled long short-term memory recurrent neural network model performs the best compared to other existing methods on both the datasets with respect to temporal cross-correlation, mean squared error, and capturing the extremes.

Recurrent headache and interpersonal violence in adolescence: the roles of psychological distress, loneliness and family cohesion: the HUNT study.

PubMed

Stensland, Synne Oien; Thoresen, Siri; Wentzel-Larsen, Tore; Zwart, John-Anker; Dyb, Grete

2014-06-10

Recurrent headache is the most common and disabling pain condition in adolescence. Co-occurrence of psychosocial adversity is associated with increased risk of chronification and functional impairment. Exposure to interpersonal violence seems to constitute an important etiological factor. Thus, knowledge of the multiple pathways linking interpersonal violence to recurrent headache could help guide preventive and clinical interventions. In the present study we explored a hypothetical causal model where the link between exposure to interpersonal violence and recurrent headache is mediated in parallel through loneliness and psychological distress. Higher level of family cohesion and male sex is hypothesized to buffer the adverse effect of exposure to interpersonal violence on headache. The model was assessed using data from the cross-sectional, population-based Young-HUNT 3 study of Norwegian adolescents, conducted from 2006-2008. A cohort of 10 464 adolescents were invited. The response rate was 73% (7620), age ranged from 12 and 20 years, and 50% (3832) were girls. The study comprised self-report measures of exposure to interpersonal violence, loneliness, psychological distress and family cohesion, in addition to a validated interview on headache, meeting the International Classification of Headache Disorders criteria. Recurrent headache was defined as headache recurring at least monthly during the past year, and sub-classified into monthly and weekly headache, which served as separate outcomes. In Conditional Process Analysis, loneliness and psychological distress consistently posed as parallel mediating mechanisms, indirectly linking exposure to interpersonal violence to recurrent headache. We found no substantial moderating effect of family cohesion or sex. Loneliness and psychological distress seem to play crucial roles in the relationship between exposure to interpersonal violence and recurrent headache. To facilitate coping and recovery, it may be helpful to account for these factors in preventive and clinical interventions. Trauma-informed, social relationship-based interventions may represent a major opportunity to alter trajectories of recurrent headache.

Osteosarcoma of the spine: prognostic variables for local recurrence and overall survival, a multicenter ambispective study.

PubMed

Dekutoski, Mark B; Clarke, Michelle J; Rose, Peter; Luzzati, Alessandro; Rhines, Laurence D; Varga, Peter P; Fisher, Charles G; Chou, Dean; Fehlings, Michael G; Reynolds, Jeremy J; Williams, Richard; Quraishi, Nasir A; Germscheid, Niccole M; Sciubba, Daniel M; Gokaslan, Ziya L; Boriani, Stefano

2016-07-01

OBJECTIVE Primary spinal osteosarcomas are rare and aggressive neoplasms. Poor outcomes can occur, as obtaining marginal margins is technically demanding; further Enneking-appropriate en bloc resection can have significant morbidity. The goal of this study is to identify prognostic variables for local recurrence and mortality in surgically treated patients diagnosed with a primary osteosarcoma of the spine. METHODS A multicenter ambispective database of surgically treated patients with primary spine osteosarcomas was developed by AOSpine Knowledge Forum Tumor. Patient demographic, diagnosis, treatment, perioperative morbidity, local recurrence, and cross-sectional survival data were collected. Tumors were classified in 2 cohorts: Enneking appropriate (EA) and Enneking inappropriate (EI), as defined by pathology margin matching Enneking-recommended surgical margins. Prognostic variables were analyzed in reference to local recurrence and survival. RESULTS Between 1987 and 2012, 58 patients (32 female patients) underwent surgical treatment for primary spinal osteosarcoma. Patients were followed for a mean period of 3.5 ± 3.5 years (range 0.5 days to 14.3 years). The median survival for the entire cohort was 6.7 years postoperative. Twenty-four (41%) patients died, and 17 (30%) patients suffered a local recurrence, 10 (59%) of whom died. Twenty-nine (53%) patients underwent EA resection while 26 (47%) patients underwent EI resection with a postoperative median survival of 6.8 and 3.7 years, respectively (p = 0.048). EI patients had a higher rate of local recurrence than EA patients (p = 0.001). Patient age, previous surgery, biopsy type, tumor size, spine level, and chemotherapy timing did not significantly influence recurrence and survival. CONCLUSIONS Osteosarcoma of the spine presents a significant challenge, and most patients die in spite of aggressive surgery. There is a significant decrease in recurrence and an increase in survival with en bloc resection (EA) when compared with intralesional resection (EI). The effect of adjuvant and neoadjuvant chemotherapeutics, as well as method of biopsy, requires further exploration.

Recurrent headache and interpersonal violence in adolescence: the roles of psychological distress, loneliness and family cohesion: the HUNT study

PubMed Central

2014-01-01

Background Recurrent headache is the most common and disabling pain condition in adolescence. Co-occurrence of psychosocial adversity is associated with increased risk of chronification and functional impairment. Exposure to interpersonal violence seems to constitute an important etiological factor. Thus, knowledge of the multiple pathways linking interpersonal violence to recurrent headache could help guide preventive and clinical interventions. In the present study we explored a hypothetical causal model where the link between exposure to interpersonal violence and recurrent headache is mediated in parallel through loneliness and psychological distress. Higher level of family cohesion and male sex is hypothesized to buffer the adverse effect of exposure to interpersonal violence on headache. Methods The model was assessed using data from the cross-sectional, population-based Young-HUNT 3 study of Norwegian adolescents, conducted from 2006–2008. A cohort of 10 464 adolescents were invited. The response rate was 73% (7620), age ranged from 12 and 20 years, and 50% (3832) were girls. The study comprised self-report measures of exposure to interpersonal violence, loneliness, psychological distress and family cohesion, in addition to a validated interview on headache, meeting the International Classification of Headache Disorders criteria. Recurrent headache was defined as headache recurring at least monthly during the past year, and sub-classified into monthly and weekly headache, which served as separate outcomes. Results In Conditional Process Analysis, loneliness and psychological distress consistently posed as parallel mediating mechanisms, indirectly linking exposure to interpersonal violence to recurrent headache. We found no substantial moderating effect of family cohesion or sex. Conclusions Loneliness and psychological distress seem to play crucial roles in the relationship between exposure to interpersonal violence and recurrent headache. To facilitate coping and recovery, it may be helpful to account for these factors in preventive and clinical interventions. Trauma-informed, social relationship-based interventions may represent a major opportunity to alter trajectories of recurrent headache. PMID:24912800

High-Grade Serous Ovarian Cancer: Use of Machine Learning to Predict Abdominopelvic Recurrence on CT on the Basis of Serial Cancer Antigen 125 Levels.

PubMed

Shinagare, Atul B; Balthazar, Patricia; Ip, Ivan K; Lacson, Ronilda; Liu, Joyce; Ramaiya, Nikhil; Khorasani, Ramin

2018-05-19

The aim of this study was to use machine learning to predict abdominal recurrence on CT on the basis of serial cancer antigen 125 (CA125) levels in patients with advanced high-grade serous ovarian cancer on surveillance. This institutional review board-approved, HIPAA-compliant, retrospective, hypothesis-generating study included all 57 patients (mean age, 61 ± 11.2 years) with advanced high-grade serous ovarian cancer who underwent cytoreductive surgery from January to December 2012, followed by surveillance abdominopelvic CT and corresponding CA125 levels. A blinded radiologist reviewed abdominopelvic CT studies until recurrence was noted. Four measures of CA125 were assessed: actual CA125 levels at the time of CT, absolute change since prior CT, relative change since prior CT, and rate of change since prior CT. Using machine learning, support vector machine models were optimized and evaluated using 10-fold cross-validation to determine the CA125 measure most predictive of abdominal recurrence. The association of the most accurate CA125 measure was further analyzed using Cox proportional-hazards model along with age, tumor size, stage, and degree of cytoreduction. Rate of change in CA125 was most predictive of abdominal recurrence in a linear kernel support vector machine model and was significantly higher preceding CT studies showing abdominal recurrence (median 13.2 versus 0.6 units/month; P = .007). On multivariate analysis, a higher rate of CA125 increase was significantly associated with recurrence (hazard ratio, 1.02 per 10 units change; 95% confidence interval, 1.0006-1.04; P = .04). A higher rate of CA125 increase is associated with abdominal recurrence. The rate of increase of CA125 may help in the selection of patients who are most likely to benefit from abdominopelvic CT in surveillance of ovarian cancer. Copyright © 2018 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Three variations of the laryngeal nerve in the same patient: a case report

PubMed Central

2011-01-01

Introduction A non-recurrent course is a rare anatomic variation of the inferior laryngeal nerve (ILN). Bilateral extra-laryngeal bifurcation of the ILN seldom occurs before its laryngeal entry. Anastomosis between the ILN and cervical sympathetic chain is another rare anatomic feature. The prevalence of extra-laryngeal branching of the non-recurrent nerve is unknown. We present an example of triple anatomic variations of ILNs in the same patient, and also two anatomic variations in the same nerve. Case presentation A 56-year-old Caucasian man with a large toxic multi-nodular goiter was surgically treated with total thyroidectomy. Both his right and left ILNs were identified, fully exposed and preserved along their cervical courses. We discovered many variations during bilateral exploration of the two ILNs. His right ILN was non-recurrent. This non-recurrent ILN showed a terminal division before laryngeal entry. The left nerve had a usual course as a recurrent laryngeal nerve (RLN) at his tracheaesophageal groove. We also discovered bifurcation of his RLN beginning at a neurovascular (RLN and inferior thyroid artery) crossing point. Anterior and posterior branches of both nerves entered his larynx separately. The sympathetic inferior laryngeal anastomotic branch (SILAB) between the posterior branch of his left ILN and the cervical sympathetic chain was established in the distal part of the nerve before laryngeal entry. Conclusion A non-recurrent nerve and extra-laryngeal branching of the ILN are two different variations. The coincidence of a right non-recurrent ILN and bilateral bifurcation of both nerves is a very interesting feature. SILAB is a rare additional finding as a third anatomic variation in the same patient. Extra-laryngeal terminal division of a non-recurrent ILN is an extremely unusual anatomic finding. Two anatomic variations have occurred in the same nerve, like "the variation of the variation". PMID:21722360

Proteomics and bioinformatics analysis of altered protein expression in the placental villous tissue from early recurrent miscarriage patients.

PubMed

Pan, Hai-Tao; Ding, Hai-Gang; Fang, Min; Yu, Bin; Cheng, Yi; Tan, Ya-Jing; Fu, Qi-Qin; Lu, Bo; Cai, Hong-Guang; Jin, Xin; Xia, Xian-Qing; Zhang, Tao

2018-01-01

Recurrent miscarriage (RM) affects 5% of women, it has an adverse emotional impact on women. Because of the complexities of early development, the mechanism of recurrent miscarriage is still unclear. We hypothesized that abnormal placenta leads to early recurrent miscarriage (ERM). The aim of this study was to identify ERM associated factors in human placenta villous tissue using proteomics. Investigation of these differences in protein expression in parallel profiling is essential to understand the comprehensive pathophysiological mechanism underlying recurrent miscarriage (RM). To gain more insight into mechanisms of recurrent miscarriage (RM), a comparative proteome profile of the human placenta villous tissue in normal and RM pregnancies was analyzed using iTRAQ technology and bioinformatics analysis used by Ingenuity Pathway Analysis (IPA) software. In this study, we employed an iTRAQ based proteomics analysis of four placental villous tissues from patients with early recurrent miscarriage (ERM) and four from normal pregnant women. Finally, we identified 2805 proteins and 79,998 peptides between patients with RM and normal matched group. Further analysis identified 314 differentially expressed proteins in placental villous tissue (≥1.3-fold, Student's t-test, p < 0.05); 209 proteins showed the increased expression while 105 proteins showed decreased expression. These 314 proteins were analyzed by Ingenuity Pathway Analysis (IPA) and were found to play important roles in the growth of embryo. Furthermore, network analysis show that Angiotensinogen (AGT), MAPK14 and Prothrombin (F2) are core factors in early embryonic development. We used another 8 independent samples (4 cases and 4 controls) to cross validation of the proteomic data. This study has identified several proteins that are associated with early development, these results may supply new insight into mechanisms behind recurrent miscarriage. Copyright © 2017 Elsevier Ltd. All rights reserved.

Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing.

PubMed

Parvaresh, Laila; Crighton, Taryn; Martinez, Elena; Bustamante, Andrea; Chen, Sharon; Sintchenko, Vitali

2018-06-07

The recurrence of tuberculosis (TB) disease in treated patients can serve as a marker of the efficacy of TB control programs. Recurrent disease represents either endogenous reactivation with the same strain of Mycobacterium tuberculosis due to non-compliance or inadequate therapy or exogenous reinfection with a new strain. Genotyping or whole genome sequencing (WGS) of M. tuberculosis isolates from initial and recurrent cases can differentiate between reinfection and reactivation. This study examined cases of recurrent TB in New South Wales, Australia, using genotyping and WGS. Culture-confirmed TB cases diagnosed at least 12 months apart between January 2011 and December 2016 were included. Isolates of M. tuberculosis from patients were compared using 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-24) typing and WGS. Eighteen cases of recurrent disease were identified but isolates from only 15 (83%) were available for study. MIRU-24 findings classified 13 (13/15; 87%) as reactivation and two (13%), as reinfection. Sequencing 13 cultivable paired isolates demonstrated 11 reactivations and two reinfections. There was genomic similarity in 10 out of 13 pairs while one case (1/13; 8%) had 12 SNPS differences. Two other cases (2/13;15%) had > 200 SNPs differences and were classified as reinfection. No phenotypic or genomic evidence of drug resistance was observed. TB control programs can achieve consistently low rates of recurrent disease in low incidence settings. WGS of implicated isolates augments the differentiation between reactivation and reinfection and indicates that the majority of recurrences are due to reactivation rather than reinfection. Predominance of reactivation over reinfection indicates high-quality public health practices and a low risk of local transmission. This study was approved by the Western Sydney Local Health District (WSLHD) Human Research Ethics Committee (HREC Ref: AU RED LNR/17/WMEAD/190; SSA Ref: LNR SSA/17/WMEAD/191).

Endogenously determined cycles: empirical evidence from livestock industries.

PubMed

McCullough, Michael P; Huffaker, Ray; Marsh, Thomas L

2012-04-01

This paper applies the techniques of phase space reconstruction and recurrence quantification analysis to investigate U.S. livestock cycles in relation to recent literature on the business cycle. Results are presented for pork and cattle cycles, providing empirical evidence that the cycles themselves have slowly diminished. By comparing the evolution of production processes for the two livestock cycles we argue that the major cause for this moderation is largely endogenous. The analysis suggests that previous theoretical models relying solely on exogenous shocks to create cyclical patterns do not fully capture changes in system dynamics. Specifically, the biological constraint in livestock dynamics has become less significant while technology and information are relatively more significant. Concurrently, vertical integration of the supply chain may have improved inventory management, all resulting in a small, less deterministic, cyclical effect.

Scrub Typhus Incidence Modeling with Meteorological Factors in South Korea.

PubMed

Kwak, Jaewon; Kim, Soojun; Kim, Gilho; Singh, Vijay P; Hong, Seungjin; Kim, Hung Soo

2015-06-29

Since its recurrence in 1986, scrub typhus has been occurring annually and it is considered as one of the most prevalent diseases in Korea. Scrub typhus is a 3rd grade nationally notifiable disease that has greatly increased in Korea since 2000. The objective of this study is to construct a disease incidence model for prediction and quantification of the incidences of scrub typhus. Using data from 2001 to 2010, the incidence Artificial Neural Network (ANN) model, which considers the time-lag between scrub typhus and minimum temperature, precipitation and average wind speed based on the Granger causality and spectral analysis, is constructed and tested for 2011 to 2012. Results show reliable simulation of scrub typhus incidences with selected predictors, and indicate that the seasonality in meteorological data should be considered.

Scrub Typhus Incidence Modeling with Meteorological Factors in South Korea

PubMed Central

Kwak, Jaewon; Kim, Soojun; Kim, Gilho; Singh, Vijay P.; Hong, Seungjin; Kim, Hung Soo

2015-01-01

Since its recurrence in 1986, scrub typhus has been occurring annually and it is considered as one of the most prevalent diseases in Korea. Scrub typhus is a 3rd grade nationally notifiable disease that has greatly increased in Korea since 2000. The objective of this study is to construct a disease incidence model for prediction and quantification of the incidences of scrub typhus. Using data from 2001 to 2010, the incidence Artificial Neural Network (ANN) model, which considers the time-lag between scrub typhus and minimum temperature, precipitation and average wind speed based on the Granger causality and spectral analysis, is constructed and tested for 2011 to 2012. Results show reliable simulation of scrub typhus incidences with selected predictors, and indicate that the seasonality in meteorological data should be considered. PMID:26132479

The utility of faecal calprotectin to predict post-operative recurrence in Crohńs disease.

PubMed

Herranz Bachiller, Maria Teresa; Barrio Andres, Jesus; Fernandez Salazar, Luis; Ruiz-Zorrilla, Rafael; Sancho Del Val, Lorena; Atienza Sanchez, Ramon

2016-01-01

Endoscopic recurrence in Crohńs disease occurs in up to 80% of patients during the first year after surgery. Due to this, these patients need close monitoring. Faecal calprotectin has been proposed to be used as a non-invasive marker to monitor inflammatory activity. Up to now the use of faecal markers in endoscopic recurrence has been scarcely studied and with contradictory results. This was a cross-sectional observational study of diagnostic validity. It included all patients with Crohńs disease (CD) and ileocolic resection retrospectively who had had an ileocolonoscopy and a determination of faecal calprotectin before this colonoscopy, from 2007 to 2015. Ninety-seven patients were included. We observed that the mean value of faecal calprotectin increased as the Rutgeerts score increased. The variable of that most statistical significance obtained in bivariate analysis was faecal calprotectin (p < 0.0001). Area under curve (AUC) of faecal calprotectin in endoscopic recurrence was 0.74 (95% CI: 0.644-0.842), and an optimal cut-off of 60 mcrgr/gr, obtained a score of 0.45 using Youden test. This indicated that calprotectin would have 88% Sensitivity and 58% Specificity in detecting any recurrence, the NPV was approximately 83,9%. None of the other variables studied had a significant correlation. Faecal calprotectin predicts endoscopic recurrence in CD patients who have gone through surgery, however the cut-off point is still a problem so we cannot recommend calprotectin as a substitute of colonoscopy for CD monitoring and treatment adjustment.

Interaction between specific forms of childhood maltreatment and the serotonin transporter gene (5-HTT) in recurrent depressive disorder

PubMed Central

Fisher, Helen L.; Cohen-Woods, Sarah; Hosang, Georgina M.; Korszun, Ania; Owen, Mike; Craddock, Nick; Craig, Ian W.; Farmer, Anne E.; McGuffin, Peter; Uher, Rudolf

2013-01-01

Background There is inconsistent evidence of interaction between stressful events and a serotonin transporter promoter polymorphism (5-HTTLPR) in depression. Recent studies have indicated that the moderating effect of 5-HTTLPR may be strongest when adverse experiences have occurred in childhood and the depressive symptoms persist over time. However, it is unknown whether this gene-environment interaction is present for recurrent depressive disorder and different forms of maltreatment. Therefore, patients with recurrent clinically diagnosed depression and controls screened for absence of depression were utilised to examine the moderating effect of 5-HTTLPR on associations between specific forms of childhood adversity and recurrent depression. Method A sample of 227 recurrent unipolar depression cases and 228 never psychiatrically ill controls completed the Childhood Trauma Questionnaire to assess exposure to sexual, physical and emotional abuse, physical and emotional neglect in childhood. DNA extracted from blood or cheek swabs was genotyped for the short (s) and long (l) alleles of 5-HTTLPR. Results All forms of childhood maltreatment were reported as more severe by cases than controls. There was no direct association between 5-HTTLPR and depression. Significant interactions with additive and recessive 5-HTTLPR genetic models were found for overall severity of maltreatment, sexual abuse and to a lesser degree for physical neglect, but not other maltreatment types. Limitations The cross-sectional design limits causal inference. Retrospective report of childhood adversity may have reduced the accuracy of the findings. Conclusions This study provides support for the role of interplay between 5-HTTLPR and a specific early environmental risk in recurrent depressive disorder. PMID:22840631

DESIGN CHARACTERISTICS OF THE IDAHO NATIONAL LABORATORY HIGH-TEMPERATURE GAS-COOLED TEST REACTOR

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

Sterbentz, James; Bayless, Paul; Strydom, Gerhard

2016-11-01

Uncertainty and sensitivity analysis is an indispensable element of any substantial attempt in reactor simulation validation. The quantification of uncertainties in nuclear engineering has grown more important and the IAEA Coordinated Research Program (CRP) on High-Temperature Gas Cooled Reactor (HTGR) initiated in 2012 aims to investigate the various uncertainty quantification methodologies for this type of reactors. The first phase of the CRP is dedicated to the estimation of cell and lattice model uncertainties due to the neutron cross sections co-variances. Phase II is oriented towards the investigation of propagated uncertainties from the lattice to the coupled neutronics/thermal hydraulics core calculations.more » Nominal results for the prismatic single block (Ex.I-2a) and super cell models (Ex.I-2c) have been obtained using the SCALE 6.1.3 two-dimensional lattice code NEWT coupled to the TRITON sequence for cross section generation. In this work, the TRITON/NEWT-flux-weighted cross sections obtained for Ex.I-2a and various models of Ex.I-2c is utilized to perform a sensitivity analysis of the MHTGR-350 core power densities and eigenvalues. The core solutions are obtained with the INL coupled code PHISICS/RELAP5-3D, utilizing a fixed-temperature feedback for Ex. II-1a.. It is observed that the core power density does not vary significantly in shape, but the magnitude of these variations increases as the moderator-to-fuel ratio increases in the super cell lattice models.« less

Irregular-regular mode oscillations inside plasma bubble and its fractal analysis in glow discharge magnetized plasma

NASA Astrophysics Data System (ADS)

Megalingam, Mariammal; Hari Prakash, N.; Solomon, Infant; Sarma, Arun; Sarma, Bornali

2017-04-01

Experimental evidence of different kinds of oscillations in floating potential fluctuations of glow discharge magnetized plasma is being reported. A spherical gridded cage is inserted into the ambient plasma volume for creating plasma bubbles. Plasma is produced between a spherical mesh grid and chamber. The spherical mesh grid of 80% optical transparency is connected to the positive terminal of power supply and considered as anode. Two Langmuir probes are kept in the ambient plasma to measure the floating potential fluctuations in different positions within the system, viz., inside and outside the spherical mesh grid. At certain conditions of discharge voltage (Vd) and magnetic field, irregular to regular mode appears, and it shows chronological changes with respect to magnetic field. Further various nonlinear analyses such as Recurrence Plot, Hurst exponent, and Lyapunov exponent have been carried out to investigate the dynamics of oscillation at a range of discharge voltages and external magnetic fields. Determinism, entropy, and Lmax are important measures of Recurrence Quantification Analysis which indicate an irregular to regular transition in the dynamics of the fluctuations. Furthermore, behavior of the plasma oscillation is characterized by the technique called multifractal detrended fluctuation analysis to explore the nature of the fluctuations. It reveals that it has a multifractal nature and behaves as a long range correlated process.

N1N8-bis(gamma-glutamyl)spermidine cross-linking in epidermal-cell envelopes. Comparison of cross-link levels in normal and psoriatic cell envelopes.

PubMed Central

Martinet, N; Beninati, S; Nigra, T P; Folk, J E

1990-01-01

N1N8-Bis(gamma-glutamyl)spermidine was found in exhaustive proteolytic digests of isolated cell envelopes from human epidermis at levels comparable with those of epsilon-(gamma-glutamyl)lysine. Significantly higher than normal amounts of these compounds, particularly the bis(gamma-glutamyl)polyamine, were observed in envelopes from afflicted areas (scales) of psoriatic patients. These findings support the notions that N1N8-bis(gamma-glutamyl)spermidine, like epsilon-(gamma-glutamyl)lysine, functions in cell envelopes as an enzyme-generated protein cross-link and stabilizing force and that individuals with the chronic, recurrent skin disease, psoriasis, exhibit in involved epidermis abnormal cell-envelope-protein cross-linking. PMID:2241917

Dictating photoreactivity through restricted bond rotations: cross-photoaddition of atropisomeric acrylimide derivatives under UV/visible-light irradiation.

PubMed

Iyer, Akila; Jockusch, Steffen; Sivaguru, J

2014-11-13

Nonbiaryl atropisomeric acrylimides underwent facile [2 + 2] photocycloaddition leading to cross-cyclobutane adducts with very high stereospecificity (enantiomeric excess (ee): 99% and diastereomeric excess (de): 99%). The photoreactions proceeded smoothly in isotropic media for both direct and triplet sensitized irradiations. The reactions were also found to be very efficient in the solid state where the same cross-cyclobutane adduct was observed. Photophysical studies enabled us to understand the excited-state photochemistry of acrylimides. The triplet energy was found to be ∼63 kcal/mol. The reactions proceeded predominantly via a singlet excited state upon direct irradiation with very poor intersystem crossing that was ascertained by quantification of the generated singlet oxygen. The reactions progressed smoothly with triplet sensitization with UV or visible-light irradiations. Laser flash photolysis experiments established the triplet transient of atropisomeric acrylimides with a triplet lifetime at room temperature of ∼40 ns.

Lumbar muscle structure and function in chronic versus recurrent low back pain: a cross-sectional study.

PubMed

Goubert, Dorien; De Pauw, Robby; Meeus, Mira; Willems, Tine; Cagnie, Barbara; Schouppe, Stijn; Van Oosterwijck, Jessica; Dhondt, Evy; Danneels, Lieven

2017-09-01

Heterogeneity exists within the low back pain (LBP) population. Some patients recover after every pain episode, whereas others suffer daily from LBP complaints. Until now, studies rarely make a distinction between recurrent low back pain (RLBP) and chronic low back pain (CLBP), although both are characterized by a different clinical picture. Clinical experiences also indicate that heterogeneity exists within the CLBP population. Muscle degeneration, like atrophy, fat infiltration, alterations in muscle fiber type, and altered muscle activity, compromises proper biomechanics and motion of the spinal units in LBP patients. The amount of alterations in muscle structure and muscle function of the paraspinal muscles might be related to the recurrence or chronicity of LBP. The aim of this experimental study is to evaluate differences in muscle structure (cross-sectional area and lean muscle fat index) and muscle activity of the multifidus (MF) and erector spinae (ES) during trunk extension, in patients with RLBP, non-continuous CLBP, and continuous CLBP. This cross-sectional study took place in the university hospital of Ghent, Belgium. Muscle structure characteristics and muscle activity were assessed by magnetic resonance imaging (MRI). Fifty-five adults with non-specific LBP (24 RLBP in remission, 15 non-continuous CLBP, 16 continuous CLBP) participated in this study. Total cross-sectional area, muscle cross-sectional area, fat cross-sectional area, lean muscle fat index, T2-rest and T2-shift were assessed. A T1-weighted Dixon MRI scan was used to evaluate spinal muscle cross-sectional area and fat infiltration in the lumbar MF and ES. Muscle functional MRI was used to evaluate the muscle activity of the lumbar MF and ES during a lumbar extension exercise. Before and after the exercise, a pain assessment was performed. This study was supported by grants from the Special Research Fund of Ghent University (DEF12/AOP/022) without potential conflict of interest-associated biases in the text of the paper. Fat cross-sectional area and lean muscle fat index were significantly higher in MF and ES in continuous CLBP compared with non-continuous CLBP and RLBP (p<.05). No differencesbetween groups were found for total cross-sectional area and muscle cross-sectional area in MF or ES (p>.05). Also, no significant differences between groups for T2-rest were established. T2-shift, however, was significantly lower in MF and ES in RLBP compared with, respectively, non-continuous CLBP and continuous CLBP (p<.05). These results indicate a higher amount of fat infiltration in the lumbar muscles, in the absence of clear atrophy, in continuous CLBP compared with RLBP. A lower metabolic activity of the lumbar muscles was seen in RLBP replicating a relative lower intensity in contractions performed by the lumbar muscles in RLBP compared with non-continuous and continuous CLBP. In conclusion, RLBP differs from continuous CLBP for both muscle structure and muscle function, whereas non-continuous CLBP seems comparable with RLBP for lumbar muscle structure and with continuous CLBP for lumbar muscle function. These results underline the differences in muscle structure and muscle function between different LBP populations. Copyright © 2017 Elsevier Inc. All rights reserved.

Combined preputial advancement and phallopexy as a revision technique for treating paraphimosis in a dog.

PubMed

Wasik, S M; Wallace, A M

2014-11-01

A 7-year-old neutered male Jack Russell terrier-cross was presented for signs of recurrent paraphimosis, despite previous surgical enlargement of the preputial ostium. Revision surgery was performed using a combination of preputial advancement and phallopexy, which resulted in complete and permanent coverage of the glans penis by the prepuce, and at 1 year postoperatively, no recurrence of paraphimosis had been observed. The combined techniques allow preservation of the normal penile anatomy, are relatively simple to perform and provide a cosmetic result. We recommend this combination for the treatment of paraphimosis in the dog, particularly when other techniques have failed. © 2014 Australian Veterinary Association.

Comparison of machine learning and semi-quantification algorithms for (I123)FP-CIT classification: the beginning of the end for semi-quantification?

PubMed

Taylor, Jonathan Christopher; Fenner, John Wesley

2017-11-29

Semi-quantification methods are well established in the clinic for assisted reporting of (I123) Ioflupane images. Arguably, these are limited diagnostic tools. Recent research has demonstrated the potential for improved classification performance offered by machine learning algorithms. A direct comparison between methods is required to establish whether a move towards widespread clinical adoption of machine learning algorithms is justified. This study compared three machine learning algorithms with that of a range of semi-quantification methods, using the Parkinson's Progression Markers Initiative (PPMI) research database and a locally derived clinical database for validation. Machine learning algorithms were based on support vector machine classifiers with three different sets of features: Voxel intensities Principal components of image voxel intensities Striatal binding radios from the putamen and caudate. Semi-quantification methods were based on striatal binding ratios (SBRs) from both putamina, with and without consideration of the caudates. Normal limits for the SBRs were defined through four different methods: Minimum of age-matched controls Mean minus 1/1.5/2 standard deviations from age-matched controls Linear regression of normal patient data against age (minus 1/1.5/2 standard errors) Selection of the optimum operating point on the receiver operator characteristic curve from normal and abnormal training data Each machine learning and semi-quantification technique was evaluated with stratified, nested 10-fold cross-validation, repeated 10 times. The mean accuracy of the semi-quantitative methods for classification of local data into Parkinsonian and non-Parkinsonian groups varied from 0.78 to 0.87, contrasting with 0.89 to 0.95 for classifying PPMI data into healthy controls and Parkinson's disease groups. The machine learning algorithms gave mean accuracies between 0.88 to 0.92 and 0.95 to 0.97 for local and PPMI data respectively. Classification performance was lower for the local database than the research database for both semi-quantitative and machine learning algorithms. However, for both databases, the machine learning methods generated equal or higher mean accuracies (with lower variance) than any of the semi-quantification approaches. The gain in performance from using machine learning algorithms as compared to semi-quantification was relatively small and may be insufficient, when considered in isolation, to offer significant advantages in the clinical context.

Piloting a European Employer Survey on Skill Needs: Illustrative Findings. Research Paper No 36

ERIC Educational Resources Information Center

Sofroniou, Nicholas, Ed.; Zukersteinova, Alena, Ed.

2013-01-01

Today, information and data on skills development come mainly from household and employees surveys: trends in the labour market, demand and supply of skills, data on skill mismatch and skills obsolescence. Recurrent analysis of individual cross-sectional data and their extrapolation into the future indicates significant structural changes over…

From cutting-edge pointwise cross-section to groupwise reaction rate: A primer

NASA Astrophysics Data System (ADS)

Sublet, Jean-Christophe; Fleming, Michael; Gilbert, Mark R.

2017-09-01

The nuclear research and development community has a history of using both integral and differential experiments to support accurate lattice-reactor, nuclear reactor criticality and shielding simulations, as well as verification and validation efforts of cross sections and emitted particle spectra. An important aspect to this type of analysis is the proper consideration of the contribution of the neutron spectrum in its entirety, with correct propagation of uncertainties and standard deviations derived from Monte Carlo simulations, to the local and total uncertainty in the simulated reactions rates (RRs), which usually only apply to one application at a time. This paper identifies deficiencies in the traditional treatment, and discusses correct handling of the RR uncertainty quantification and propagation, including details of the cross section components in the RR uncertainty estimates, which are verified for relevant applications. The methodology that rigorously captures the spectral shift and cross section contributions to the uncertainty in the RR are discussed with quantified examples that demonstrate the importance of the proper treatment of the spectrum profile and cross section contributions to the uncertainty in the RR and subsequent response functions. The recently developed inventory code FISPACT-II, when connected to the processed nuclear data libraries TENDL-2015, ENDF/B-VII.1, JENDL-4.0u or JEFF-3.2, forms an enhanced multi-physics platform providing a wide variety of advanced simulation methods for modelling activation, transmutation, burnup protocols and simulating radiation damage sources terms. The system has extended cutting-edge nuclear data forms, uncertainty quantification and propagation methods, which have been the subject of recent integral and differential, fission, fusion and accelerators validation efforts. The simulation system is used to accurately and predictively probe, understand and underpin a modern and sustainable understanding of the nuclear physics that is so important for many areas of science and technology; advanced fission and fuel systems, magnetic and inertial confinement fusion, high energy, accelerator physics, medical application, isotope production, earth exploration, astrophysics and homeland security.

Reference Cross Sections for Charged-particle Monitor Reactions

NASA Astrophysics Data System (ADS)

Hermanne, A.; Ignatyuk, A. V.; Capote, R.; Carlson, B. V.; Engle, J. W.; Kellett, M. A.; Kibédi, T.; Kim, G.; Kondev, F. G.; Hussain, M.; Lebeda, O.; Luca, A.; Nagai, Y.; Naik, H.; Nichols, A. L.; Nortier, F. M.; Suryanarayana, S. V.; Takács, S.; Tárkányi, F. T.; Verpelli, M.

2018-02-01

Evaluated cross sections of beam-monitor reactions are expected to become the de-facto standard for cross-section measurements that are performed over a very broad energy range in accelerators in order to produce particular radionuclides for industrial and medical applications. The requirements for such data need to be addressed in a timely manner, and therefore an IAEA coordinated research project was launched in December 2012 to establish or improve the nuclear data required to characterise charged-particle monitor reactions. An international team was assembled to recommend more accurate cross-section data over a wide range of targets and projectiles, undertaken in conjunction with a limited number of measurements and more extensive evaluations of the decay data of specific radionuclides. Least-square evaluations of monitor-reaction cross sections including uncertainty quantification have been undertaken for charged-particle beams of protons, deuterons, 3He- and 4He-particles. Recommended beam monitor reaction data with their uncertainties are available at the IAEA-NDS medical portal http://www-nds.iaea.org/medical/monitor_reactions.html.

CrossFit-related cervical internal carotid artery dissection.

PubMed

Lu, Albert; Shen, Peter; Lee, Paul; Dahlin, Brian; Waldau, Ben; Nidecker, Anna E; Nundkumar, Anoop; Bobinski, Matthew

2015-08-01

CrossFit is a high-intensity strength and conditioning program that has gained popularity over the past decade. Potential injuries associated with CrossFit training have been suggested in past reports. We report three cases of cervical carotid dissection that are associated with CrossFit workouts. Patient 1 suffered a distal cervical internal carotid artery (ICA) dissection near the skull base and a small infarct in Wernicke's area. He was placed on anticoagulation and on follow-up has near complete recovery. Patient 2 suffered a proximal cervical ICA dissection that led to arterial occlusion and recurrent middle cerebral artery territory infarcts and significant neurological sequelae. Patient 3 had a skull base ICA dissection that led to a partial Horner's syndrome but no cerebral infarct. While direct causality cannot be proven, intense CrossFit workouts may have led to the ICA dissections in these patients.

Quantification of silver nanoparticle uptake and distribution within individual human macrophages by FIB/SEM slice and view.

PubMed

Guehrs, Erik; Schneider, Michael; Günther, Christian M; Hessing, Piet; Heitz, Karen; Wittke, Doreen; López-Serrano Oliver, Ana; Jakubowski, Norbert; Plendl, Johanna; Eisebitt, Stefan; Haase, Andrea

2017-03-21

Quantification of nanoparticle (NP) uptake in cells or tissues is very important for safety assessment. Often, electron microscopy based approaches are used for this purpose, which allow imaging at very high resolution. However, precise quantification of NP numbers in cells and tissues remains challenging. The aim of this study was to present a novel approach, that combines precise quantification of NPs in individual cells together with high resolution imaging of their intracellular distribution based on focused ion beam/ scanning electron microscopy (FIB/SEM) slice and view approaches. We quantified cellular uptake of 75 nm diameter citrate stabilized silver NPs (Ag 75 Cit) into an individual human macrophage derived from monocytic THP-1 cells using a FIB/SEM slice and view approach. Cells were treated with 10 μg/ml for 24 h. We investigated a single cell and found in total 3138 ± 722 silver NPs inside this cell. Most of the silver NPs were located in large agglomerates, only a few were found in clusters of fewer than five NPs. Furthermore, we cross-checked our results by using inductively coupled plasma mass spectrometry and could confirm the FIB/SEM results. Our approach based on FIB/SEM slice and view is currently the only one that allows the quantification of the absolute dose of silver NPs in individual cells and at the same time to assess their intracellular distribution at high resolution. We therefore propose to use FIB/SEM slice and view to systematically analyse the cellular uptake of various NPs as a function of size, concentration and incubation time.

Simultaneous quantification of adalimumab and infliximab in human plasma by liquid chromatography-tandem mass spectrometry.

PubMed

Jourdil, Jean-François; Némoz, Benjamin; Gautier-Veyret, Elodie; Romero, Charlotte; Stanke-Labesque, Françoise

2018-03-30

Adalimumab (ADA) and infliximab (IFX) are therapeutic monoclonal antibodies (TMabs) targeting tumor necrosis factor-alpha (TNFα). They are used to treat inflammatory diseases. Clinical trials have suggested that therapeutic drug monitoring for ADA or IFX could improve treatment response and cost-effectiveness. However, ADA and IFX were quantified by ELISA in all these studies, and the discrepancies between the results obtained raise questions about their reliability.We describe here the validation of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous quantification of ADA and IFX in human samples. Full-length antibodies labeled with stable isotopes were added to plasma samples as an internal standard. Samples were then prepared using Mass Spectrometry Immuno Assay (MSIA) followed by trypsin digestion prior ADA and IFX quantification by LC-MS/MS.ADA and IFX were quantified in serum from patients treated with ADA (n=21) or IFX (n=22), and the concentrations obtained were compared with those obtained with a commercial ELISA kit. The chromatography run lasted 8.6 minutes and the quantification range was 1 to 26 mg/L. The method was reproducible, repeatable and accurate. For both levels of internal quality control, for ADA and IFX inter and intra-day coefficients of variation and accuracies were all within 15%, in accordance with FDA recommendations. No significant cross-contamination effect was noted.Good agreement was found between LC-MS/MS and ELISA results, for both ADA and IFX. This LC-MS/MS method can be used for the quantification of ADA and IFX in a single analytical run and for the optimization of LC-MS/MS resource use in clinical pharmacology laboratories.

Differentiation of women with premenstrual dysphoric disorder, recurrent brief depression, and healthy controls by daily mood rating dynamics.

PubMed

Pincus, Steven M; Schmidt, Peter J; Palladino-Negro, Paula; Rubinow, David R

2008-04-01

Enhanced statistical characterization of mood-rating data holds the potential to more precisely classify and sub-classify recurrent mood disorders like premenstrual dysphoric disorder (PMDD) and recurrent brief depressive disorder (RBD). We applied several complementary statistical methods to differentiate mood rating dynamics among women with PMDD, RBD, and normal controls (NC). We compared three subgroups of women: NC (n=8); PMDD (n=15); and RBD (n=9) on the basis of daily self-ratings of sadness, study lengths between 50 and 120 days. We analyzed mean levels; overall variability, SD; sequential irregularity, approximate entropy (ApEn); and a quantification of the extent of brief and staccato dynamics, denoted 'Spikiness'. For each of SD, irregularity (ApEn), and Spikiness, we showed highly significant subgroup differences, ANOVA0.001 for each statistic; additionally, many paired subgroup comparisons showed highly significant differences. In contrast, mean levels were indistinct among the subgroups. For SD, normal controls had much smaller levels than the other subgroups, with RBD intermediate. ApEn showed PMDD to be significantly more regular than the other subgroups. Spikiness showed NC and RBD data sets to be much more staccato than their PMDD counterparts, and appears to suitably characterize the defining feature of RBD dynamics. Compound criteria based on these statistical measures discriminated diagnostic subgroups with high sensitivity and specificity. Taken together, the statistical suite provides well-defined specifications of each subgroup. This can facilitate accurate diagnosis, and augment the prediction and evaluation of response to treatment. The statistical methodologies have broad and direct applicability to behavioral studies for many psychiatric disorders, and indeed to similar analyses of associated biological signals across multiple axes.

Multiplex Droplet Digital PCR Quantification of Recurrent Somatic Mutations in Diffuse Large B-Cell and Follicular Lymphoma.

PubMed

Alcaide, Miguel; Yu, Stephen; Bushell, Kevin; Fornika, Daniel; Nielsen, Julie S; Nelson, Brad H; Mann, Koren K; Assouline, Sarit; Johnson, Nathalie A; Morin, Ryan D

2016-09-01

A plethora of options to detect mutations in tumor-derived DNA currently exist but each suffers limitations in analytical sensitivity, cost, or scalability. Droplet digital PCR (ddPCR) is an appealing technology for detecting the presence of specific mutations based on a priori knowledge and can be applied to tumor biopsies, including formalin-fixed paraffin embedded (FFPE) tissues. More recently, ddPCR has gained popularity in its utility in quantifying circulating tumor DNA. We have developed a suite of novel ddPCR assays for detecting recurrent mutations that are prevalent in common B-cell non-Hodgkin lymphomas (NHLs), including diffuse large B-cell lymphoma, follicular lymphoma, and lymphoplasmacytic lymphoma. These assays allowed the differentiation and counting of mutant and wild-type molecules using one single hydrolysis probe. We also implemented multiplexing that allowed the simultaneous detection of distinct mutations and an "inverted" ddPCR assay design, based on employing probes matching wild-type alleles, capable of detecting the presence of multiple single nucleotide polymorphisms. The assays successfully detected and quantified somatic mutations commonly affecting enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) (Y641) and signal transducer and activator of transcription 6 (STAT6) (D419) hotspots in fresh tumor, FFPE, and liquid biopsies. The "inverted" ddPCR approach effectively reported any single nucleotide variant affecting either of these 2 hotspots as well. Finally, we could effectively multiplex hydrolysis probes targeting 2 additional lymphoma-related hotspots: myeloid differentiation primary response 88 (MYD88; L265P) and cyclin D3 (CCND3; I290R). Our suite of ddPCR assays provides sufficient analytical sensitivity and specificity for either the invasive or noninvasive detection of multiple recurrent somatic mutations in B-cell NHLs. © 2016 American Association for Clinical Chemistry.

Using recurrence plot for determinism analysis of EEG recordings in genetic absence epilepsy rats.

PubMed

Ouyang, Gaoxiang; Li, Xiaoli; Dang, Chuangyin; Richards, Douglas A

2008-08-01

Understanding the transition of brain activity towards an absence seizure is a challenging task. In this paper, we use recurrence quantification analysis to indicate the deterministic dynamics of EEG series at the seizure-free, pre-seizure and seizure states in genetic absence epilepsy rats. The determinism measure, DET, based on recurrence plot, was applied to analyse these three EEG datasets, each dataset containing 300 single-channel EEG epochs of 5-s duration. Then, statistical analysis of the DET values in each dataset was carried out to determine whether their distributions over the three groups were significantly different. Furthermore, a surrogate technique was applied to calculate the significance level of determinism measures in EEG recordings. The mean (+/-SD) DET of EEG was 0.177+/-0.045 in pre-seizure intervals. The DET values of pre-seizure EEG data are significantly higher than those of seizure-free intervals, 0.123+/-0.023, (P<0.01), but lower than those of seizure intervals, 0.392+/-0.110, (P<0.01). Using surrogate data methods, the significance of determinism in EEG epochs was present in 25 of 300 (8.3%), 181 of 300 (60.3%) and 289 of 300 (96.3%) in seizure-free, pre-seizure and seizure intervals, respectively. Results provide some first indications that EEG epochs during pre-seizure intervals exhibit a higher degree of determinism than seizure-free EEG epochs, but lower than those in seizure EEG epochs in absence epilepsy. The proposed methods have the potential of detecting the transition between normal brain activity and the absence seizure state, thus opening up the possibility of intervention, whether electrical or pharmacological, to prevent the oncoming seizure.

Brief communication: Landslide motion from cross correlation of UAV-derived morphological attributes

NASA Astrophysics Data System (ADS)

Peppa, Maria V.; Mills, Jon P.; Moore, Phil; Miller, Pauline E.; Chambers, Jonathan E.

2017-12-01

Unmanned aerial vehicles (UAVs) can provide observations of high spatio-temporal resolution to enable operational landslide monitoring. In this research, the construction of digital elevation models (DEMs) and orthomosaics from UAV imagery is achieved using structure-from-motion (SfM) photogrammetric procedures. The study examines the additional value that the morphological attribute of openness, amongst others, can provide to surface deformation analysis. Image-cross-correlation functions and DEM subtraction techniques are applied to the SfM outputs. Through the proposed integrated analysis, the automated quantification of a landslide's motion over time is demonstrated, with implications for the wider interpretation of landslide kinematics via UAV surveys.

A prospective randomised cross-over study of the effect of insulin analogues and human insulin on the frequency of severe hypoglycaemia in patients with type 1 diabetes and recurrent hypoglycaemia (the HypoAna trial): study rationale and design

PubMed Central

2012-01-01

Background Severe hypoglycaemia still represents a significant problem in insulin-treated diabetes. Most patients do not experience severe hypoglycaemia often. However, 20% of patients with type 1 diabetes experience recurrent severe hypoglycaemia corresponding to at least two episodes per year. The effect of insulin analogues on glycaemic control has been documented in large trials, while their effect on the frequency of severe hypoglycaemia is less clear, especially in patients with recurrent severe hypoglycaemia. The HypoAna Trial is designed to investigate whether short-acting and long-acting insulin analogues in comparison with human insulin are superior in reducing the occurrence of severe hypoglycaemic episodes in patients with recurrent hypoglycaemia. This paper reports the study design of the HypoAna Trial. Methods/design The study is a Danish two-year investigator-initiated, prospective, randomised, open, blinded endpoint (PROBE), multicentre, cross-over trial investigating the effect of insulin analogues versus human insulin on the frequency of severe hypoglycaemia in subjects with type 1 diabetes. Patients are randomised to treatment with basal-bolus therapy with insulin detemir / insulin aspart or human NPH insulin / human regular insulin in random order. The major inclusion criterion is history of two or more episodes of severe hypoglycaemia in the preceding year. Discussion In contrast to almost all other studies in this field the HypoAna Trial includes only patients with major problems with hypoglycaemia. The HypoAna Trial will elucidate whether basal-bolus regimen with short-acting and long-acting insulin analogues in comparison with human insulin are superior in reducing occurrence of severe hypoglycaemic episodes in hypoglycaemia prone patients with type 1 diabetes. http://www.clinicaltrials.gov: NCT00346996. PMID:22727048

Response to low-dose herbicide selection in self-pollinated Avena fatua.

PubMed

Busi, Roberto; Girotto, Marcelo; Powles, Stephen B

2016-03-01

When applied at the correct plant stage and dose, herbicides are highly toxic to plants. At reduced, low herbicide doses (below the recommended dose) plants can survive and display continuous and quantitative variation in dose-survival responses. Recurrent (directional) selection studies can reveal whether such a phenotypic variation in plant survival response to low herbicide dose is heritable and leads to herbicide resistance. In a common experimental garden study, we have subjected a susceptible population of self-pollinated hexaploid Avena fatua to low-dose recurrent selection with the ACCase-inhibiting herbicide diclofop-methyl for three consecutive generations. Significant differences in response to low-dose diclofop-methyl selection were observed between the selected progenies and parent plants, with a twofold diclofop-methyl resistance and cross-resistance to ALS-inhibiting herbicides. Thus, the capacity of self-pollinated A. fatua to respond to low-dose herbicide selection is marginal, and it is much lower than in cross-pollinated L. rigidum. Lolium rigidum in the same experiment evolved 40-fold diclofop-methyl resistance by progressive enrichment of quantitative resistance-endowing traits. Cross-pollination rate, genetic variation and ploidy levels are identified as possible drivers affecting the contrasting capacity of Avena versus Lolium plants to respond to herbicide selection and the subsequent likelihood of resistance evolution at low herbicide dose usage. © 2015 Society of Chemical Industry.

Risk of Recurrent Pancreatitis and Progression to Chronic Pancreatitis After a First Episode of Acute Pancreatitis.

PubMed

Ahmed Ali, Usama; Issa, Yama; Hagenaars, Julia C; Bakker, Olaf J; van Goor, Harry; Nieuwenhuijs, Vincent B; Bollen, Thomas L; van Ramshorst, Bert; Witteman, Ben J; Brink, Menno A; Schaapherder, Alexander F; Dejong, Cornelis H; Spanier, B W Marcel; Heisterkamp, Joos; van der Harst, Erwin; van Eijck, Casper H; Besselink, Marc G; Gooszen, Hein G; van Santvoort, Hjalmar C; Boermeester, Marja A

2016-05-01

Patients with a first episode of acute pancreatitis can develop recurrent or chronic pancreatitis (CP). However, little is known about the incidence or risk factors for these events. We performed a cross-sectional study of 669 patients with a first episode of acute pancreatitis admitted to 15 Dutch hospitals from December 2003 through March 2007. We collected information on disease course, outpatient visits, and hospital readmissions, as well as results from imaging, laboratory, and histology studies. Standardized follow-up questionnaires were sent to all available patients to collect information on hospitalizations and interventions for pancreatic disease, abdominal pain, steatorrhea, diabetes mellitus, medications, and alcohol and tobacco use. Patients were followed up for a median time period of 57 months. Primary end points were recurrent pancreatitis and CP. Risk factors were evaluated using regression analysis. The cumulative risk was assessed using Kaplan-Meier analysis. Recurrent pancreatitis developed in 117 patients (17%), and CP occurred in 51 patients (7.6%). Recurrent pancreatitis developed in 12% of patients with biliary disease, 24% of patients with alcoholic etiology, and 25% of patients with disease of idiopathic or other etiologies; CP occurred in 3%, 16%, and 10% of these patients, respectively. Etiology, smoking, and necrotizing pancreatitis were independent risk factors for recurrent pancreatitis and CP. Acute Physiology and Chronic Health Evaluation II scores at admission also were associated independently with recurrent pancreatitis. The cumulative risk for recurrent pancreatitis over 5 years was highest among smokers at 40% (compared with 13% for nonsmokers). For alcohol abusers and current smokers, the cumulative risks for CP were similar-approximately 18%. In contrast, the cumulative risk of CP increased to 30% in patients who smoked and abused alcohol. Based on a retrospective analysis of patients admitted to Dutch hospitals, a first episode of acute pancreatitis leads to recurrent pancreatitis in 17% of patients, and almost 8% of patients progress to CP within 5 years. Progression was associated independently with alcoholic etiology, smoking, and a history of pancreatic necrosis. Smoking is the predominant risk factor for recurrent disease, whereas the combination of alcohol abuse and smoking produces the highest cumulative risk for chronic pancreatitis. Copyright © 2016 AGA Institute. Published by Elsevier Inc. All rights reserved.

Simple Quantification of Pentosidine in Human Urine and Plasma by High-Performance Liquid Chromatography

PubMed Central

Lee, Ji Sang; Chung, Yoon-Sok; Chang, Sun Young

2017-01-01

Pentosidine is an advanced glycation end-product (AGE) and fluorescent cross-link compound. A simple high-performance liquid chromatographic (HPLC) method was developed for the detection and quantification of pentosidine in human urine and plasma. The mobile phase used a gradient system to improve separation of pentosidine from endogenous peaks, and chromatograms were monitored by fluorescent detector set at excitation and emission wavelengths of 328 and 378 nm, respectively. The retention time for pentosidine was 24.3 min and the lower limits of quantification (LLOQ) in human urine and plasma were 1 nM. The intraday assay precisions (coefficients of variation) were generally low and found to be in the range of 5.19–7.49% and 4.96–8.78% for human urine and plasma, respectively. The corresponding values of the interday assay precisions were 9.45% and 4.27%. Accuracies (relative errors) ranged from 87.9% to 115%. Pentosidine was stable in a range of pH solutions, human urine, and plasma. In summary, this HPLC method can be applied in future preclinical and clinical evaluation of pentosidine in the diabetic patients. PMID:29181026

Quantification of Methane and Ammonia Emissions in a Naturally Ventilated Barn by Using Defined Criteria to Calculate Emission Rates.

PubMed

Schmithausen, Alexander J; Schiefler, Inga; Trimborn, Manfred; Gerlach, Katrin; Südekum, Karl-Heinz; Pries, Martin; Büscher, Wolfgang

2018-05-16

Extensive experimentation on individual animals in respiration chambers has already been carried out to evaluate the potential of dietary changes and opportunities to mitigate CH₄ emissions from ruminants. Although it is difficult to determine the air exchange rate of open barn spaces, measurements at the herd level should provide similarly reliable and robust results. The primary objective of this study was (1) to define a validity range (data classification criteria (DCC)) for the variables of wind velocity and wind direction during long-term measurements at barn level; and (2) to apply this validity range to a feeding trial in a naturally cross-flow ventilated dairy barn. The application of the DCC permitted quantification of CH₄ and NH₃ emissions during a feeding trial consisting of four periods. Differences between the control group (no supplement) and the experimental group fed a ration supplemented with condensed Acacia mearnsii tannins (CT) became apparent. Notably, CT concentrations of 1% and 3% of ration dry matter did not reduce CH₄ emissions. In contrast, NH₃ emissions decreased 34.5% when 3% CT was supplemented. The data confirm that quantification of trace gases in a naturally ventilated barn at the herd level is possible.

Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3D segmentation algorithms

PubMed Central

2011-01-01

Background Image segmentation is a crucial step in quantitative microscopy that helps to define regions of tissues, cells or subcellular compartments. Depending on the degree of user interactions, segmentation methods can be divided into manual, automated or semi-automated approaches. 3D image stacks usually require automated methods due to their large number of optical sections. However, certain applications benefit from manual or semi-automated approaches. Scenarios include the quantification of 3D images with poor signal-to-noise ratios or the generation of so-called ground truth segmentations that are used to evaluate the accuracy of automated segmentation methods. Results We have developed Gebiss; an ImageJ plugin for the interactive segmentation, visualisation and quantification of 3D microscopic image stacks. We integrated a variety of existing plugins for threshold-based segmentation and volume visualisation. Conclusions We demonstrate the application of Gebiss to the segmentation of nuclei in live Drosophila embryos and the quantification of neurodegeneration in Drosophila larval brains. Gebiss was developed as a cross-platform ImageJ plugin and is freely available on the web at http://imaging.bii.a-star.edu.sg/projects/gebiss/. PMID:21668958

Relationship Between Laryngeal Electromyography and Video Laryngostroboscopy in Vocal Fold Paralysis.

PubMed

Maamary, Joel A; Cole, Ian; Darveniza, Paul; Pemberton, Cecilia; Brake, Helen Mary; Tisch, Stephen

2017-09-01

The objective of this study was to better define the relationship of laryngeal electromyography and video laryngostroboscopy in the diagnosis of vocal fold paralysis. Retrospective diagnostic cohort study with cross-sectional data analysis METHODS: Data were obtained from 57 patients with unilateral vocal fold paralysis who attended a large tertiary voice referral center. Electromyographic findings were classified according to recurrent laryngeal nerve, superior laryngeal nerve, and high vagal/combined lesions. Video laryngostroboscopy recordings were classified according to the position of the immobile fold into median, paramedian, lateral, and a foreshortened/hooded vocal fold. The position of the paralyzed vocal fold was then analyzed according to the lesion as determined by electromyography. The recurrent laryngeal nerve was affected in the majority of cases with left-sided lesions more common than right. Vocal fold position differed between recurrent laryngeal and combined vagal lesions. Recurrent laryngeal nerve lesions were more commonly associated with a laterally displaced immobile fold. No fold position was suggestive of a combined vagal lesion. The inter-rater reliability for determining fold position was high. Laryngeal electromyography is useful in diagnosing neuromuscular dysfunction of the larynx and best practice recommends its continued implementation along with laryngostroboscopy. While recurrent laryngeal nerve lesions are more likely to present with a lateral vocal fold, this does not occur in all cases. Such findings indicate that further unknown mechanisms contribute to fold position in unilateral paralysis. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A model based on temporal dynamics of fixations for distinguishing expert radiologists' scanpaths

NASA Astrophysics Data System (ADS)

Gandomkar, Ziba; Tay, Kevin; Brennan, Patrick C.; Mello-Thoms, Claudia

2017-03-01

This study investigated a model which distinguishes expert radiologists from less experienced radiologists based on features describing spatio-temporal dynamics of their eye movement during interpretation of digital mammograms. Eye movements of four expert and four less experienced radiologists were recorded during interpretation of 120 two-view digital mammograms of which 59 had biopsy proven cancers. For each scanpath, a two-dimensional recurrence plot, which represents the radiologist's refixation pattern, was generated. From each plot, six features indicating the spatio-temporal dynamics of fixations were extracted. The first feature measured the percentage of recurrent fixations; the second indicated the percentage of recurrent fixations which was fixated later in several consecutive fixations; the third measured the percentage of recurrent fixations that form a repeated sequence of fixations and the fourth assessed whether the recurrent fixations were occurring sequentially close together. The number of switches between the two mammographic views was also measured, as was the average number of consecutive fixations in each view before switching. These six features along with total time on case and average fixation duration were fed into a support vector machine whose performance was evaluated using 10-fold cross validation. The model achieved a sensitivity of 86.3% and a specificity of 85.2% for distinguishing experts' scanpaths. The obtained result suggests that spatio-temporal dynamics of eye movements can characterize expertise level and has potential applications for monitoring the development of expertise among radiologists as a result of different training regimes and continuing education schemes.

[Recurrent wheezing: prevalence and associated factors in infants from Buenos Aires City, Argentina].

PubMed

Szulman, Gabriela Aída; Freilij, Héctor; Behrends, Ilse; Gentile, Ángela; Mallol, Javier

The episodes of bronchial obstruction at early age constitute a frequent problem in Pediatrics. The aim of this study was to evaluate the prevalence of recurrent wheezing in infants in Buenos Aires City, as well as to identify any associated factors. Cross-sectional study performed from 2011 to 2012 in the Children Hospital Ricardo Gutiérrez, Buenos Aires City, as part of the International Study of Wheezing in Infants. A validated questionnaire was applied to parents of infants aged between 12 and 15 months. The prevalence of wheezing, mostly the recurrent episodes (three or more), and their probable associated factors were evaluated. Data were statistically analyzed with χ 2 , Fisher's test, binary and logistics multiple regression analysis. The significance level was 0.05. Over 1063 infants, 58.9% (confidence interval (CI) 95% 55.9-61.9) presented at least one episode of wheezing and 26.3% (CI95% 23.8-29.9) three or more episodes (recurrent wheezing). Risk factors associated to wheezing were male gender (p=0.001), six or more episodes of cold during the first year of life (p <0.0001), age at first cold <4 months (p <0.0001); pneumonia (p <0.0001) and smoking during pregnancy (tobacco) (p=0.01). For recurrent wheezing, risk factors we considered as six or more episodes of cold during the first year of life (p <0.0001), early (< 4 month of age) onset wheezing (p <0.0001) and nocturnal wheezing (p <0.0001). The prevalence of recurrent wheezing among infants in Buenos Aires Ciy was high (26.3%). Some identified associated factors can be preventable. Copyright © 2017 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

Anastomotic Leaks After Restorative Resections for Rectal Cancer Compromise Cancer Outcomes and Survival.

PubMed

Lu, Zheqin R; Rajendran, Nirooshun; Lynch, A Craig; Heriot, Alexander G; Warrier, Satish K

2016-03-01

Anastomotic leaks after restorative resections for rectal cancer may lead to worse long-term outcomes. The purpose of this study was to evaluate the best current evidence assessing anastomotic leaks in rectal cancer resections with curative intent and their impact on survival and cancer recurrence. A meta-analysis was performed using MEDLINE, EMBASE, and Cochrane search engines for relevant studies published between January 1982 and January 2015. Preferred Reporting Items for Systematic Reviews and Meta-Analyses methodology was used to screen and select relevant studies for the review using key words "colorectal surgery; colorectal neoplasm; rectal neoplasm" and "anastomotic leak." Anastomotic leak groups were compared with nonanastomotic leak groups. ORs were calculated from binary data for local recurrence, distant recurrence, and cancer-specific mortality. A random-effects model was then used to calculate pooled ORs with 95% CIs. Eleven studies with 13,655 patients met the inclusion criteria. This included 5 prospective cohort and 6 retrospective cohort studies. Median follow-up was 60 months. Higher cancer-specific mortality was noted in the leak group with an OR of 1.30 (95% CI, 1.04-1.62; p < 0.05). Local recurrences were more likely in rectal cancer resections complicated by anastomotic leaks (OR = 1.61 (95% CI, 1.25-2.09); p < 0.001). Distant recurrence was not more likely in the anastomotic leak group (OR = 1.07 (95% CI, 0.87-1.33); p = 0.52). All 11 studies are level 3 evidence cohort studies. Additional sensitivity analyses were performed to minimize cross-study heterogeneity. Anastomotic leaks after restorative resections for rectal cancer adversely impact cancer-specific mortality and local recurrence.

Interaction between specific forms of childhood maltreatment and the serotonin transporter gene (5-HTT) in recurrent depressive disorder.

PubMed

Fisher, Helen L; Cohen-Woods, Sarah; Hosang, Georgina M; Korszun, Ania; Owen, Mike; Craddock, Nick; Craig, Ian W; Farmer, Anne E; McGuffin, Peter; Uher, Rudolf

2013-02-15

There is inconsistent evidence of interaction between stressful events and a serotonin transporter promoter polymorphism (5-HTTLPR) in depression. Recent studies have indicated that the moderating effect of 5-HTTLPR may be strongest when adverse experiences have occurred in childhood and the depressive symptoms persist over time. However, it is unknown whether this gene-environment interaction is present for recurrent depressive disorder and different forms of maltreatment. Therefore, patients with recurrent clinically diagnosed depression and controls screened for the absence of depression were utilised to examine the moderating effect of 5-HTTLPR on associations between specific forms of childhood adversity and recurrent depression. A sample of 227 recurrent unipolar depression cases and 228 never psychiatrically ill controls completed the Childhood Trauma Questionnaire to assess exposure to sexual, physical and emotional abuse, physical and emotional neglect in childhood. DNA extracted from blood or cheek swabs was genotyped for the short (s) and long (l) alleles of 5-HTTLPR. All forms of childhood maltreatment were reported as more severe by cases than controls. There was no direct association between 5-HTTLPR and depression. Significant interactions with additive and recessive 5-HTTLPR genetic models were found for overall severity of maltreatment, sexual abuse and to a lesser degree for physical neglect, but not other maltreatment types. The cross-sectional design limits causal inference. Retrospective report of childhood adversity may have reduced the accuracy of the findings. This study provides support for the role of interplay between 5-HTTLPR and a specific early environmental risk in recurrent depressive disorder. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of cytoplasmic diversity on post anthesis heat tolerance in wheat

USDA-ARS?s Scientific Manuscript database

The nuclear genomes of ten alloplasmic lines were substituted by backcrossing four or five times using ‘Karl 92’, ‘Ventnor’, ‘U1275’ and ‘Jagger’ as recurrent parents to study the cytoplasmic effects on heat tolerance. During the final backcross, reciprocal crosses were made to develop NILs (Near Is...

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga.

PubMed

Arbelaez, Juan D; Moreno, Laura T; Singh, Namrata; Tung, Chih-Wei; Maron, Lyza G; Ospina, Yolima; Martinez, César P; Grenier, Cécile; Lorieux, Mathias; McCouch, Susan

Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/ O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/ O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.

Involved LEEP excision margins as predictor of residual/recurrent disease in HIV-positive and HIV-negative women in a low-resource setting.

PubMed

van Bogaert, Louis-Jacques

2015-04-01

To describe the accuracy of the diagnosis of involved excision margins after loop electrosurgical excision procedure (LEEP) in a low-resource setting. Cross-sectional study of 176 LEEPs indicated for a cytological report of high-grade squamous intraepithelial lesion (HGSIL). A total of 72 HIV-positive and 104 HIV-negative women with cervical intraepithelial neoplasia (CIN) ≥ 2 on their LEEP histology report with involved excision margins were enrolled in the study. All patients underwent either a repeat LEEP or a hysterectomy. The specimens were evaluated for residual/recurrent CIN ≥ 2 or less. Persistent/recurrent CIN ≥ 2 was diagnosed in 139 (79.4%) instances and microinvasive squamous cell carcinoma in 6 (3.4%). Thirty (17.2%) showed CIN1. The persistence/recurrence rate was 72.2% and 88.5% in HIV-positive and HIV-negative women, respectively (χ2 = 7.5, p = 0.006). In > 80% the diagnosis of involved excision margins was confirmed, a positive predictive value of 82.4%. In the absence of more accurate follow-up methods such as HPV testing or co-testing with cytology, a correct diagnosis of margin status, especially when involved, is an important guide to further management and follow-up.

Brain Dynamics in Predicting Driving Fatigue Using a Recurrent Self-Evolving Fuzzy Neural Network.

PubMed

Liu, Yu-Ting; Lin, Yang-Yin; Wu, Shang-Lin; Chuang, Chun-Hsiang; Lin, Chin-Teng

2016-02-01

This paper proposes a generalized prediction system called a recurrent self-evolving fuzzy neural network (RSEFNN) that employs an on-line gradient descent learning rule to address the electroencephalography (EEG) regression problem in brain dynamics for driving fatigue. The cognitive states of drivers significantly affect driving safety; in particular, fatigue driving, or drowsy driving, endangers both the individual and the public. For this reason, the development of brain-computer interfaces (BCIs) that can identify drowsy driving states is a crucial and urgent topic of study. Many EEG-based BCIs have been developed as artificial auxiliary systems for use in various practical applications because of the benefits of measuring EEG signals. In the literature, the efficacy of EEG-based BCIs in recognition tasks has been limited by low resolutions. The system proposed in this paper represents the first attempt to use the recurrent fuzzy neural network (RFNN) architecture to increase adaptability in realistic EEG applications to overcome this bottleneck. This paper further analyzes brain dynamics in a simulated car driving task in a virtual-reality environment. The proposed RSEFNN model is evaluated using the generalized cross-subject approach, and the results indicate that the RSEFNN is superior to competing models regardless of the use of recurrent or nonrecurrent structures.

Cognitive processing speed is related to fall frequency in older adults with multiple sclerosis.

PubMed

Sosnoff, Jacob J; Balantrapu, Swathi; Pilutti, Lara A; Sandroff, Brian M; Morrison, Steven; Motl, Robert W

2013-08-01

To examine mobility, balance, fall risk, and cognition in older adults with multiple sclerosis (MS) as a function of fall frequency. Retrospective, cross-sectional design. University research laboratory. Community-dwelling persons with MS (N=27) aged between 50 and 75 years were divided into 2 groups-single-time (n=11) and recurrent (n=16; >2 falls/12 mo) fallers-on the basis of fall history. Not applicable. Mobility was assessed using a variety of measures including Multiple Sclerosis Walking Scale-12, walking speed (Timed 25-Foot Walk test), endurance (6-Minute Walk test), and functional mobility (Timed Up and Go test). Balance was assessed with the Berg Balance Scale, posturography, and self-reported balance confidence. Fall risk was assessed with the Physiological Profile Assessment. Cognitive processing speed was quantified with the Symbol Digit Modalities Test and the Paced Auditory Serial Addition Test. Recurrent fallers had slower cognitive processing speed than single-time fallers (P ≤.01). There was no difference in mobility, balance, or fall risk between recurrent and single-time fallers (P>.05). Results indicated that cognitive processing speed is associated with fall frequency and may have implications for fall prevention strategies targeting recurrent fallers with MS. Copyright © 2013 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Prospectively identified deficits in sagittal plane hip-ankle coordination in female athletes who sustain a second anterior cruciate ligament injury after anterior cruciate ligament reconstruction and return to sport.

PubMed

Paterno, Mark V; Kiefer, Adam W; Bonnette, Scott; Riley, Michael A; Schmitt, Laura C; Ford, Kevin R; Myer, Gregory D; Shockley, Kevin; Hewett, Timothy E

2015-12-01

Athletes who return to sport after anterior cruciate ligament reconstruction are at increased risk of future ACL injury. Altered coordination of lower extremity motion may increase this risk. The purpose of this study was to prospectively determine if altered lower extremity coordination patterns exist in athletes who go on to sustain a 2nd anterior cruciate ligament injury. Sixty-one female athletes who were cleared to return to sport after anterior cruciate ligament reconstruction were included. Hip-ankle coordination was assessed prior to return to sport with a dynamic postural coordination task. Within 12 months, 14 patients sustained a 2nd ACL injury. Fourteen matched subjects were selected for comparative analysis. Cross-recurrence quantification analysis characterized hip-ankle coordination patterns. A group × target speed (slow vs. fast) × leg (involved vs. uninvolved) analysis of variance was used to identify differences. A main effect of group (P = 0.02) indicated that the single injury group exhibited more stable hip-ankle coordination [166.2 (18.9)] compared to the 2nd injury group [108.4 (10.1)]. A leg × group interaction was also observed (P = .04). The affected leg of the single injury group exhibited more stable coordination [M = 187.1 (23.3)] compared to the affected leg of the 2nd injury group [M = 110.13 (9.8)], P = 0.03. Hip-ankle coordination was altered in female athletes who sustained a 2nd anterior cruciate ligament injury after return to sport. Failure to coordinate lower extremity movement in the absence of normal knee proprioception may place the knee at risk. Copyright © 2015 Elsevier Ltd. All rights reserved.

Prospectively Identified Deficits in Sagittal Plane Hip-Ankle Coordination in Female Athletes who Sustain a Second Anterior Cruciate Ligament Injury after Anterior Cruciate Ligament Reconstruction and Return to Sport

PubMed Central

Paterno, Mark V.; Kiefer, Adam W.; Bonnette, Scott; Riley, Michael A.; Schmitt, Laura C.; Ford, Kevin R.; Myer, Gregory D.; Shockley, Kevin; Hewett, Timothy E.

2015-01-01

Background Athletes who return to sport after anterior cruciate ligament reconstruction are at increased risk of future ACL injury. Altered coordination of lower extremity motion may increase this risk. The purpose of this study was to prospectively determine if altered lower extremity coordination patterns exist in athletes who go on to sustain a 2nd anterior cruciate ligament injury. Methods Sixty-one female athletes who were medically cleared to return to sport after anterior cruciate ligament reconstruction were included. Hip-ankle coordination was assessed prior to return to sport with a dynamic postural coordination task. Within 12 months, 14 patients sustained a 2nd ACL injury. Fourteen matched subjects were selected for comparative analysis. Cross-recurrence quantification analysis characterized hip-ankle coordination patterns. A group × target speed (slow vs. fast) × leg (involved vs. uninvolved) analysis of variance was used to identify coordination differences. Findings A main effect of group (p = 0.02) indicated that the single injury group exhibited more stable hip-ankle coordination [166.2 (18.9)] compared to the 2nd injury group [108.4 (10.1)]. A leg × group interaction was also observed (p = .04). The affected leg of the single injury group exhibited more stable coordination [M = 187.1 (23.3)] compared to the affected leg of the 2nd injury group [M = 110.13 (9.8)], p = 0.03. Interpretation Hip-ankle coordination was altered in female athletes who sustained a 2nd anterior cruciate ligament injury after return to sport. Failure to coordinate lower extremity movement in the absence of normal knee proprioception may place the knee at high-risk. PMID:26416200

Identification and quantification analysis of nonlinear dynamics properties of combustion instability in a diesel engine

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

Yang, Li-Ping, E-mail: yangliping302@hrbeu.edu.cn; Ding, Shun-Liang; Song, En-Zhe

The cycling combustion instabilities in a diesel engine have been analyzed based on chaos theory. The objective was to investigate the dynamical characteristics of combustion in diesel engine. In this study, experiments were performed under the entire operating range of a diesel engine (the engine speed was changed from 600 to 1400 rpm and the engine load rate was from 0% to 100%), and acquired real-time series of in-cylinder combustion pressure using a piezoelectric transducer installed on the cylinder head. Several methods were applied to identify and quantitatively analyze the combustion process complexity in the diesel engine including delay-coordinate embedding, recurrencemore » plot (RP), Recurrence Quantification Analysis, correlation dimension (CD), and the largest Lyapunov exponent (LLE) estimation. The results show that the combustion process exhibits some determinism. If LLE is positive, then the combustion system has a fractal dimension and CD is no more than 1.6 and within the diesel engine operating range. We have concluded that the combustion system of diesel engine is a low-dimensional chaotic system and the maximum values of CD and LLE occur at the lowest engine speed and load. This means that combustion system is more complex and sensitive to initial conditions and that poor combustion quality leads to the decrease of fuel economy and the increase of exhaust emissions.« less

Association between Short Physical Performance Battery and falls in older people: the Progetto Veneto Anziani Study.

PubMed

Veronese, Nicola; Bolzetta, Francesco; Toffanello, Elena Debora; Zambon, Sabina; De Rui, Marina; Perissinotto, Egle; Coin, Alessandra; Corti, Maria-Chiara; Baggio, Giovannella; Crepaldi, Gaetano; Sergi, Giuseppe; Manzato, Enzo

2014-06-01

It is known that weakness in the lower limbs is associated with recurrent falls in old people. Among the tests routinely used to assess lower extremity strength, the Short Physical Performance Battery (SPPB) is one of those used most often, but its relationship with recurrent falls is poorly investigated. We aimed to determine if SPPB scores are related to recurrent falling in a sample of 2710 older-aged people, and to ascertain which test in the SPPB is most strongly associated with a higher rate of falls. In this cross-sectional study, we demonstrated that participants scoring 0-6 in the SPPB were more likely to be recurrent fallers than those scoring 10-12 (odds ratio [OR]=3.46, 95% confidence interval [CI] 2.04-5.88 in women; OR=3.82, 95% CI 1.77- 8.52, in men). SPPB scores of 7-9 were only associated with women being more likely to be recurrent fallers (OR=2.03, 95% CI 1.28-3.22). When the SPPB items were analyzed separately, even a lower score in gait speed for women was significantly associated with the presence of recurrent falls (OR=2.11; 95% CI 1.04-4.30), whereas in men only a significant increase in the time taken to complete the five timed chair stands test was associated with a higher rate of falls (OR=2.75; 95% CI 1.21-6.23). In conclusion, our study demonstrated that SPPB scores ≤6 are associated with a higher fall rate in old people of both genders; in females, even an SPPB score between 7 and 9 identifies subjects at a higher likelihood of being recurrent fallers. Among the single items of the SPPB, the most strongly associated with falls were gait speed in women and the five timed chair stands test in men.

Association Between Short Physical Performance Battery and Falls in Older People: The Progetto Veneto Anziani Study

PubMed Central

Bolzetta, Francesco; Toffanello, Elena Debora; Zambon, Sabina; De Rui, Marina; Perissinotto, Egle; Coin, Alessandra; Corti, Maria-Chiara; Baggio, Giovannella; Crepaldi, Gaetano; Sergi, Giuseppe; Manzato, Enzo

2014-01-01

Abstract It is known that weakness in the lower limbs is associated with recurrent falls in old people. Among the tests routinely used to assess lower extremity strength, the Short Physical Performance Battery (SPPB) is one of those used most often, but its relationship with recurrent falls is poorly investigated. We aimed to determine if SPPB scores are related to recurrent falling in a sample of 2710 older-aged people, and to ascertain which test in the SPPB is most strongly associated with a higher rate of falls. In this cross-sectional study, we demonstrated that participants scoring 0–6 in the SPPB were more likely to be recurrent fallers than those scoring 10–12 (odds ratio [OR]=3.46, 95% confidence interval [CI] 2.04–5.88 in women; OR=3.82, 95% CI 1.77– 8.52, in men). SPPB scores of 7–9 were only associated with women being more likely to be recurrent fallers (OR=2.03, 95% CI 1.28–3.22). When the SPPB items were analyzed separately, even a lower score in gait speed for women was significantly associated with the presence of recurrent falls (OR=2.11; 95% CI 1.04–4.30), whereas in men only a significant increase in the time taken to complete the five timed chair stands test was associated with a higher rate of falls (OR=2.75; 95% CI 1.21–6.23). In conclusion, our study demonstrated that SPPB scores ≤6 are associated with a higher fall rate in old people of both genders; in females, even an SPPB score between 7 and 9 identifies subjects at a higher likelihood of being recurrent fallers. Among the single items of the SPPB, the most strongly associated with falls were gait speed in women and the five timed chair stands test in men. PMID:24387140

Quantification of the Effect of Cross-shear on the Wear of Conventional and Highly Cross-linked UHMWPE

PubMed Central

Kang, Lu; Galvin, Alison L.; Brown, Thomas D.; Jin, Zhongmin; Fisher, John

2008-01-01

A computational model has been developed to quantify the degree of cross-shear of a polyethylene pin articulating against a metallic plate, based on the direct simulation of a multidirectional pin-on-plate wear machine. The principal molecular orientation (PMO) was determined for each polymer site. The frictional work in the direction perpendicular to the PMO was assumed to produce the greatest orientation softening (Wang et al., 1997). The cross-shear ratio (CS) was defined as the frictional work perpendicular to the PMO direction, divided by the total frictional work. Cross-shear on the pin contact surface was location-specific, and of continuously changing magnitude because the direction of frictional force continuously changed due to pin rotation. The polymer pin motion was varied from a purely linear track (CS=0) up to a maximum rotation of ±55° (CS=0.254). The relationship between wear factors (K) measured experimentally and theoretically predicted CS was defined using logarithmic functions for both conventional and highly cross-linked UHMWPE. Cross-shear increased the apparent wear factor for both polyethylenes by more than 5-fold compared to unidirectional wear. PMID:17936763

Toward a dynamical theory of body movement in musical performance

PubMed Central

Demos, Alexander P.; Chaffin, Roger; Kant, Vivek

2014-01-01

Musicians sway expressively as they play in ways that seem clearly related to the music, but quantifying the relationship has been difficult. We suggest that a complex systems framework and its accompanying tools for analyzing non-linear dynamical systems can help identify the motor synergies involved. Synergies are temporary assemblies of parts that come together to accomplish specific goals. We assume that the goal of the performer is to convey musical structure and expression to the audience and to other performers. We provide examples of how dynamical systems tools, such as recurrence quantification analysis (RQA), can be used to examine performers' movements and relate them to the musical structure and to the musician's expressive intentions. We show how detrended fluctuation analysis (DFA) can be used to identify synergies and discover how they are affected by the performer's expressive intentions. PMID:24904490

Prospective study of single-stage repair of contaminated hernias using a biologic porcine tissue matrix: the RICH Study.

PubMed

Itani, Kamal M F; Rosen, Michael; Vargo, Daniel; Awad, Samir S; Denoto, George; Butler, Charles E

2012-09-01

In the presence of contamination, the repair of a ventral incisional hernia (VIH) is challenging. The presence of comorbidities poses an additional risk for postoperative wound events and hernia recurrence. To date, very few studies describe the outcomes of VIH repair in this high-risk population. A prospective, multicenter, single-arm, the Repair of Infected or Contaminated Hernias study was performed to study the clinical outcomes of open VIH repair of contaminated abdominal defects with a non-cross-linked, porcine, acellular dermal matrix, Strattice. Of 85 patients who consented to participate, 80 underwent open VIH repair with Strattice. Hernia defects were 'clean-contaminated' (n = 39), 'contaminated' (n = 39), or 'dirty' (n = 2), and the defects were classified as grade 3 (n = 60) or grade 4 (n = 20). The midline was restored, and primary closure was achieved in 64 patients; the defect was bridged in 16 patients. At 24 months, 53 patients (66%) experienced 95 wound events. There were 28 unique, infection-related events in 24 patients. Twenty-two patients experienced seromas, all but 5 of which were transient and required no intervention. No unanticipated adverse events occurred, and no tissue matrix required complete excision. There were 22 hernia (28%) recurrences by month 24. There was no correlation between infection-related events and hernia recurrence. The use of the intact, non-cross-linked, porcine, acellular dermal matrix, Strattice, in the repair of contaminated VIH in high-risk patients allowed for successful, single-stage reconstruction in >70% of patients followed for 24 months after repair. Published by Mosby, Inc.

Identification and quantification of major maillard cross-links in human serum albumin and lens protein. Evidence for glucosepane as the dominant compound.

PubMed

Biemel, Klaus M; Friedl, D Alexander; Lederer, Markus O

2002-07-12

Glycation reactions leading to protein modifications (advanced glycation end products) contribute to various pathologies associated with the general aging process and long term complications of diabetes. However, only few relevant compounds have so far been detected in vivo. We now report on the first unequivocal identification of the lysine-arginine cross-links glucosepane 5, DOGDIC 6, MODIC 7, and GODIC 8 in human material. For their accurate quantification by coupled liquid chromatography-electrospray ionization mass spectrometry, (13)C-labeled reference compounds were synthesized independently. Compounds 5-8 are formed via the alpha-dicarbonyl compounds N(6)-(2,3-dihydroxy-5,6-dioxohexyl)-l-lysinate (1a,b), 3-deoxyglucosone (), methylglyoxal (), and glyoxal (), respectively. The protein-bound dideoxyosone 1a,b seems to be of prime significance for cross-linking because it presumably is not detoxified by mammalian enzymes as readily as 2-4. Hence, the follow-up product glucosepane 5 was found to be the dominant compound. Up to 42.3 pmol of 5/mg of protein was identified in human serum albumin of diabetics; the level of 5 correlates markedly with the glycated hemoglobin HbA(1c). In the water-insoluble fraction of lens proteins from normoglycemics, concentration of 5 ranges between 132.3 and 241.7 pmol/mg. The advanced glycoxidation end product GODIC 8 is elevated significantly in brunescent lenses, indicating enhanced oxidative stress in this material. Compounds 5-8 thus appear predestined as markers for pathophysiological processes.

Assessment of real-time PCR based methods for quantification of pollen-mediated gene flow from GM to conventional maize in a field study.

PubMed

Pla, Maria; La Paz, José-Luis; Peñas, Gisela; García, Nora; Palaudelmàs, Montserrat; Esteve, Teresa; Messeguer, Joaquima; Melé, Enric

2006-04-01

Maize is one of the main crops worldwide and an increasing number of genetically modified (GM) maize varieties are cultivated and commercialized in many countries in parallel to conventional crops. Given the labeling rules established e.g. in the European Union and the necessary coexistence between GM and non-GM crops, it is important to determine the extent of pollen dissemination from transgenic maize to other cultivars under field conditions. The most widely used methods for quantitative detection of GMO are based on real-time PCR, which implies the results are expressed in genome percentages (in contrast to seed or grain percentages). Our objective was to assess the accuracy of real-time PCR based assays to accurately quantify the contents of transgenic grains in non-GM fields in comparison with the real cross-fertilization rate as determined by phenotypical analysis. We performed this study in a region where both GM and conventional maize are normally cultivated and used the predominant transgenic maize Mon810 in combination with a conventional maize variety which displays the characteristic of white grains (therefore allowing cross-pollination quantification as percentage of yellow grains). Our results indicated an excellent correlation between real-time PCR results and number of cross-fertilized grains at Mon810 levels of 0.1-10%. In contrast, Mon810 percentage estimated by weight of grains produced less accurate results. Finally, we present and discuss the pattern of pollen-mediated gene flow from GM to conventional maize in an example case under field conditions.

Tracking ink composition on Herculaneum papyrus scrolls: quantification and speciation of lead by X-ray based techniques and Monte Carlo simulations.

PubMed

Tack, Pieter; Cotte, Marine; Bauters, Stephen; Brun, Emmanuel; Banerjee, Dipanjan; Bras, Wim; Ferrero, Claudio; Delattre, Daniel; Mocella, Vito; Vincze, Laszlo

2016-02-08

The writing in carbonized Herculaneum scrolls, covered and preserved by the pyroclastic events of the Vesuvius in 79 AD, was recently revealed using X-ray phase-contrast tomography, without the need of unrolling the sensitive scrolls. Unfortunately, some of the text is difficult to read due to the interference of the papyrus fibers crossing the written text vertically and horizontally. Recently, lead was found as an elemental constituent in the writing, rendering the text more clearly readable when monitoring the lead X-ray fluorescence signal. Here, several hypotheses are postulated for the origin and state of lead in the papyrus writing. Multi-scale X-ray fluorescence micro-imaging, Monte Carlo quantification and X-ray absorption microspectroscopy experiments are used to provide additional information on the ink composition, in an attempt to determine the origin of the lead in the Herculaneum scrolls and validate the postulated hypotheses.

Robust tumor morphometry in multispectral fluorescence microscopy

NASA Astrophysics Data System (ADS)

Tabesh, Ali; Vengrenyuk, Yevgen; Teverovskiy, Mikhail; Khan, Faisal M.; Sapir, Marina; Powell, Douglas; Mesa-Tejada, Ricardo; Donovan, Michael J.; Fernandez, Gerardo

2009-02-01

Morphological and architectural characteristics of primary tissue compartments, such as epithelial nuclei (EN) and cytoplasm, provide important cues for cancer diagnosis, prognosis, and therapeutic response prediction. We propose two feature sets for the robust quantification of these characteristics in multiplex immunofluorescence (IF) microscopy images of prostate biopsy specimens. To enable feature extraction, EN and cytoplasm regions were first segmented from the IF images. Then, feature sets consisting of the characteristics of the minimum spanning tree (MST) connecting the EN and the fractal dimension (FD) of gland boundaries were obtained from the segmented compartments. We demonstrated the utility of the proposed features in prostate cancer recurrence prediction on a multi-institution cohort of 1027 patients. Univariate analysis revealed that both FD and one of the MST features were highly effective for predicting cancer recurrence (p <= 0.0001). In multivariate analysis, an MST feature was selected for a model incorporating clinical and image features. The model achieved a concordance index (CI) of 0.73 on the validation set, which was significantly higher than the CI of 0.69 for the standard multivariate model based solely on clinical features currently used in clinical practice (p < 0.0001). The contributions of this work are twofold. First, it is the first demonstration of the utility of the proposed features in morphometric analysis of IF images. Second, this is the largest scale study of the efficacy and robustness of the proposed features in prostate cancer prognosis.

Automated fluorescent miscroscopic image analysis of PTBP1 expression in glioma

PubMed Central

Becker, Aline; Elder, Brad; Puduvalli, Vinay; Winter, Jessica; Gurcan, Metin

2017-01-01

Multiplexed immunofluorescent testing has not entered into diagnostic neuropathology due to the presence of several technical barriers, amongst which includes autofluorescence. This study presents the implementation of a methodology capable of overcoming the visual challenges of fluorescent microscopy for diagnostic neuropathology by using automated digital image analysis, with long term goal of providing unbiased quantitative analyses of multiplexed biomarkers for solid tissue neuropathology. In this study, we validated PTBP1, a putative biomarker for glioma, and tested the extent to which immunofluorescent microscopy combined with automated and unbiased image analysis would permit the utility of PTBP1 as a biomarker to distinguish diagnostically challenging surgical biopsies. As a paradigm, we utilized second resections from patients diagnosed either with reactive brain changes (pseudoprogression) and recurrent glioblastoma (true progression). Our image analysis workflow was capable of removing background autofluorescence and permitted quantification of DAPI-PTBP1 positive cells. PTBP1-positive nuclei, and the mean intensity value of PTBP1 signal in cells. Traditional pathological interpretation was unable to distinguish between groups due to unacceptably high discordance rates amongst expert neuropathologists. Our data demonstrated that recurrent glioblastoma showed more DAPI-PTBP1 positive cells and a higher mean intensity value of PTBP1 signal compared to resections from second surgeries that showed only reactive gliosis. Our work demonstrates the potential of utilizing automated image analysis to overcome the challenges of implementing fluorescent microscopy in diagnostic neuropathology. PMID:28282372

Indication for Computed Tomography Scan in Shoulder Instability: Sensitivity and Specificity of Standard Radiographs to Predict Bone Defects After Traumatic Anterior Glenohumeral Instability.

PubMed

Delage Royle, Audrey; Balg, Frédéric; Bouliane, Martin J; Canet-Silvestri, Fanny; Garant-Saine, Laurianne; Sheps, David M; Lapner, Peter; Rouleau, Dominique M

2017-10-01

Quantifying glenohumeral bone loss is key in preoperative surgical planning for a successful Bankart repair. Simple radiographs can accurately measure bone defects in cases of recurrent shoulder instability. Cohort study (diagnosis); Level of evidence, 2. A true anteroposterior (AP) view, alone and in combination with an axillary view, was used to evaluate the diagnostic properties of radiographs compared with computed tomography (CT) scan, the current gold standard, to predict significant bone defects in 70 patients. Sensitivity, specificity, and positive and negative predictive values were evaluated and compared. Detection of glenoid bone loss on plain film radiographs, with and without axillary view, had a sensitivity of 86% for both views and a specificity of 73% and 64% with and without the axillary view, respectively. For detection of humeral bone loss, the sensitivity was 8% and 17% and the specificity was 98% and 91% with and without the axillary view, respectively. Regular radiographs would have missed 1 instance of significant bone loss on the glenoid side and 20 on the humeral side. Interobserver reliabilities were moderate for glenoid detection (κ = 0.473-0.503) and poor for the humeral side (κ = 0.278-0.336). Regular radiographs showed suboptimal sensitivity, specificity, and reliability. Therefore, CT scan should be considered in the treatment algorithm for accurate quantification of bone loss to prevent high rates of recurrent instability.

Treatment for incarcerated indirect hernia with "Cross-Internal Ring" inguinal oblique incision in children.

PubMed

Yan, Xue-Qiang; Yang, Jun; Zheng, Nan-Nan; Kuang, Hou-Fang; Duan, Xu-Fei; Bian, Hong-Qiang

2017-01-01

This study aims to evaluate the utility of the "Cross-Internal Ring" inguinal oblique incision for the surgical treatment of incarcerated indirect hernia (IIH) complicated with severe abdominal distension. Patients of IIH complicated with severe abdominal distension were reviewed retrospectively. All patients received operation through the "Cross-Internal Ring" inguinal oblique incision. There were totally 13 patients were included, male to female ratio was 9-4. The time for patients to resume oral feeding varying from 2 to 5 days after operation, no complications include delayed intestinal perforation, intra-abdominal abscess, and incision infection happened. Average postoperative hospital stay was 5.2 days. All cases were followed up for 6-18 months. No recurrence or iatrogenic cryptorchidism happened. "Cross-Internal Ring" inguinal oblique incision is a simple, safe, and reliable surgical method to treat pediatric IIH complicated with severe abdominal distension.

Recurrence networks from multivariate signals for uncovering dynamic transitions of horizontal oil-water stratified flows

NASA Astrophysics Data System (ADS)

Gao, Zhong-Ke; Zhang, Xin-Wang; Jin, Ning-De; Donner, Reik V.; Marwan, Norbert; Kurths, Jürgen

2013-09-01

Characterizing the mechanism of drop formation at the interface of horizontal oil-water stratified flows is a fundamental problem eliciting a great deal of attention from different disciplines. We experimentally and theoretically investigate the formation and transition of horizontal oil-water stratified flows. We design a new multi-sector conductance sensor and measure multivariate signals from two different stratified flow patterns. Using the Adaptive Optimal Kernel Time-Frequency Representation (AOK TFR) we first characterize the flow behavior from an energy and frequency point of view. Then, we infer multivariate recurrence networks from the experimental data and investigate the cross-transitivity for each constructed network. We find that the cross-transitivity allows quantitatively uncovering the flow behavior when the stratified flow evolves from a stable state to an unstable one and recovers deeper insights into the mechanism governing the formation of droplets at the interface of stratified flows, a task that existing methods based on AOK TFR fail to work. These findings present a first step towards an improved understanding of the dynamic mechanism leading to the transition of horizontal oil-water stratified flows from a complex-network perspective.

Thyrotropin receptor autoantibodies and early miscarriages in patients with Hashimoto thyroiditis: a case-control study.

PubMed

Toulis, Konstantinos A; Goulis, Dimitrios G; Tsolakidou, Konstantina; Hilidis, Ilias; Fragkos, Marios; Polyzos, Stergios A; Gerofotis, Antonios; Kita, Marina; Bili, Helen; Vavilis, Dimitrios; Daniilidis, Michail; Tarlatzis, Basil C; Papadimas, Ioannis

2013-08-01

We have previously hypothesized that early miscarriage in women with Hashimoto thyroiditis might be the result of a cross-reactivity process, in which blocking autoantibodies against thyrotropin receptor (TSHr-Ab) antagonize hCG action on its receptor on the corpus luteum. To test this hypothesis from the clinical perspective, we investigated the presence of TSHr-Ab in Hashimoto thyroiditis patients with apparently unexplained, first-trimester recurrent miscarriages compared to that in Hashimoto thyroiditis patients with documented normal fertility. A total of 86 subjects (43 cases and 43 age-matched controls) were finally included in a case-control study. No difference in the prevalence of TSHr-Ab positivity was detected between cases and controls (Fisher's exact test, p value = 1.00). In patients with recurrent miscarriages, TSHr-Ab concentrations did not predict the number of miscarriages (univariate linear regression, p value = 0.08). These results were robust in sensitivity analyses, including only cases with full investigation or those with three or more miscarriages. We conclude that no role could be advocated for TSHr-Ab in the aetiology of recurrent miscarriages in women with Hashimoto thyroiditis.

Quantification of indium in steel using PIXE

NASA Astrophysics Data System (ADS)

Oliver, A.; Miranda, J.; Rickards, J.; Cheang, J. C.

1989-04-01

The quantitative analysis of steel for endodontics tools was carried out using low-energy protons (≤ 700 keV). A computer program for a thick-target analysis which includes enhancement due to secondary fluorescence was used. In this experiment the L-lines of indium are enhanced due to the proximity of other elements' K-lines to the indium absorption edge. The results show that the ionization cross section expression employed to evaluate this magnitude is important.

ANALYSIS OF FACTORS AFFECTING OUTCOME OF ULTRASOUND-GUIDED RADIOFREQUENCY HEAT ABLATION FOR TREATMENT OF PRIMARY HYPERPARATHYROIDISM IN DOGS.

PubMed

Bucy, Daniel; Pollard, Rachel; Nelson, Richard

2017-01-01

Radiofrequency (RF) parathyroid ablation is a noninvasive treatment for hyperparathyroidism in dogs. There are no published data assessing factors associated with RF parathyroid ablation success or failure in order to guide patient selection and improve outcome. The purpose of this retrospective analytical study was to determine whether imaging findings, biochemical data, or concurrent diseases were associated with RF heat ablation treatment failure. For inclusion in the study, dogs must have had a clinical diagnosis of primary hyperparathyroidism, undergone cervical ultrasound and RF ablation of abnormal parathyroid tissue, and must have had at least 3 months of follow-up information available following the date of ultrasound-guided parathyroid ablation. Dogs were grouped based on those with recurrent or persistent hypercalcemia and those without recurrent or persistent hypercalcemia following therapy. Parathyroid nodule size, thyroid lobe size, nodule location, and presence of concurrent disease were recorded. Recurrence of hypercalcemia occurred in 9/32 dogs that had ablation of abnormal parathyroid tissue (28%) and one patient had persistent hypercalcemia (3%) following parathyroid ablation. Nodule width (P = 0.036), height (P = 0.028), and largest cross-sectional area (P = 0.023) were larger in dogs that had recurrent or persistent hypercalcemia following ablation. Hypothyroidism was more common in dogs with recurrent disease (P = 0.044). Radiofrequency ablation was successful in 22/32 (69%) dogs. Larger parathyroid nodule size and/or concurrent hypothyroidism were associated with treatment failure in dogs that underwent ultrasound-guided RF parathyroid nodule ablation. © 2016 American College of Veterinary Radiology.

Chronic bacterial prostatitis in men with spinal cord injury.

PubMed

Krebs, Jörg; Bartel, Peter; Pannek, Jürgen

2014-12-01

Recurrent urinary tract infections (UTI) are a major problem affecting spinal cord injury (SCI) patients and may stem from chronic bacterial prostatitis. We have therefore investigated the presence of chronic bacterial prostatitis and its role in the development of recurrent symptomatic UTI in SCI men. This study is a prospective cross-sectional investigation of bacterial prostatitis in SCI men in a single SCI rehabilitation center. In 50 men with chronic SCI presenting for a routine urologic examination, urine samples before and after prostate massage were taken for microbiologic investigation and white blood cell counting. Furthermore, patient characteristics, bladder diary details, and the annual rate of symptomatic UTI were collected retrospectively. No participant reported current symptoms of UTI or prostatitis. In most men (39/50, 78 %), the microbiologic analysis of the post-massage urine sample revealed growth of pathogenic bacteria. The majority of these men (32/39, 82 %) also presented with mostly (27/39, 69 %) the same pathogenic bacteria in the pre-massage sample. There was no significant (p = 0.48) difference in the number of symptomatic UTI in men with a positive post-massage culture compared with those with a negative culture. No significant (p = 0.67) difference in the frequency distribution of positive versus negative post-massage cultures was detected between men with recurrent and sporadic UTI. Most SCI men are affected by asymptomatic bacterial prostatitis; however, bacterial prostatitis does not play a major role in the development of recurrent UTI. The indication for antibiotic treatment of chronic bacterial prostatitis in asymptomatic SCI men with recurrent UTI is questionable.

Frequency Of Different Risk Factors Associated With Recurrent Urinary Tract Infection Among Postmenopausal Women.

PubMed

Jameel, Sadia; Mahmud, Syed Nayer

2016-01-01

Urinary Tract Infection is one of the most common infections encountered by women. These infections have the tendency to recur. In order to identify women at risk of recurrence there is a need to identify risk factors associated with it. Among women, factors predisposing to recurrent infections are not much explored. The study was done with an objective to determine different risk factors associated with recurrent UTI among postmenopausal women. This was a cross sectional study conducted at the Out Patient Department of Nephrology in Shifa International Hospital Islamabad over a period of six months, June 6th to December 5th 2012. Information regarding demographics and risk factors were recorded on a predesigned pro forma. A descriptive analysis was done for quantitative variables like age and qualitative variables like marital status and frequency of different risk factors. Stratification of risk factors according to age was also done. Hundred females were enrolled into the study after informed consent. The mean age of the study population was 64.4±9.48. 97% of the population was married. Out of 100 patients, 42 had high post-void volume, 35 had urinary incontinence and 17 patients were having cystocele. According to age stratification, most frequently affected age group was between 51-60 years (38%), followed by 61-70 years (36%), then 25% in more than 70 years, whereas only 1% was between 41-50 years. Recurrent UTI in postmenopausal females is most frequently associated with high post void volume and most frequently affected age group is between 51-60 years.

Oral antiviral therapy for prevention of genital herpes outbreaks in immunocompetent and nonpregnant patients.

PubMed

Le Cleach, Laurence; Trinquart, Ludovic; Do, Giao; Maruani, Annabel; Lebrun-Vignes, Benedicte; Ravaud, Philippe; Chosidow, Olivier

2014-08-03

Genital herpes is caused by herpes simplex virus 1 (HSV-1) or 2 (HSV-2). Some infected people experience outbreaks of genital herpes, typically, characterized by vesicular and erosive localized painful genital lesions. To compare the effectiveness and safety of three oral antiviral drugs (acyclovir, famciclovir and valacyclovir) prescribed to suppress genital herpes outbreaks in non-pregnant patients. We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, the search portal of the World Health Organization International Clinical Trials Registry Platform and pharmaceutical company databases up to February 2014. We also searched US Food and Drug Administration databases and proceedings of seven congresses to a maximum of 10 years. We contacted trial authors and pharmaceutical companies. We selected parallel-group and cross-over randomized controlled trials including patients with recurrent genital herpes caused by HSV, whatever the type (HSV-1, HSV-2, or undetermined), with at least four recurrences per year (trials concerning human immunodeficiency virus (HIV)-positive patients or pregnant women were not eligible) and comparing suppressive oral antiviral treatment with oral acyclovir, famciclovir, and valacyclovir versus placebo or another suppressive oral antiviral treatment. Two review authors independently selected eligible trials and extracted data. The Risk of bias tool was used to assess risk of bias. Treatment effect was measured by the risk ratio (RR) of having at least one genital herpes recurrence. Pooled RRs were derived by conventional pairwise meta-analyses. A network meta-analysis allowed for estimation of all possible two-by-two comparisons between antiviral drugs. A total of 26 trials (among which six had a cross-over design) were included. Among the 6950 randomly assigned participants, 54% (range 0 to 100%) were female, mean age was 35 years (range 26 to 45.1), and the mean number of recurrences per year was 11 (range 6.3 to 17.8). Duration of treatment was two to 12 months. Risk of bias was considered high for half of the studies and unclear for the other half. A total of 14 trials compared acyclovir versus placebo, four trials compared valacyclovir versus placebo and 2 trials compared valacyclovir versus no treatment. Three trials compared famciclovir versus placebo. Two trials compared valacyclovir versus famciclovir and one trial compared acyclovir versus valacyclovir versus placebo.We analyzed data from 22 trials for the outcome: risk of having at least one clinical recurrence. We could not obtain the outcome data for four trials. In placebo-controlled trials, there was a low quality evidence that the risk of having at least one clinical recurrence was reduced with acyclovir (nine parallel-group trials, n = 2049; pooled RR 0.48, 95% confidence interval (CI) 0.39 to 0.58), valacyclovir (four trials, n = 1788; pooled RR 0.41, 95% CI 0.24 to 0.69), or famciclovir (two trials, n = 732; pooled RR 0.57, 95% CI 0.50 to 0.64). The six cross-over trials showed larger treatment effects on average than the parallel-group trials. We found evidence of a small-study effect for acyclovir placebo-controlled trials (adjusted pooled RR 0.61, 95% CI 0.49 to 0.75). In analyzing parallel-group trials by daily dose, no clear evidence was found of a dose-response relationship for any drug. In head-to-head trials, the risk of having at least one recurrence was increased with valacyclovir rather than acyclovir (one trial, n = 1345; RR 1.16, 95% CI 1.01 to 1.34) and was not significantly different from that seen with famciclovir as compared with valacyclovir (one trial, n = 320; RR 1.18, 95% CI 0.86 to 1.63).We included 16 parallel-arm trials in a network meta-analysis and we were unable to determine which of the drugs was most effective in reducing the risk of at least one clinical recurrence (after adjustment for small-study effects, pooled RR 0.83, 95% CI 0.61 to 1.11 for valacyclovir vs acyclovir; pooled RR 1.04, 95% CI, 0.71 to 1.49 for famciclovir vs acyclovir; and pooled RR 1.26, 95% CI 0.89 to 1.75 for famciclovir vs valacyclovir). Safety data were sought but were reported as total numbers of adverse events. Owing to risk of bias and inconsistency, there is low quality evidence that suppressive antiviral therapy with acyclovir, valacyclovir or famciclovir in pacients experiencing at least four recurrences of genital herpes per year decreases the number of pacients with at least one recurrence as compared with placebo. Network meta-analysis of the few direct comparisons and the indirect comparisons did not show superiority of one drug over another.

Synthesis and enzymatic degradation of epichlorohydrin cross-linked pectins.

PubMed

Semdé, Rasmané; Moës, André J; Devleeschouwer, Michel J; Amighi, Karim

2003-02-01

The water solubility of pectin was successfully decreased by cross-linking with increasing amounts of epichlorohydrin in the reaction media. The initial molar ratios of epichlorohydrin/ galacturonic acid monomer in the reaction mixtures were 0, 0.37, 0.56, 0.74, 1.00, 1.47, and 2.44. The resulting epichlorohydrin cross-linked pectins were thus referred to as C-LP0, C-LP37, C-LP56, C-LP75, C-LP100, C-LP150, and C-LP250, respectively. Methoxylation degrees ranged from 60.5 +/- 0.9% to 68.0 +/- 0.6%, and the effective cross-linking degrees, determined by quantification of the hydroxyl anions consumed during the reaction, were 0, 17.8, 26.0, 38.3, 46.5, 53.5, and 58.7%. respectively. After incubating the different cross-linked pectins (0.5% w/v) in 25 mL of 0.05 M acetate-phosphate buffer (pH 4.5), containing 50 microL of Pectinex Ultra SP-L (pectinolytic enzymes), between 60 and 80% of the pectin osidic bounds were broken in less than 1 hr. Moreover, increasing the cross-linking degree only resulted in a weak slowing on the enzymatic degradation velocity.

Flood of February 1980 along the Agua Fria River, Maricopa County, Arizona

USGS Publications Warehouse

Thomsen, B.W.

1980-01-01

The flood of February 20, 1980, along the Agua Fria River below Waddell Dam, Maricopa County, Ariz., was caused by heavy rains during February 13-20. The runoff filled Lake Pleasant and resulted in the largest release--66,600 cubic feet per second--from the reservoir since it was built in 1927; the maximum inflow to the reservoir was about 73,300 cubic feet per second. The area inundated by the releases includes about 28 miles along the channel from the mouth of the Agua Fria River to the Beardsley Canal flume crossing 5 miles downstream from Waddell Dam. The flood of 1980 into Lake Pleasant has a recurrence interval of about 47 years, whereas the flood of record (1919) has a recurrence interval of about 100 years. (USGS)

Screening of the unrecognised bipolar disorders among outpatients with recurrent depressive disorder: a cross-sectional study in psychiatric hospital in Morocco.

PubMed

Bouchra, Oneib; Maria, Sabir; Abderazak, Ouanass

2017-01-01

The bipolar disorder is often misdiagnosed in particular among outpatients with recurrent depression. Indeed, this work confirmed that the unrecognised bipolar disorder is common among depressed outpatients, which were younger, unemployed, single or divorced with a low socio-economic level. These socio-demographics data gives us an idea about the disability experienced by the unknown bipolar patients. Also, we demonstrate that the under-diagnosis bipolar disorder was associated with the earliest onset age of a depressive episode and it was more prevalent in depressed patients with suicidal ideation and suicide attempts. These factors should be taken into account when we screen for the unknowm bipolar disorder, especially type II to improve the early diagnosis and the quality of life of these patients.

VAVUQ, Python and Matlab freeware for Verification and Validation, Uncertainty Quantification

NASA Astrophysics Data System (ADS)

Courtney, J. E.; Zamani, K.; Bombardelli, F. A.; Fleenor, W. E.

2015-12-01

A package of scripts is presented for automated Verification and Validation (V&V) and Uncertainty Quantification (UQ) for engineering codes that approximate Partial Differential Equations (PDFs). The code post-processes model results to produce V&V and UQ information. This information can be used to assess model performance. Automated information on code performance can allow for a systematic methodology to assess the quality of model approximations. The software implements common and accepted code verification schemes. The software uses the Method of Manufactured Solutions (MMS), the Method of Exact Solution (MES), Cross-Code Verification, and Richardson Extrapolation (RE) for solution (calculation) verification. It also includes common statistical measures that can be used for model skill assessment. Complete RE can be conducted for complex geometries by implementing high-order non-oscillating numerical interpolation schemes within the software. Model approximation uncertainty is quantified by calculating lower and upper bounds of numerical error from the RE results. The software is also able to calculate the Grid Convergence Index (GCI), and to handle adaptive meshes and models that implement mixed order schemes. Four examples are provided to demonstrate the use of the software for code and solution verification, model validation and uncertainty quantification. The software is used for code verification of a mixed-order compact difference heat transport solver; the solution verification of a 2D shallow-water-wave solver for tidal flow modeling in estuaries; the model validation of a two-phase flow computation in a hydraulic jump compared to experimental data; and numerical uncertainty quantification for 3D CFD modeling of the flow patterns in a Gust erosion chamber.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

PubMed Central

Röst, Hannes L.; Liu, Yansheng; D’Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C.; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-01-01

Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets. PMID:27479329

Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0)).

PubMed

Hu, Kaifeng; Westler, William M; Markley, John L

2011-02-16

Quantitative one-dimensional (1D) (1)H NMR spectroscopy is a useful tool for determining metabolite concentrations because of the direct proportionality of signal intensity to the quantity of analyte. However, severe signal overlap in 1D (1)H NMR spectra of complex metabolite mixtures hinders accurate quantification. Extension of 1D (1)H to 2D (1)H-(13)C HSQC leads to the dispersion of peaks along the (13)C dimension and greatly alleviates peak overlapping. Although peaks are better resolved in 2D (1)H-(13)C HSQC than in 1D (1)H NMR spectra, the simple proportionality of cross peaks to the quantity of individual metabolites is lost by resonance-specific signal attenuation during the coherence transfer periods. As a result, peaks for individual metabolites usually are quantified by reference to calibration data collected from samples of known concentration. We show here that data from a series of HSQC spectra acquired with incremented repetition times (the time between the end of the first (1)H excitation pulse to the beginning of data acquisition) can be extrapolated back to zero time to yield a time-zero 2D (1)H-(13)C HSQC spectrum (HSQC(0)) in which signal intensities are proportional to concentrations of individual metabolites. Relative concentrations determined from cross peak intensities can be converted to absolute concentrations by reference to an internal standard of known concentration. Clustering of the HSQC(0) cross peaks by their normalized intensities identifies those corresponding to metabolites present at a given concentration, and this information can assist in assigning these peaks to specific compounds. The concentration measurement for an individual metabolite can be improved by averaging the intensities of multiple, nonoverlapping cross peaks assigned to that metabolite.

Multimodal Imaging and Lighting Bias Correction for Improved μPAD-based Water Quality Monitoring via Smartphones

NASA Astrophysics Data System (ADS)

McCracken, Katherine E.; Angus, Scott V.; Reynolds, Kelly A.; Yoon, Jeong-Yeol

2016-06-01

Smartphone image-based sensing of microfluidic paper analytical devices (μPADs) offers low-cost and mobile evaluation of water quality. However, consistent quantification is a challenge due to variable environmental, paper, and lighting conditions, especially across large multi-target μPADs. Compensations must be made for variations between images to achieve reproducible results without a separate lighting enclosure. We thus developed a simple method using triple-reference point normalization and a fast-Fourier transform (FFT)-based pre-processing scheme to quantify consistent reflected light intensity signals under variable lighting and channel conditions. This technique was evaluated using various light sources, lighting angles, imaging backgrounds, and imaging heights. Further testing evaluated its handle of absorbance, quenching, and relative scattering intensity measurements from assays detecting four water contaminants - Cr(VI), total chlorine, caffeine, and E. coli K12 - at similar wavelengths using the green channel of RGB images. Between assays, this algorithm reduced error from μPAD surface inconsistencies and cross-image lighting gradients. Although the algorithm could not completely remove the anomalies arising from point shadows within channels or some non-uniform background reflections, it still afforded order-of-magnitude quantification and stable assay specificity under these conditions, offering one route toward improving smartphone quantification of μPAD assays for in-field water quality monitoring.

The Accuracy of Al and Cu Film Thickness Determinations and the Implications for Electron Probe Microanalysis.

PubMed

Matthews, Mike B; Kearns, Stuart L; Buse, Ben

2018-04-01

The accuracy to which Cu and Al coatings can be determined, and the effect this has on the quantification of the substrate, is investigated. Cu and Al coatings of nominally 5, 10, 15, and 20 nm were sputter coated onto polished Bi using two configurations of coater: One with the film thickness monitor (FTM) sensor colocated with the samples, and one where the sensor is located to one side. The FTM thicknesses are compared against those calculated from measured Cu Lα and Al Kα k-ratios using PENEPMA, GMRFilm, and DTSA-II. Selected samples were also cross-sectioned using focused ion beam. Both systems produced repeatable coatings, the thickest coating being approximately four times the thinnest coating. The side-located FTM sensor indicated thicknesses less than half those of the software modeled results, propagating on to 70% errors in substrate quantification at 5 kV. The colocated FTM sensor produced errors in film thickness and substrate quantification of 10-20%. Over the range of film thicknesses and accelerating voltages modeled both the substrate and coating k-ratios can be approximated by linear trends as functions of film thickness. The Al films were found to have a reduced density of ~2 g/cm2.

A new automated quantification algorithm for the detection and evaluation of focal liver lesions with contrast-enhanced ultrasound.

PubMed

Gatos, Ilias; Tsantis, Stavros; Spiliopoulos, Stavros; Skouroliakou, Aikaterini; Theotokas, Ioannis; Zoumpoulis, Pavlos; Hazle, John D; Kagadis, George C

2015-07-01

Detect and classify focal liver lesions (FLLs) from contrast-enhanced ultrasound (CEUS) imaging by means of an automated quantification algorithm. The proposed algorithm employs a sophisticated segmentation method to detect and contour focal lesions from 52 CEUS video sequences (30 benign and 22 malignant). Lesion detection involves wavelet transform zero crossings utilization as an initialization step to the Markov random field model toward the lesion contour extraction. After FLL detection across frames, time intensity curve (TIC) is computed which provides the contrast agents' behavior at all vascular phases with respect to adjacent parenchyma for each patient. From each TIC, eight features were automatically calculated and employed into the support vector machines (SVMs) classification algorithm in the design of the image analysis model. With regard to FLLs detection accuracy, all lesions detected had an average overlap value of 0.89 ± 0.16 with manual segmentations for all CEUS frame-subsets included in the study. Highest classification accuracy from the SVM model was 90.3%, misdiagnosing three benign and two malignant FLLs with sensitivity and specificity values of 93.1% and 86.9%, respectively. The proposed quantification system that employs FLLs detection and classification algorithms may be of value to physicians as a second opinion tool for avoiding unnecessary invasive procedures.

Quantification of the Keto-Hydroperoxide (HOOCH2OCHO) and Other Elusive Intermediates during Low-Temperature Oxidation of Dimethyl Ether.

PubMed

Moshammer, Kai; Jasper, Ahren W; Popolan-Vaida, Denisia M; Wang, Zhandong; Bhavani Shankar, Vijai Shankar; Ruwe, Lena; Taatjes, Craig A; Dagaut, Philippe; Hansen, Nils

2016-10-04

This work provides new temperature-dependent mole fractions of elusive intermediates relevant to the low-temperature oxidation of dimethyl ether (DME). It extends the previous study of Moshammer et al. [ J. Phys. Chem. A 2015 , 119 , 7361 - 7374 ] in which a combination of a jet-stirred reactor and molecular beam mass spectrometry with single-photon ionization via tunable synchrotron-generated vacuum-ultraviolet radiation was used to identify (but not quantify) several highly oxygenated species. Here, temperature-dependent concentration profiles of 17 components were determined in the range of 450-1000 K and compared to up-to-date kinetic modeling results. Special emphasis is paid toward the validation and application of a theoretical method for predicting photoionization cross sections that are hard to obtain experimentally but essential to turn mass spectral data into mole fraction profiles. The presented approach enabled the quantification of the hydroperoxymethyl formate (HOOCH 2 OCH 2 O), which is a key intermediate in the low-temperature oxidation of DME. The quantification of this keto-hydroperoxide together with the temperature-dependent concentration profiles of other intermediates including H 2 O 2 , HCOOH, CH 3 OCHO, and CH 3 OOH reveals new opportunities for the development of a next-generation DME combustion chemistry mechanism.

The impact of recurrent throat infection on children and their families.

PubMed

Howel, Denise; Webster, Simon; Hayes, Jane; Barton, Andrew; Donaldson, Liam

2002-06-01

Recurrent throat problems in children are common and have an impact on the family. The appropriateness of surgery will depend on both clinical and social factors. The aim of this study was to assess the impact on the whole family when a child is suffering from recurrent throat problems, and investigate related parental attitudes. A total of 1190 parents of children in northern England for whom tonsillectomy or adeno-tonsillectomy was a possible treatment option were sent a questionnaire covering social and clinical issues such as children's symptoms, the impact on family life and parental attitudes. The majority of children had experienced more than four episodes in the previous year, had their sleep affected and time off school. Most parents were worried and reported disruption to the family, including taking time off work and cross-infection. Parental disruption, worry and eagerness for surgery were significantly associated with the duration of episodes of throat problems and the number of episodes in the previous year, but not with duration of tonsillitis. Time off school, or parental time off work was significantly associated with parental worry and disruption, but not with eagerness for surgery. This work highlights the impact of recurrent throat problems and related parental attitudes, and will aid in striking a balance between clinical requirements and the needs and wishes of the family.

HOMFLYPT polynomial is the best quantifier for topological cascades of vortex knots

NASA Astrophysics Data System (ADS)

Ricca, Renzo L.; Liu, Xin

2018-02-01

In this paper we derive and compare numerical sequences obtained by adapted polynomials such as HOMFLYPT, Jones and Alexander-Conway for the topological cascade of vortex torus knots and links that progressively untie by a single reconnection event at a time. Two cases are considered: the alternate sequence of knots and co-oriented links (with positive crossings) and the sequence of two-component links with oppositely oriented components (negative crossings). New recurrence equations are derived and sequences of numerical values are computed. In all cases the adapted HOMFLYPT polynomial proves to be the best quantifier for the topological cascade of torus knots and links.

Restoration of pseudo-self-compatibility (PSC) in derivatives of a high-PSC × no-PSC cross in Nemesia strumosa Benth.

PubMed

Robacker, C D; Ascher, P D

1978-05-01

Mean PSC increased following each generation of recurrent selection in F1, F2 and F3 Nemesia strumosa families derived from a cross of a 100% PSC plant to an unrelated 0% PSC plant. The first 100% PSC individuals occurred in the F4. Populations derived through sib pollination tended to have higher PSC means than lines derived through self pollination. One F3 family showed a three-fold higher PSC level when pollinated in the green-house than when pollinated in the growth chamber, while another F3 family similarly pollinated showed no change in PSC.

Factors controlling volume errors through 2D gully erosion assessment: guidelines for optimal survey design

NASA Astrophysics Data System (ADS)

Castillo, Carlos; Pérez, Rafael

2017-04-01

The assessment of gully erosion volumes is essential for the quantification of soil losses derived from this relevant degradation process. Traditionally, 2D and 3D approaches has been applied for this purpose (Casalí et al., 2006). Although innovative 3D approaches have recently been proposed for gully volume quantification, a renewed interest can be found in literature regarding the useful information that cross-section analysis still provides in gully erosion research. Moreover, the application of methods based on 2D approaches can be the most cost-effective approach in many situations such as preliminary studies with low accuracy requirements or surveys under time or budget constraints. The main aim of this work is to examine the key factors controlling volume error variability in 2D gully assessment by means of a stochastic experiment involving a Monte Carlo analysis over synthetic gully profiles in order to 1) contribute to a better understanding of the drivers and magnitude of gully erosion 2D-surveys uncertainty and 2) provide guidelines for optimal survey designs. Owing to the stochastic properties of error generation in 2D volume assessment, a statistical approach was followed to generate a large and significant set of gully reach configurations to evaluate quantitatively the influence of the main factors controlling the uncertainty of the volume assessment. For this purpose, a simulation algorithm in Matlab® code was written, involving the following stages: - Generation of synthetic gully area profiles with different degrees of complexity (characterized by the cross-section variability) - Simulation of field measurements characterised by a survey intensity and the precision of the measurement method - Quantification of the volume error uncertainty as a function of the key factors In this communication we will present the relationships between volume error and the studied factors and propose guidelines for 2D field surveys based on the minimal survey densities required to achieve a certain accuracy given the cross-sectional variability of a gully and the measurement method applied. References Casali, J., Loizu, J., Campo, M.A., De Santisteban, L.M., Alvarez-Mozos, J., 2006. Accuracy of methods for field assessment of rill and ephemeral gully erosion. Catena 67, 128-138. doi:10.1016/j.catena.2006.03.005

Retrospective cross-sectional pilot study of rifaximin dosing for the prevention of recurrent hepatic encephalopathy.

PubMed

Lyon, Kelsey C; Likar, Eric; Martello, Jay L; Regier, Michael

2017-09-01

Standard treatment for hepatic encephalopathy (HE) includes medications that reduce ammonia and bacterial translocation in the gut. Rifaximin can be used off-label for the reduction of overt HE. The study purpose was to determine efficacy of traditional rifaximin dosing (400 mg three times daily) compared with newer dosing (550 mg twice daily) via readmission rates for the prevention of recurrent HE. This was a retrospective, observational, cross-sectional pilot study conducted in a tertiary medical center. A total of 226 patients 18-89 years of age with documentation of HE via ICD-9 code who started rifaximin therapy while inpatient between April 2009 and June 2014 were evaluated. Data collected included rifaximin dosing, other medications used to treat HE, duration of therapy, time to readmission, and various laboratory values. There were no differences in readmission rates at 30 days, 60 days, or 6 months between treatment groups. Additionally, there was no difference in the odds of readmission between the treatment groups (OR = 0.77, 95% CI: [0.201, 4.365], P = 0.718). Patients had a low overall probability of readmission over the observational period. Based on average wholesale price data, the cost for a 9-day supply of rifaximin for the 400-mg dosing regimen is $952.56 versus $605.16 for the 550-mg dosing regimen. The rifaximin 550-mg dosing strategy should be utilized in hospitalized patients for the prevention of recurrent HE as there was no difference in readmission rate or time to readmission between dosing groups. The 550-mg regimen had a lower acquisition cost for a 9-day duration of treatment in the studied institution. © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Quantification of malondialdehyde and 4-hydroxynonenal adducts to lysine residues in native and oxidized human low-density lipoprotein.

PubMed Central

Requena, J R; Fu, M X; Ahmed, M U; Jenkins, A J; Lyons, T J; Baynes, J W; Thorpe, S R

1997-01-01

Malondialdehyde (MDA) and 4-hydroxynonenal (HNE) are major end-products of oxidation of polyunsaturated fatty acids, and are frequently measured as indicators of lipid peroxidation and oxidative stress in vivo. MDA forms Schiff-base adducts with lysine residues and cross-links proteins in vitro; HNE also reacts with lysines, primarily via a Michael addition reaction. We have developed methods using NaBH4 reduction to stabilize these adducts to conditions used for acid hydrolysis of protein, and have prepared reduced forms of lysine-MDA [3-(N epsilon-lysino)propan-1-ol (LM)], the lysine-MDA-lysine iminopropene cross-link [1,3-di(N epsilon-lysino)propane (LML)] and lysine-HNE [3-(N epsilon-lysino)-4-hydroxynonan-l-ol (LHNE)]. Gas chromatography/MS assays have been developed for quantification of the reduced compounds in protein. RNase incubated with MDA or HNE was used as a model for quantification of the adducts by gas chromatography/MS. There was excellent agreement between measurement of MDA bound to RNase as LM and LML, and as thiobarbituric acid-MDA adducts measured by HPLC; these adducts accounted for 70-80% of total lysine loss during the reaction with MDA. LM and LML (0.002-0.12 mmol/ mol of lysine) were also found in freshly isolated low-density lipoprotein (LDL) from healthy subjects. LHNE was measured in RNase treated with HNE, but was not detectable in native LDL. LM, LML and LHNE increased in concert with the formation of conjugated dienes during the copper-catalysed oxidation of LDL, but accounted for modification of < 1% of lysine residues in oxidized LDL. These results are the first report of direct chemical measurement of MDA and HNE adducts to lysine residues in LDL. LM, LML and LHNE should be useful as biomarkers of lipid peroxidative modification of protein and of oxidative stress in vitro and in vivo. PMID:9078279

Simultaneous Detection of Human C-Terminal p53 Isoforms by Single Template Molecularly Imprinted Polymers (MIPs) Coupled with Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)-Based Targeted Proteomics.

PubMed

Jiang, Wenting; Liu, Liang; Chen, Yun

2018-03-06

Abnormal expression of C-terminal p53 isoforms α, β, and γ can cause the development of cancers including breast cancer. To date, much evidence has demonstrated that these isoforms can differentially regulate target genes and modulate their expression. Thus, quantification of individual isoforms may help to link clinical outcome to p53 status and to improve cancer patient treatment. However, there are few studies on accurate determination of p53 isoforms, probably due to sequence homology of these isoforms and also their low abundance. In this study, a targeted proteomics assay combining molecularly imprinted polymers (MIPs) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed for simultaneous quantification of C-terminal p53 isoforms. Isoform-specific surrogate peptides (i.e., KPLDGEYFTLQIR (peptide-α) for isoform α, KPLDGEYFTLQDQTSFQK (peptide-β) for isoform β, and KPLDGEYFTLQMLLDLR (peptide-γ) for isoform γ) were first selected and used in both MIPs enrichment and mass spectrometric detection. The common sequence KPLDGEYFTLQ of these three surrogate peptides was used as single template in MIPs. In addition to optimization of imprinting conditions and characterization of the prepared MIPs, binding affinity and cross-reactivity of the MIPs for each surrogate peptide were also evaluated. As a result, a LOQ of 5 nM was achieved, which was >15-fold more sensitive than that without MIPs. Finally, the assay was validated and applied to simultaneous quantitative analysis of C-terminal p53 isoforms α, β, and γ in several human breast cell lines (i.e., MCF-10A normal cells, MCF-7 and MDA-MB-231 cancer cells, and drug-resistant MCF-7/ADR cancer cells). This study is among the first to employ single template MIPs and cross-reactivity phenomenon to select isoform-specific surrogate peptides and enable simultaneous quantification of protein isoforms in LC-MS/MS-based targeted proteomics.

Development of a high stability pointing mechanism for wide application

NASA Technical Reports Server (NTRS)

Brunnen, A. J. D.; Bentall, R. H.

1982-01-01

A recurrent requirement of spaceborne instruments and communications equipment is that of accurate pointing. This need is recognizable in such diverse applications as Star Sensor trimming, Momentum Wheel gimballing, in-orbit adjustment or alignment of equipment, inter-satellite communication and Antenna Pointing. A pointing mechanism of novel design having several advantages over the more conventional gimbal, centre-pivoted, or cross axis pointing concepts is described.

A recurrence matrix method for the analysis of longitudinal and torsional vibrations in non-uniform multibranch beams with variable boundary conditions

NASA Technical Reports Server (NTRS)

Davis, R. B.; Stephens, M. V.

1974-01-01

An approximate method for calculating the longitudinal and torsional natural frequencies and associated modal data of a beamlike, variable cross section multibranch structure is presented. The procedure described is the numerical integration of the first order differential equations that characterize the beam element in longitudinal motion and that satisfy the appropriate boundary conditions.

Sciatic neurosteatosis: Relationship with age, gender, obesity and height.

PubMed

Ratner, Shayna; Khwaja, Raamis; Zhang, Lihua; Xi, Yin; Dessouky, Riham; Rubin, Craig; Chhabra, Avneesh

2018-04-01

To evaluate inter-reader performance for cross-sectional area and fat quantification of bilateral sciatic nerves on MRI and assess correlations with anthropometrics. In this IRB-approved, HIPPA-compliant study, three readers performed a cross-sectional analysis of 3T lumbosacral plexus MRIs over an 18-month period. Image slices were evaluated at two levels (A and B). The sciatic nerve was outlined using a free hand region of interest tool on PACS. Proton-density fat fraction (FF) and cross-sectional areas were recorded. Inter-reader agreement was assessed using intra-class correlation coefficient (ICC). Spearman correlation coefficients were used for correlations with age, BMI and height and Wilcoxon rank sum test was used to assess gender differences. A total of 67 patients were included in this study with male to female ratio of 1:1. Inter-reader agreement was good to excellent for FF measurements at both levels (ICC=0.71-0.90) and poor for sciatic nerve areas (ICC=0.08-0.27). Positive correlations of sciatic FF and area were seen with age (p value<0.05). Males had significantly higher sciatic intraneural fat than females (p<0.05). Fat quantification MRI is highly reproducible with significant positive correlations of sciatic FF and area with age, which may have implications for MRI diagnosis of sciatic neuropathy. • MR proton density fat fraction is highly reproducible at multiple levels. • Sciatic intraneural fat is positively correlated with increasing age (p < 0.05). • Positive correlations exist between bilateral sciatic nerve areas and age (p < 0.05). • Males had significantly higher sciatic intraneural fat than females (p < 0.05).

Determination of chlorpropham (CIPC) residues, in the concrete flooring of potato stores, using quantitative (HPLC UV/VIS) and qualitative (GCMS) methods.

PubMed

Douglas, Leisa; MacKinnon, Gillian; Cook, Gordon; Duncan, Harry; Briddon, Adrian; Seamark, Steven

2018-03-01

Isopropyl-N-(3-chlorophenyl) carbamate (CIPC, common name Chlorpropham) is commonly used for post-harvest sprout inhibition in stored potatoes. It is applied as a thermal fog which results in loss to the fabric of the store and the atmosphere. Recently, there have been concerns in the United Kingdom because of cross contamination of other crop commodities that were stored in buildings with a history of CIPC usage. This cross contamination may have occurred because of retained residues in the fabric of the stores. The retention of CIPC in concrete is poorly understood; therefore the requirement for a robust analytical method for the detection and quantification of CIPC in concrete is a critical first step in tackling this problem. A method using High-Performance Liquid Chromatography with ultraviolet detection (HPLC UV/VIS) was validated. CIPC recoveries at three concentration levels (0.4, 4.0 and 40.0 μg g -1 ) were in the range of 90.7-97.0% with relative standard deviations between 2.14 and 3.01%. The limits of detection and quantification were 0.03 and 0.1 μg g -1 , respectively. This study confirmed that CIPC was persistent in concrete to a depth of 4 cm, with >90% within the top 1 cm of the flooring. Copyright © 2017 Elsevier Ltd. All rights reserved.

A method to separate and quantify the effects of indentation size, residual stress and plastic damage when mapping properties using instrumented indentation

NASA Astrophysics Data System (ADS)

Hou, X. D.; Jennett, N. M.

2017-11-01

Instrumented indentation is a convenient and increasingly rapid method of high resolution mapping of surface properties. There is, however, significant untapped potential for the quantification of these properties, which is only possible by solving a number of serious issues that affect the absolute values for mechanical properties obtained from small indentations. The three most pressing currently are the quantification of: the indentation size effect (ISE), residual stress, and pile-up and sink-in—which is itself affected by residual stress and ISE. Hardness based indentation mapping is unable to distinguish these effects. We describe a procedure that uses an elastic modulus as an internal reference and combines the information available from an indentation modulus map, a hardness map, and a determination of the ISE coefficient (using self-similar geometry indentation) to correct for the effects of stress, pile up and the indentation size effect, to leave a quantified map of plastic damage and grain refinement hardening in a surface. This procedure is used to map the residual stress in a cross-section of the machined surface of a previously stress free metal. The effect of surface grinding is compared to milling and is shown to cause different amounts of work hardening, increase in residual stress, and surface grain size reduction. The potential use of this procedure for mapping coatings in cross-section is discussed.

Rapid steroid hormone quantification for congenital adrenal hyperplasia (CAH) in dried blood spots using UPLC liquid chromatography-tandem mass spectrometry.

PubMed

Janzen, Nils; Sander, Stefanie; Terhardt, Michael; Steuerwald, Ulrike; Peter, Michael; Das, Anibh M; Sander, Johannes

2011-12-11

Newborn screening for congenital adrenal hyperplasia (CAH) is usually done by quantifying 17α-hydroxyprogesterone using immunoassay. However, this test produces high rates of false positive results caused by cross reacting steroids. Therefore we have developed a selective and specific method with a short run time (1.25 min) for quantification of 17α-hydroxyprogesterone, 21-deoxycortisol, 11-deoxycortisol, 11-deoxycorticosterone and cortisol from dried blood spots. The extraction procedure is very simple and steroid separation is ensured on a BEH C18 column and an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Analysis was done in positive ionization mode (ESI+) and recorded in multiple reaction monitoring mode (MRM). The method gave linear results for all steroids over a range of 5-200 (cortisol: 12.5-500)nmol/L with coefficients of regression >0.992. Absolute recovery was >64.1%. Across the analytical range the inter-assay coefficient of variation (CV) was <3%. Newborn blood samples of patients with confirmed 21-CAH and 11-CAH could clearly be distinguished from samples of unaffected newborns falsely positive on immunoassay. The method is not influenced by cross reactions as found on immunoassay. Analysis of dried blood spots shows that this method is sensitive and fast enough to allow rapid analysis and can therefore improve the newborn screening program. Copyright © 2011 Elsevier Inc. All rights reserved.

Uncertainty Quantification Techniques of SCALE/TSUNAMI

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

Rearden, Bradley T; Mueller, Don

2011-01-01

The Standardized Computer Analysis for Licensing Evaluation (SCALE) code system developed at Oak Ridge National Laboratory (ORNL) includes Tools for Sensitivity and Uncertainty Analysis Methodology Implementation (TSUNAMI). The TSUNAMI code suite can quantify the predicted change in system responses, such as k{sub eff}, reactivity differences, or ratios of fluxes or reaction rates, due to changes in the energy-dependent, nuclide-reaction-specific cross-section data. Where uncertainties in the neutron cross-section data are available, the sensitivity of the system to the cross-section data can be applied to propagate the uncertainties in the cross-section data to an uncertainty in the system response. Uncertainty quantification ismore » useful for identifying potential sources of computational biases and highlighting parameters important to code validation. Traditional validation techniques often examine one or more average physical parameters to characterize a system and identify applicable benchmark experiments. However, with TSUNAMI correlation coefficients are developed by propagating the uncertainties in neutron cross-section data to uncertainties in the computed responses for experiments and safety applications through sensitivity coefficients. The bias in the experiments, as a function of their correlation coefficient with the intended application, is extrapolated to predict the bias and bias uncertainty in the application through trending analysis or generalized linear least squares techniques, often referred to as 'data adjustment.' Even with advanced tools to identify benchmark experiments, analysts occasionally find that the application models include some feature or material for which adequately similar benchmark experiments do not exist to support validation. For example, a criticality safety analyst may want to take credit for the presence of fission products in spent nuclear fuel. In such cases, analysts sometimes rely on 'expert judgment' to select an additional administrative margin to account for gap in the validation data or to conclude that the impact on the calculated bias and bias uncertainty is negligible. As a result of advances in computer programs and the evolution of cross-section covariance data, analysts can use the sensitivity and uncertainty analysis tools in the TSUNAMI codes to estimate the potential impact on the application-specific bias and bias uncertainty resulting from nuclides not represented in available benchmark experiments. This paper presents the application of methods described in a companion paper.« less

Impact of Nuclear Data Uncertainties on Advanced Fuel Cycles and their Irradiated Fuel - a Comparison between Libraries

NASA Astrophysics Data System (ADS)

Díez, C. J.; Cabellos, O.; Martínez, J. S.

2014-04-01

The uncertainties on the isotopic composition throughout the burnup due to the nuclear data uncertainties are analysed. The different sources of uncertainties: decay data, fission yield and cross sections; are propagated individually, and their effect assessed. Two applications are studied: EFIT (an ADS-like reactor) and ESFR (Sodium Fast Reactor). The impact of the uncertainties on cross sections provided by the EAF-2010, SCALE6.1 and COMMARA-2.0 libraries are compared. These Uncertainty Quantification (UQ) studies have been carried out with a Monte Carlo sampling approach implemented in the depletion/activation code ACAB. Such implementation has been improved to overcome depletion/activation problems with variations of the neutron spectrum.

Clinical review: improving the measurement of serum thyroglobulin with mass spectrometry.

PubMed

Hoofnagle, Andrew N; Roth, Mara Y

2013-04-01

Serum thyroglobulin (Tg) measurements are central to the management of patients treated for differentiated thyroid carcinoma. For decades, Tg measurements have relied on methods that are subject to interference by commonly found substances in human serum and plasma, such as Tg autoantibodies. As a result, many patients need additional imaging studies to rule out cancer persistence or recurrence that could be avoided with more sensitive and specific testing methods. The aims of this review are to: 1) briefly review the interferences common to Tg immunoassays; 2) introduce readers to liquid chromatography-tandem mass spectrometry as a method for quantifying proteins in human serum/plasma; and 3) discuss the potential benefits and limitations of the method in the quantification of serum Tg. Mass spectrometric methods have traditionally lacked the sensitivity, robustness, and throughput to be useful clinical assays. These methods failed to meet the necessary clinical benchmarks due to the nature of the mass spectrometry workflow and instrumentation. Over the past few years, there have been major advances in reagents, automation, and instrumentation for the quantification of proteins using mass spectrometry. More recently, methods using mass spectrometry to detect and quantify Tg have been developed and are of sufficient quality to be used in the management of patients. Novel serum Tg assays that use mass spectrometry may avoid the issue of autoantibody interference and other problems with currently available immunoassays for Tg. Prospective studies are needed to fully understand the potential benefits of novel Tg assays to patients and care providers.

[Clinical value of para-recurrent laryngeal nerve lymphadenectomy for middle thoracic esophageal squamous cell carcinoma].

PubMed

Wang, Zhen; Liu, Shuoyan

2015-09-01

To analyze the pattern of lymphatic metastasis in middle thoracic esophageal squamous cell carcinoma (ESCC) with different T staging and to investigate the clinical value of para-recurrent laryngeal nerve lymphadenectomy. Clinicopathological data of 717 patients with middle thoracic ESCC undergoing Mckeown esophagectomy plus three-field lymph node dissection in Fujian Provincial Hospital from January 1999 to December 2007 were analyzed retrospectively. Lymph node metastatic rates of different T stages were calculated. Clinical value of each station lymphadenectomy, especially the para-recurrent laryngeal nerve lymphadenectomy, was evaluated by the efficacy index (EI, cross product of one station metastatic rate and 5-year survival of patient with positive lymph nodes of above station). Rates of lymph node metastasis were 29.0% (18/62), 61.1% (91/149) and 64.8% (328/506) in stage T1, T2 and T3 patients respectively. Despite T staging, metastatic rates of right para-recurrent laryngeal nerve lymph node (rRLN LN) were 21.0% (13/62), 28.9% (43/149) and 29.4% (149/506) in stage T1, T2 and T3 patients respectively, which was the most common among all lymph node stations. Metastatic rates of left para-recurrent laryngeal nerve lymph node (lRLN LN) were the second, with 8.1% (5/62), 17.4% (26/149) and 24.7% (125/506) in stage T1, T2, T3 patients respectively. Follow-up period lasted more than 5 years. The 5-year survival rates of positive rRLN LN were 53.8%, 39.5% and 32.2% in stage T1, T2 and T3 patients respectively, whose EI values were 11.3, 11.4 and 9.5 respectively. The 5-year survival rates of positive lRLN LN were 40.0%, 34.6% and 40.0% in stage T1, T2 and T3 patients respectively, whose EI values were 3.2, 6.0 and 9.9 respectively. Bilateral para-recurrent laryngeal nerve lymph nodes are the common sites of metastasis in middle thoracic esophageal squamous cell carcinoma. Right para-recurrent laryngeal nerve lymphadenectomy is of high clinical value despite the T staging. Left para-recurrent laryngeal nerve lymphadenectomy has better efficacy in stage T2 and T3 patients, but is limited in stage T1 patients.

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

PubMed

Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

[Association between suicidal behaviour and cyclothymic temperament in patients with recurrent depressive disorder].

PubMed

Mechri, Anwar; Kerkeni, Neila; Hassine, Rym; Khalfaoui, Sana; Touati, Imen; Bacha, Miloud

2013-01-01

Suicidal behaviour is a major health problem, particularly among patients with depressive disorders. To determine the frequency of suicidal behavior among sample of patients with recurrent depressive disorder and to explore the relationship between suicidal behavior and cyclothymic temperament in these patients. This was a cross-sectional study bearing on 98 patients (43 men and 55 women, mean age of 46.8 ± 9.9 years) followed for recurrent depressive disorder according to the criteria of DSM-IV recruited during partial or complete recovery interval. Information about suicidal behavior was collected from medical records. Cyclothymic temperament (CT) was assessed using the cyclothymic subscale (21 items). Patients who had scores above the threshold score of 10 and were considered as cyclothymic (CT+ group) and other patients were considered non-cyclothymic (CT- group). History of suicide attempts were reported in 22.4% of patients. The mean number of previous suicide attempts was significantly higher among patients in the TC+ group (0.7 ± 1.4) versus 0.2 ± 0.6 for patients in the TC- group (p=0.01). Recurrent thoughts of death and suicide attempts in the last depressive episode, were significantly higher in the CT+ group, with a 57.5% versus 24.6% in the CT- group, (p=0.001) and 33.3% versus 10.7% in the TC- group (p=0.006). A multivariate analysis retained the TC as an independent factor associated with suicidal behavior, with two other factors: the young age of patients and the frequency of previous hospitalizations. Our findings the frequency of suicidal behavior and suggest the involvement of CT in the increased risk of suicide among patients with recurrent depressive disorder.

Hope and mood changes throughout the primary brain tumor illness trajectory

PubMed Central

Acquaye, Alvina A.; Lin, Lin; Vera-Bolanos, Elizabeth; Gilbert, Mark R.; Armstrong, Terri S.

2016-01-01

Background The ambiguity of defining hope impacts the level of readiness faced by health care professionals treating patients with glioma, a disease with unpredictable outcomes. This study describes the report of hope and the relationship between hope and mood in adult brain tumor patients at various points in the illness trajectory. Methods This was a cross-sectional study with data collection including use of the Herth Hope Index (HHI), the Profile of Mood States-Short Form (POMS-SF), and clinical information. Descriptive statistics were used to report sample characteristics. Spearman's rho and Mann-Whitney tests were used to compare and differentiate scores. Results Eighty-two patients ranging in age from 22 to 78 years (median, 44.5 y) participated in the study. Patients were primarily male (57.3%), married (76.8%), and had a high-grade glioma (35.4%). Nearly half had recurrence, and more than 20% were on active treatment. The overall HHI total score for the sample was 41.32 (range: 13–48). Patients with recurrence had a lower HHI interconnectedness (median = 14.00) score and higher total mood disturbance (median = 14.00) compared with patients without recurrence (median = 15.00 and median = 0.00, respectively; P < .05). All negative mood states on the POMS-SF were negatively correlated with HHI subscales. Conclusions Overall, patients reporting more hope also reported less overall mood disturbance As expected, patients with tumor recurrence reported lower hope and higher mood disturbance than those who were newly diagnosed or without recurrence. Targeting interventions specifically tailored to an individual's needs for improvement in quality of life throughout the disease course may include measures to address hope in order to facilitate positive coping strategies. PMID:26109686

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

PubMed

Renault, Victor; Tost, Jörg; Pichon, Fabien; Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

2017-01-01

Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. aCNViewer@cephb.fr.

Variable carbon losses from recurrent fires in drained tropical peatlands.

PubMed

Konecny, Kristina; Ballhorn, Uwe; Navratil, Peter; Jubanski, Juilson; Page, Susan E; Tansey, Kevin; Hooijer, Aljosja; Vernimmen, Ronald; Siegert, Florian

2016-04-01

Tropical peatland fires play a significant role in the context of global warming through emissions of substantial amounts of greenhouse gases. However, the state of knowledge on carbon loss from these fires is still poorly developed with few studies reporting the associated mass of peat consumed. Furthermore, spatial and temporal variations in burn depth have not been previously quantified. This study presents the first spatially explicit investigation of fire-driven tropical peat loss and its variability. An extensive airborne Light Detection and Ranging data set was used to develop a prefire peat surface modelling methodology, enabling the spatially differentiated quantification of burned area depth over the entire burned area. We observe a strong interdependence between burned area depth, fire frequency and distance to drainage canals. For the first time, we show that relative burned area depth decreases over the first four fire events and is constant thereafter. Based on our results, we revise existing peat and carbon loss estimates for recurrent fires in drained tropical peatlands. We suggest values for the dry mass of peat fuel consumed that are 206 t ha(-1) for initial fires, reducing to 115 t ha(-1) for second, 69 t ha(-1) for third and 23 t ha(-1) for successive fires, which are 58-7% of the current IPCC Tier 1 default value for all fires. In our study area, this results in carbon losses of 114, 64, 38 and 13 t C ha(-1) for first to fourth fires, respectively. Furthermore, we show that with increasing proximity to drainage canals both burned area depth and the probability of recurrent fires increase and present equations explaining burned area depth as a function of distance to drainage canal. This improved knowledge enables a more accurate approach to emissions accounting and will support IPCC Tier 2 reporting of fire emissions. © 2015 John Wiley & Sons Ltd.

Deciphering membrane-associated molecular processes in target tissue of autoimmune uveitis by label-free quantitative mass spectrometry.

PubMed

Hauck, Stefanie M; Dietter, Johannes; Kramer, Roxane L; Hofmaier, Florian; Zipplies, Johanna K; Amann, Barbara; Feuchtinger, Annette; Deeg, Cornelia A; Ueffing, Marius

2010-10-01

Autoimmune uveitis is a blinding disease presenting with autoantibodies against eye-specific proteins as well as autoagressive T cells invading and attacking the immune-privileged target tissue retina. The molecular events enabling T cells to invade and attack the tissue have remained elusive. Changes in membrane protein expression patterns between diseased and healthy stages are especially interesting because initiating events of disease will most likely occur at membranes. Since disease progression is accompanied with a break-down of the blood-retinal barrier, serum-derived proteins mask the potential target tissue-related changes. To overcome this limitation, we used membrane-enriched fractions derived from retinas of the only available spontaneous animal model for the disease equine recurrent uveitis, and compared expression levels by a label-free LC-MSMS-based strategy to healthy control samples. We could readily identify a total of 893 equine proteins with 57% attributed to the Gene Ontology project term "membrane." Of these, 179 proteins were found differentially expressed in equine recurrent uveitis tissue. Pathway enrichment analyses indicated an increase in proteins related to antigen processing and presentation, TNF receptor signaling, integrin cell surface interactions and focal adhesions. Additionally, loss of retina-specific proteins reflecting decrease of vision was observed as well as an increase in Müller glial cell-specific proteins indicating glial reactivity. Selected protein candidates (caveolin 1, integrin alpha 1 and focal adhesion kinase) were validated by immunohistochemistry and tissue staining pattern pointed to a significant increase of these proteins at the level of the outer limiting membrane which is part of the outer blood-retinal barrier. Taken together, the membrane enrichment in combination with LC-MSMS-based label-free quantification greatly increased the sensitivity of the comparative tissue profiling and resulted in detection of novel molecular pathways related to equine recurrent uveitis.

Detection and Quantification of Viable and Nonviable Trypanosoma cruzi Parasites by a Propidium Monoazide Real-Time Polymerase Chain Reaction Assay

PubMed Central

Cancino-Faure, Beatriz; Fisa, Roser; Alcover, M. Magdalena; Jimenez-Marco, Teresa; Riera, Cristina

2016-01-01

Molecular techniques based on real-time polymerase chain reaction (qPCR) allow the detection and quantification of DNA but are unable to distinguish between signals from dead or live cells. Because of the lack of simple techniques to differentiate between viable and nonviable cells, the aim of this study was to optimize and evaluate a straightforward test based on propidium monoazide (PMA) dye action combined with a qPCR assay (PMA-qPCR) for the selective quantification of viable/nonviable epimastigotes of Trypanosoma cruzi. PMA has the ability to penetrate the plasma membrane of dead cells and covalently cross-link to the DNA during exposure to bright visible light, thereby inhibiting PCR amplification. Different concentrations of PMA (50–200 μM) and epimastigotes of the Maracay strain of T. cruzi (1 × 105–10 parasites/mL) were assayed; viable and nonviable parasites were tested and quantified by qPCR with a TaqMan probe specific for T. cruzi. In the PMA-qPCR assay optimized at 100 μM PMA, a significant qPCR signal reduction was observed in the nonviable versus viable epimastigotes treated with PMA, with a mean signal reduction of 2.5 logarithm units and a percentage of signal reduction > 98%, in all concentrations of parasites assayed. This signal reduction was also observed when PMA-qPCR was applied to a mixture of live/dead parasites, which allowed the detection of live cells, except when the concentration of live parasites was low (10 parasites/mL). The PMA-qPCR developed allows differentiation between viable and nonviable epimastigotes of T. cruzi and could thus be a potential method of parasite viability assessment and quantification. PMID:27139452

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data*

PubMed Central

Mitchell, Christopher J.; Kim, Min-Sik; Na, Chan Hyun; Pandey, Akhilesh

2016-01-01

Quantitative mass spectrometry data necessitates an analytical pipeline that captures the accuracy and comprehensiveness of the experiments. Currently, data analysis is often coupled to specific software packages, which restricts the analysis to a given workflow and precludes a more thorough characterization of the data by other complementary tools. To address this, we have developed PyQuant, a cross-platform mass spectrometry data quantification application that is compatible with existing frameworks and can be used as a stand-alone quantification tool. PyQuant supports most types of quantitative mass spectrometry data including SILAC, NeuCode, 15N, 13C, or 18O and chemical methods such as iTRAQ or TMT and provides the option of adding custom labeling strategies. In addition, PyQuant can perform specialized analyses such as quantifying isotopically labeled samples where the label has been metabolized into other amino acids and targeted quantification of selected ions independent of spectral assignment. PyQuant is capable of quantifying search results from popular proteomic frameworks such as MaxQuant, Proteome Discoverer, and the Trans-Proteomic Pipeline in addition to several standalone search engines. We have found that PyQuant routinely quantifies a greater proportion of spectral assignments, with increases ranging from 25–45% in this study. Finally, PyQuant is capable of complementing spectral assignments between replicates to quantify ions missed because of lack of MS/MS fragmentation or that were omitted because of issues such as spectra quality or false discovery rates. This results in an increase of biologically useful data available for interpretation. In summary, PyQuant is a flexible mass spectrometry data quantification platform that is capable of interfacing with a variety of existing formats and is highly customizable, which permits easy configuration for custom analysis. PMID:27231314

Toward automatic segmentation and quantification of tumor and stroma in whole-slide images of H and E stained rectal carcinomas

NASA Astrophysics Data System (ADS)

Geessink, Oscar G. F.; Baidoshvili, Alexi; Freling, Gerard; Klaase, Joost M.; Slump, Cornelis H.; van der Heijden, Ferdinand

2015-03-01

Visual estimation of tumor and stroma proportions in microscopy images yields a strong, Tumor-(lymph)Node- Metastasis (TNM) classification-independent predictor for patient survival in colorectal cancer. Therefore, it is also a potent (contra)indicator for adjuvant chemotherapy. However, quantification of tumor and stroma through visual estimation is highly subject to intra- and inter-observer variability. The aim of this study is to develop and clinically validate a method for objective quantification of tumor and stroma in standard hematoxylin and eosin (H and E) stained microscopy slides of rectal carcinomas. A tissue segmentation algorithm, based on supervised machine learning and pixel classification, was developed, trained and validated using histological slides that were prepared from surgically excised rectal carcinomas in patients who had not received neoadjuvant chemotherapy and/or radiotherapy. Whole-slide scanning was performed at 20× magnification. A total of 40 images (4 million pixels each) were extracted from 20 whole-slide images at sites showing various relative proportions of tumor and stroma. Experienced pathologists provided detailed annotations for every extracted image. The performance of the algorithm was evaluated using cross-validation by testing on 1 image at a time while using the other 39 images for training. The total classification error of the algorithm was 9.4% (SD = 3.2%). Compared to visual estimation by pathologists, the algorithm was 7.3 times (P = 0.033) more accurate in quantifying tissues, also showing 60% less variability. Automatic tissue quantification was shown to be both reliable and practicable. We ultimately intend to facilitate refined prognostic stratification of (colo)rectal cancer patients and enable better personalized treatment.

Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids.

PubMed

Li, Zhao; Liu, Yong; Wei, Qingquan; Liu, Yuanjie; Liu, Wenwen; Zhang, Xuelian; Yu, Yude

2016-01-01

Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm(2) area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10(-1) to 4 × 10(-3) copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings.

Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids

PubMed Central

Li, Zhao; Liu, Yong; Wei, Qingquan; Liu, Yuanjie; Liu, Wenwen; Zhang, Xuelian; Yu, Yude

2016-01-01

Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm2 area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10-1 to 4 × 10-3 copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings. PMID:27074005

Prolonged remission from hepatic encephalopathy with rifaximin: results of a placebo crossover analysis

PubMed Central

Bajaj, J S; Barrett, A C; Bortey, E; Paterson, C; Forbes, W P

2015-01-01

Background Rifaximin therapy reduced risk of hepatic encephalopathy (HE) recurrence and HE-related hospitalisations during a 6-month, randomised, placebo-controlled trial (RCT) and a 24-month open-label maintenance (OLM) study. However, the impact of crossover from placebo to rifaximin therapy is unclear. Aim To study the impact of crossing over from placebo to rifaximin treatment on breakthrough HE and hospitalisation rates using a within-subjects design. Methods Adults with cirrhosis and history of overt HE episodes, currently in HE remission, received placebo during the RCT and crossed over to rifaximin 550 mg twice daily during the OLM study. Rate of breakthrough overt HE episodes, hospitalisations and incidence and rate of adverse events (AEs) were analysed during RCT and first 6 months of OLM. Results Of 82 patients randomised to placebo in the RCT who crossed over to the OLM study, 39 experienced an HE episode during the RCT compared with 14 during the OLM study (P < 0.0001). Significantly lower rates of HE events were observed with rifaximin treatment compared with placebo treatment (P < 0.0001). Rates of HE-related hospitalisation were numerically lower during rifaximin treatment compared with placebo treatment, although not significant. Rates of most common AEs, serious AEs and infection-related AEs were similar between the two treatments. Conclusions This analysis confirms the repeatability of results from the RCT on safety and efficacy of rifaximin 550 mg twice daily in reducing the risk of hepatic encephalopathy recurrence, and suggests these findings are translatable outside of a rigorous, controlled trial setting. PMID:25339518

Lung functions among patients with pulmonary tuberculosis in Dar es Salaam - a cross-sectional study.

PubMed

Manji, Mohamed; Shayo, Grace; Mamuya, Simon; Mpembeni, Rose; Jusabani, Ahmed; Mugusi, Ferdinand

2016-04-23

Approximately 40-60 % of patients remain sufferers of sequela of obstructive, restrictive or mixed patterns of lung disease despite treatment for pulmonary tuberculosis (PTB). The prevalence of these abnormalities in Tanzania remains unknown. A descriptive cross-sectional study was carried out among 501 patients with PTB who had completed at least 20 weeks of treatment. These underwent spirometry and their lung functions were classified as normal or abnormal (obstructive, restrictive or mixed). Logistic regression models were used to explore factors associated with abnormal lung functions. Abnormal lung functions were present in 371 (74 %) patients. There were 210 (42 %) patients with obstructive, 65 (13 %) patients with restrictive and 96 (19 %) patients with mixed patterns respectively. Significant factors associated with abnormal lung functions included recurrent PTB (Adj OR 2.8, CI 1.274 - 6.106), Human Immunodeficiency Virus (HIV) negative status (Adj OR 1.7, CI 1.055 - 2.583), age more than 40 years (Adj OR 1.7, CI 1.080 - 2.804) and male sex (Adj OR 1.7, CI 1.123 - 2.614). The prevalence of abnormal lung functions is high and it is associated with male sex, age older than 40 years, recurrent PTB and HIV negative status.

Polyunsaturated Fatty Acids and Recurrent Mood Disorders: Phenomenology, Mechanisms, and Clinical Application

PubMed Central

Messamore, Erik; Almeida, Daniel M.; Jandacek, Ronald J.; McNamara, Robert K.

2017-01-01

A body of evidence has implicated dietary deficiency in omega-3 polyunsaturated fatty acids (n-3 PUFA), including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), in the pathophysiology and etiology of recurrent mood disorders including major depressive disorder (MDD) and bipolar disorder. Cross-national and cross-sectional evidence suggests that greater habitual intake of n-3 PUFA is associated with reduced risk for developing mood symptoms. Meta-analyses provide strong evidence that patients with mood disorders exhibit low blood n-3 PUFA levels which are associated with increased risk for the initial development of mood symptoms in response to inflammation. While the etiology of this n-3 PUFA deficit may be multifactorial, n-3 PUFA supplementation is sufficient to correct this deficit and may also have antidepressant effects. Rodent studies suggest that n-3 PUFA deficiency during perinatal development can recapitulate key neuropathological, neurochemical, and behavioral features associated with mood disorders. Clinical neuroimaging studies suggest that low n-3 PUFA biostatus is associated with abnormalities in cortical structure and function also observed in mood disorders. Collectively, these findings implicate dietary n-3 PUFA insufficiency, particularly during development, in the pathophysiology of mood dysregulation, and support implementation of routine screening for and treatment of n-3 PUFA deficiency in patients with mood disorders. PMID:28069365

Relative phase asynchrony and long-range correlation of long-term solar magnetic activity

NASA Astrophysics Data System (ADS)

Deng, Linhua

2017-07-01

Statistical signal processing is one of the most important tasks in a large amount of areas of scientific studies, such as astrophysics, geophysics, and space physics. Phase recurrence analysis and long-range persistence are the two dynamical structures of the underlying processes for the given natural phenomenon. Linear and nonlinear time series analysis approaches (cross-correlation analysis, cross-recurrence plot, wavelet coherent transform, and Hurst analysis) are combined to investigate the relative phase interconnection and long-range correlation between solar activity and geomagnetic activity for the time interval from 1932 January to 2017 January. The following prominent results are found: (1) geomagnetic activity lags behind sunspot numbers with a phase shift of 21 months, and they have a high level of asynchronous behavior; (2) their relative phase interconnections are in phase for the periodic scales during 8-16 years, but have a mixing behavior for the periodic belts below 8 years; (3) both sunspot numbers and geomagnetic activity can not be regarded as a stochastic phenomenon because their dynamical behaviors display a long-term correlation and a fractal nature. We believe that the presented conclusions could provide further information on understanding the dynamical coupling of solar dynamo process with geomagnetic activity variation, and the crucial role of solar and geomagnetic activity in the long-term climate change.

Frontal-temporal synchronization of EEG signals quantified by order patterns cross recurrence analysis during propofol anesthesia.

PubMed

Shalbaf, Reza; Behnam, Hamid; Sleigh, Jamie W; Steyn-Ross, D Alistair; Steyn-Ross, Moira L

2015-05-01

Characterizing brain dynamics during anesthesia is a main current challenge in anesthesia study. Several single channel electroencephalogram (EEG)-based commercial monitors like the Bispectral index (BIS) have suggested to examine EEG signal. But, the BIS index has obtained numerous critiques. In this study, we evaluate the concentration-dependent effect of the propofol on long-range frontal-temporal synchronization of EEG signals collected from eight subjects during a controlled induction and recovery design. We used order patterns cross recurrence plot and provide an index named order pattern laminarity (OPL) to assess changes in neuronal synchronization as the mechanism forming the foundation of conscious perception. The prediction probability of 0.9 and 0.84 for OPL and BIS specified that the OPL index correlated more strongly with effect-site propofol concentration. Also, our new index makes faster reaction to transients in EEG recordings based on pharmacokinetic and pharmacodynamic model parameters and demonstrates less variability at the point of loss of consciousness (standard deviation of 0.04 for OPL compared with 0.09 for BIS index). The result show that the OPL index can estimate anesthetic state of patient more efficiently than the BIS index in lightly sedated state with more tolerant of artifacts.

Balance ability measured with the Berg balance scale: a determinant of fall history in community-dwelling adults with leg amputation.

PubMed

Wong, Christopher Kevin; Chen, Christine C; Blackwell, Wren M; Rahal, Rana T; Benoy, Stephany A

2015-01-01

Falls are common among adults with leg amputations and associated with balance confidence. But subjective confidence is not equivalent with physical ability. This multivariate analyses of community-dwelling adults with leg amputations examined relationships among individual characteristics, falls, balance ability and balance confidence. Cross-sectional study. Community-dwelling adults with leg amputations recruited from a support group and prosthetic clinic. Subjects provided self-reported medical/fall history, prosthetic functional use, and Activities-specific Balance Confidence (ABC) questionnaire data. Balance ability was assessed with the Berg Balance Scale (BBS). Fall incidence was categorized as any fall (one or more) and recurrent falls (more than one). Multivariate logistic regression analyzed relationships within the two fall categories. Cross tabulations and ANOVA analyzed differences among subcategories. Fifty-four subjects (mean age 56.8) with various etiologies, amputation levels, and balance abilities participated. 53.7% had any fall; 25.9% had recurrent falls. Models for both fall categories correctly classified fall history in > 70% of subjects with combinations of the variables ABC, BBS, body-mass-index, and amputation level. Falls occurred regardless of clinical characteristics. Total BBS and select item scores were independent determinants of fall history. Unlike other balance-impaired populations, adults with leg amputation and better balance ability had greater odds of falling.

Dilution jet mixing program, phase 3

NASA Technical Reports Server (NTRS)

Srinivasan, R.; Coleman, E.; Myers, G.; White, C.

1985-01-01

The main objectives for the NASA Jet Mixing Phase 3 program were: extension of the data base on the mixing of single sided rows of jets in a confined cross flow to discrete slots, including streamlined, bluff, and angled injections; quantification of the effects of geometrical and flow parameters on penetration and mixing of multiple rows of jets into a confined flow; investigation of in-line, staggered, and dissimilar hole configurations; and development of empirical correlations for predicting temperature distributions for discrete slots and multiple rows of dilution holes.

Installation Restoration Program. Phase II. Confirmation/Quantification Stage 1 for Nellis Air Force Base, Nevada.

DTIC Science & Technology

1985-08-09

chemicals from the sample, thereby preventing any effects on sample chemistry and cross-contamination of subsequent samples. The laboratory quality...14 Top 3011 4 16 1 Ca 1 ch4DChief ’aquifer (water-ticurinr 16 69 53 i Lrowm clay fo.mation) L 69 1 74 5 . atar oaandand ,ravei from..0.to .750. 74 1 127...significant fraction of the Chemistry Department’s work involves data processing. Mathematical models, based upon analysis of standard solutions or

Segregated Excitatory–Inhibitory Recurrent Subnetworks in Layer 5 of the Rat Frontal Cortex

PubMed Central

Morishima, Mieko; Kobayashi, Kenta; Kato, Shigeki; Kobayashi, Kazuto; Kawaguchi, Yasuo

2017-01-01

Abstract A prominent feature of neocortical pyramidal cells (PCs) is their numerous projections to diverse brain areas. In layer 5 (L5) of the rat frontal cortex, there are 2 major subtypes of PCs that differ in their long-range axonal projections, corticopontine (CPn) cells and crossed corticostriatal (CCS) cells. The outputs of these L5 PCs can be regulated by feedback inhibition from neighboring cortical GABAergic cells. Two major subtypes of GABAergic cells are parvalbumin (PV)-positive and somatostatin (SOM)-positive cells. PV cells have a fast-spiking (FS) firing pattern, while SOM cells have a low threshold spike (LTS) and regular spiking. In this study, we found that the 2 PC subtypes in L5 selectively make recurrent connections with LTS cells. The connection patterns correlated with the morphological and physiological diversity of LTS cells. LTS cells with high input resistance (Ri) exhibited more compact dendrites and more rebound spikes than LTS cells with low Ri, which had vertically elongated dendrites. LTS subgroups differently inhibited the PC subtypes, although FS cells made nonselective connections with both projection subtypes. These results demonstrate a novel recurrent network of inhibitory and projection-specific excitatory neurons within the neocortex. PMID:29045559

On interrelations of recurrences and connectivity trends between stock indices

NASA Astrophysics Data System (ADS)

Goswami, B.; Ambika, G.; Marwan, N.; Kurths, J.

2012-09-01

Financial data has been extensively studied for correlations using Pearson's cross-correlation coefficient ρ as the point of departure. We employ an estimator based on recurrence plots - the correlation of probability of recurrence (CPR) - to analyze connections between nine stock indices spread worldwide. We suggest a slight modification of the CPR approach in order to get more robust results. We examine trends in CPR for an approximately 19-month window moved along the time series and compare them to trends in ρ. Binning CPR into three levels of connectedness (strong, moderate, and weak), we extract the trends in number of connections in each bin over time. We also look at the behavior of CPR during the dot-com bubble by shifting the time series to align their peaks. CPR mainly uncovers that the markets move in and out of periods of strong connectivity erratically, instead of moving monotonically towards increasing global connectivity. This is in contrast to ρ, which gives a picture of ever-increasing correlation. CPR also exhibits that time-shifted markets have high connectivity around the dot-com bubble of 2000. We use significance tests using twin surrogates to interpret all the measures estimated in the study.

[Methods for exposure of recurrent laryngeal nerve in thyroid surgery].

PubMed

Ma, Xiangdong; Han, Xilin; Liu, Tao; Kou, Changhua

2014-10-01

To evaluate different methods to explose recurrent laryngeal nerve (RLN) based on the location of thyroid diseses and anatomic path of the RLN, to avoid the RLN damage in thyroid surgery. A total of 755 cases underwent total lobectomy was studied retrospectively. RLN was explosed in each case. A total of 963 RLN was exposed in 755 cases, among those 658 RLN were exposed by lateral approach, 106 by inferior approach, and 199 by superior approach. It was showed that 694 RLN traveled deep to the inferior throid artery and 119 superficial to the artery, 98 through between two branches of the artery, and 62 with the cross of the nerve branches and the artery branches. Before entering larynx, 578 RLN gave off branches and 385 had no branches. Non-recurrent laryngeal nerves were found in 2 cases. There were 6 cases who presented with hoarseness after thyroidectomy and undergoing reexploration, among them RLN were legated in 4 cases and severed in 2 cases. The anatomic relation of RLN is relatively complicated. Lateral, inferior or superior aproach may be used for exposure of RLN to decrease risks of injury to the nerve.

Practice of Contemporary Dance Promotes Stochastic Postural Control in Aging

PubMed Central

Ferrufino, Lena; Bril, Blandine; Dietrich, Gilles; Nonaka, Tetsushi; Coubard, Olivier A.

2011-01-01

As society ages and the frequency of falls increases, counteracting gait and posture decline is a challenging issue for countries of the developed world. Previous studies have shown that exercise and hazard management help to improve balance and/or decrease the risks for falling in normal aging. Motor activity based on motor-skill learning, particularly dance, can also benefit balance and decreases falls with age. Recent studies have suggested that older dancers have better balance, posture, or gait than non-dancers. Additionally, clinical or laboratory measures have shown improvements in some aspects of balance after dance interventions in elderly trainees. This study examined the impact of contemporary dance (CD) and of fall prevention (FP) programs on postural control of older adults. Posturography of quiet upright stance was performed in 41 participants aged 59–86 years before and after 4.4-month training in either CD or FP once a week. Though classical statistic scores failed to show any effect, dynamic analyses of the center-of-pressure displacements revealed significant changes after training. Specifically, practice of CD enhanced the critical time interval in diffusion analysis, and reduced recurrence and mathematical stability in recurrence quantification analysis, whereas practice of FP induced or tended to induce the reverse patterns. Such effects were obtained only in the eyes open condition. We suggest that CD training based on motor improvisation favored stochastic posture inducing plasticity in motor control, while FP training based on more stereotyped behaviors did not. PMID:22232582

Tracking ink composition on Herculaneum papyrus scrolls: quantification and speciation of lead by X-ray based techniques and Monte Carlo simulations

PubMed Central

Tack, Pieter; Cotte, Marine; Bauters, Stephen; Brun, Emmanuel; Banerjee, Dipanjan; Bras, Wim; Ferrero, Claudio; Delattre, Daniel; Mocella, Vito; Vincze, Laszlo

2016-01-01

The writing in carbonized Herculaneum scrolls, covered and preserved by the pyroclastic events of the Vesuvius in 79 AD, was recently revealed using X-ray phase-contrast tomography, without the need of unrolling the sensitive scrolls. Unfortunately, some of the text is difficult to read due to the interference of the papyrus fibers crossing the written text vertically and horizontally. Recently, lead was found as an elemental constituent in the writing, rendering the text more clearly readable when monitoring the lead X-ray fluorescence signal. Here, several hypotheses are postulated for the origin and state of lead in the papyrus writing. Multi-scale X-ray fluorescence micro-imaging, Monte Carlo quantification and X-ray absorption microspectroscopy experiments are used to provide additional information on the ink composition, in an attempt to determine the origin of the lead in the Herculaneum scrolls and validate the postulated hypotheses. PMID:26854067

Determination of boron in uranium aluminum silicon alloy by spectrophotometry and estimation of expanded uncertainty in measurement

NASA Astrophysics Data System (ADS)

Ramanjaneyulu, P. S.; Sayi, Y. S.; Ramakumar, K. L.

2008-08-01

Quantification of boron in diverse materials of relevance in nuclear technology is essential in view of its high thermal neutron absorption cross section. A simple and sensitive method has been developed for the determination of boron in uranium-aluminum-silicon alloy, based on leaching of boron with 6 M HCl and H 2O 2, its selective separation by solvent extraction with 2-ethyl hexane 1,3-diol and quantification by spectrophotometry using curcumin. The method has been evaluated by standard addition method and validated by inductively coupled plasma-atomic emission spectroscopy. Relative standard deviation and absolute detection limit of the method are 3.0% (at 1 σ level) and 12 ng, respectively. All possible sources of uncertainties in the methodology have been individually assessed, following the International Organization for Standardization guidelines. The combined uncertainty is calculated employing uncertainty propagation formulae. The expanded uncertainty in the measurement at 95% confidence level (coverage factor 2) is 8.840%.

Detection and quantification of microcystins (cyanobacterial hepatotoxins) with recombinant antibody fragments isolated from a naïve human phage display library.

PubMed

McElhiney, J; Lawton, L A; Porter, A J

2000-12-01

Single-chain antibody fragments against the cyanobacterial hepatotoxin microcystin-LR were isolated from a naive human phage display library and expressed in Escherichia coli. In competition enzyme-linked immunosorbent assay (ELISA), the most sensitive antibody clone selected from the library detected free microcystin-LR with an IC(50) value of 4 microM. It was found to cross react with three other microcystin variants - microcystin-RR, microcystin-LW and microcystin-LF - and detected microcystins in extracts of the cyanobacterium Microcystis aeruginosa, found to contain the toxins by high-performance liquid chromatography (HPLC). The quantification of microcystins in these extracts by ELISA and HPLC showed good correlation. Although the antibody isolated in this study was considerably less sensitive than the polyclonal and monoclonal antibodies already available for microcystin detection, phage display technology represents a cheaper, more rapid alternative for the production of anti-microcystin antibodies than the methods currently in use.

Corneal markers of diabetic neuropathy.

PubMed

Pritchard, Nicola; Edwards, Katie; Shahidi, Ayda M; Sampson, Geoff P; Russell, Anthony W; Malik, Rayaz A; Efron, Nathan

2011-01-01

Diabetic neuropathy is a significant clinical problem that currently has no effective therapy, and in advanced cases, leads to foot ulceration and lower limb amputation. The accurate detection, characterization and quantification of this condition are important in order to define at-risk patients, anticipate deterioration, monitor progression, and assess new therapies. This review evaluates novel corneal methods of assessing diabetic neuropathy. Two new noninvasive corneal markers have emerged, and in cross-sectional studies have demonstrated their ability to stratify the severity of this disease. Corneal confocal microscopy allows quantification of corneal nerve parameters and noncontact corneal esthesiometry, the functional correlate of corneal structure, assesses the sensitivity of the cornea. Both these techniques are quick to perform, produce little or no discomfort for the patient, and are suitable for clinical settings. Each has advantages and disadvantages over traditional techniques for assessing diabetic neuropathy. Application of these new corneal markers for longitudinal evaluation of diabetic neuropathy has the potential to reduce dependence on more invasive, costly, and time-consuming assessments, such as skin biopsy.

Jellyfish collagen scaffolds for cartilage tissue engineering.

PubMed

Hoyer, Birgit; Bernhardt, Anne; Lode, Anja; Heinemann, Sascha; Sewing, Judith; Klinger, Matthias; Notbohm, Holger; Gelinsky, Michael

2014-02-01

Porous scaffolds were engineered from refibrillized collagen of the jellyfish Rhopilema esculentum for potential application in cartilage regeneration. The influence of collagen concentration, salinity and temperature on fibril formation was evaluated by turbidity measurements and quantification of fibrillized collagen. The formation of collagen fibrils with a typical banding pattern was confirmed by atomic force microscopy and transmission electron microscopy analysis. Porous scaffolds from jellyfish collagen, refibrillized under optimized conditions, were fabricated by freeze-drying and subsequent chemical cross-linking. Scaffolds possessed an open porosity of 98.2%. The samples were stable under cyclic compression and displayed an elastic behavior. Cytotoxicity tests with human mesenchymal stem cells (hMSCs) did not reveal any cytotoxic effects of the material. Chondrogenic markers SOX9, collagen II and aggrecan were upregulated in direct cultures of hMSCs upon chondrogenic stimulation. The formation of typical extracellular matrix components was further confirmed by quantification of sulfated glycosaminoglycans. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Do people with recurrent back pain constrain spinal motion during seated horizontal and downward reaching?

PubMed

Crosbie, Jack; Nascimento, Dafne Port; Filho, Ruben de Faria Negrão; Ferreira, Paulo

2013-10-01

Although the effect of symptomatic back pain on functional movement has been investigated, changes to spinal movement patterns in essentially pain-free people with a history of recurrent back pain are largely unreported. Reaching activities, important for everyday and occupational function, often present problems to such people, but have not been considered in this population. The purpose of this study was to compare the amplitude and timing of spinal and hip motions during two, seated reaching activities in people with and without a history of recurrent low back pain (RLBP). Spinal and hip motions during reaching downward and across the body, in both directions, were tracked using electromagnetic sensors. Analyses were conducted to explore the amplitudes, velocities and timings of 3D segmental movements and to compare controls with subjects with recurrent, but asymptomatic lumbar or lumbosacral pain. We detected significant differences in the amplitude and timing of movement in the lower thoracic region, with the RLBP group restricting movement and demonstrating compensatory increased motion at the hip. The lumbar region displayed no significant between-group differences. The order in which the spinal segments achieved peak velocity in cross-reaching was reversed in RLBP compared to controls, with lumbar motion leading in controls and lagging in RLBP. Subjects with a history of RLBP show a number of altered kinematic features during reaching activities which are not related to the presence or intensity of pain, but which suggest adaptive changes to movement control. © 2013.

Image of God: effect on coping and psychospiritual outcomes in early breast cancer survivors.

PubMed

Schreiber, Judith A

2011-05-01

To examine the effect of breast cancer survivors' views of God on religious coping strategies, depression, anxiety, stress, concerns about recurrence, and psychological well-being. Exploratory, cross-sectional, comparative survey. Outpatients from community and university oncology practices in the southeastern United States. 130 early breast cancer survivors (6-30 months postdiagnosis). Self-report written survey packets were mailed to practice-identified survivors. Image of God, religious coping strategies, depression, anxiety, stress, concerns about recurrence, and psychological well-being. Women who viewed God as highly engaged used more coping strategies to promote spiritual conservation in proportion to coping strategies that reflect spiritual struggle. Women who viewed God as highly engaged maintained psychological well-being when either spiritual conservation or spiritual struggle coping styles were used. No differences in variables were noted for women who viewed God as more or less angry. The belief in an engaged God is significantly related to increased psychological well-being, decreased psychological distress, and decreased concern about recurrence. Addressing survivors' issues related to psychological adjustment and concern about recurrence within their world view would allow for more personalized and effective interventions. Future research should be conducted to establish how the view that God is engaged affects coping and psychological adjustment across diverse groups of cancer survivors and groups with monotheistic, polytheistic, and naturalistic world views. This could lead to a practical method for examining the influence of these world views on individuals' responses to cancer diagnosis, treatment, and survivorship.

High prevalence of recurrent nocturnal desaturations in systemic AL amyloidosis: a cross-sectional pilot study.

PubMed

Mahmood, Shameem; Sovani, Milind; Smith, Peter; George, Leena; Quarta, Christina C; Sachchithanantham, Sajitha; Fontana, Marianna; Whelan, Carol J; Lachmann, Helen J; Gillmore, Julian D; Hawkins, Philip N; Wechalekar, Ashutosh D

2017-04-01

Cardiac involvement and/or macroglossia with soft tissue deposits are risk factors for central sleep apnoea (CSA) and obstructive sleep apnoea (OSA), and common features of systemic AL amyloidosis. Little data exist on the occurrence of sleep-disordered breathing (SDB) or recurrent nocturnal hypoxia in amyloidosis, which this study sought to investigate. A total of 72 consecutive patients with systemic amyloidosis (mean age 69 years and mean BMI 25) were evaluated for occurrence of SDB, by overnight continuous pulse oximetry, and completed Epworth Sleepiness Score (ESS) and STOPBANG questionnaires. Patients included: AL cardiac (AL-C), AL macroglossia (AL-M), AL both (AL-CM) and transthyretin (ATTR). Mean overnight oxygen saturations were 93% (SD ± 2, 95% CI 87-96) with abnormal oximetry (4% oxygen desaturation index (ODI) >5/hour): AC-C 84%, AL-M 57%, AL-CM 62% and ATTR 47%. NYHA class directly correlated with a higher 4% ODI, NYHA class I vs 3, (p = 0.01). Two-thirds of patients had STOPBANG scores >3 and abnormally high ESS scores (>10) were seen in up to 30% of patients. Recurrent nocturnal hypoxaemia, suggestive of sleep-disordered breathing, is frequent in systemic AL amyloidosis. The higher incidence in cardiac amyloidosis highlights CSA and recurrent hypoxia as possible mechanisms for morbidity/mortality in these cases. A detailed polysomnography study is planned to clarify and further investigate these findings. Copyright © 2016. Published by Elsevier B.V.

Do patients prefer mesh or anterior colporrhaphy for primary correction of anterior vaginal wall prolapse: a labelled discrete choice experiment.

PubMed

Notten, K J B; Essers, B A; Weemhoff, M; Rutten, A G H; Donners, J J A E; van Gestel, I; Kruitwagen, R F P M; Roovers, J P W R; Dirksen, C D

2015-05-01

We investigated patients' preferences for anterior colporrhaphy or mesh surgery as surgical correction of anterior vaginal wall prolapse. Labelled discrete choice experiment. Three Dutch teaching hospitals. Women with anterior vaginal wall prolapse Pelvic Organ Prolapse Quantification stage 2 or more, indicated for anterior colporrhaphy (n = 100). Discrete choice experiments are an attribute-based survey method for measuring preferences. In this experiment, women were asked to choose between two treatment scenarios, mesh surgery or anterior colporrhaphy. These surgical treatments differed in four treatment attributes: (i) recurrence rate, (ii) exposure rate, (iii) infection rate, (iv) dyspareunia. Data were analysed using a multinomial logit model. Women's preferences for anterior colporrhaphy or mesh surgery for the repair of vaginal wall prolapse. All treatment attributes, i.e. recurrence, exposure, infection and dyspareunia, proved to be significant in the woman's decision to choose mesh surgery (P < 0.001), while only two attributes out of three, recurrence and infection, were significant for anterior colporrhaphy (P < 0.001). The relative importance data showed that with regards to the four statistically significant attributes for mesh, dyspareunia was the most important attribute, and of the two significant attributes for anterior colporrhaphy, the risk of infection. Based on the attributes and levels in our discrete choice experiment, anterior colporrhaphy was preferred in 74% as a primary correction of anterior vaginal wall prolapse, followed by a preference for mesh in 26% of all choices. This study showed that next to the risk of recurrence, other aspects like risk of infection, dyspareunia and exposure play a role in the woman's preference for a surgical treatment. In addition, our results indicate that anterior colporrhaphy is preferred in the majority of the choices, followed by a preference for mesh surgery in a quarter of all choice sets. However, these results represent the average preference of a sample of women and cannot be taken as the preference of each individual. In the medical decision-making context, information from the current study should be personalised to fit patient's unique circumstances. For patients to construct their own, individual preferences, they should be well informed about the existence and magnitude of the potential benefits and risks related to either anterior colporrhaphy or mesh surgery. © 2014 Royal College of Obstetricians and Gynaecologists.

Apoptosis is increased and cell proliferation is decreased in out-of-phase endometria from infertile and recurrent abortion patients.

PubMed

Meresman, Gabriela F; Olivares, Carla; Vighi, Susana; Alfie, Margarita; Irigoyen, Marcela; Etchepareborda, Juan J

2010-10-22

Various endometrial abnormalities have been associated with luteal phase deficiency: a significant dyssynchrony in the maturation of the glandular epithelium and the stroma and a prevalence of out-of-phase endometrial biopsy specimens. Out-of phase endometrium is a controversial disorder related to failed implantation, infertility and early pregnancy loss. Given that the regulation of the apoptotic process in endometrium of luteal phase deficiency is still unknown, the aim of this study was to evaluate cell proliferation, apoptosis and the levels of the main effector caspase, caspase-3 in the luteal in-phase and out-of-phase endometrium. Thirty-seven endometrial samples from sterile or recurrent abortion patients were included in this study: 21 in-phase samples (controls) and 16 samples with out-of-phase endometrium. Biopsy specimens of eutopic endometrium were obtained from all subjects during days 21-25 of the menstrual cycle. The endometrium with endometrial maturity of cycle day 25 or less at the time of menstruation was considered out-of phase. Endometrial tissues were fixed in 10% buffered formaldehyde. For apoptosis quantification, sections were processed for in situ immunohistochemical localization of nuclei exhibiting DNA fragmentation, by the terminal deoxynucleotidyl transferase (TdT)-mediated dUTP digoxygenin nick-end labeling (TUNEL) technique. Expressions of Proliferating Cell Nuclear Antigen (PCNA) as a marker of cell proliferation, and of cleaved caspase-3 as a marker of apoptosis, were assessed by immunohistochemistry in the luteal in-phase and out-of-phase endometrium from infertile and recurrent abortion patients. Luteal out-of-phase endometrium had increased apoptosis levels compared to in-phase endometrium (p < 0.05). Caspase-3 evaluation confirmed these results: the luteal out-of-phase endometrium showed augmented cleaved caspase-3 expression (p < 0.005). As well, our data demonstrated that the luteal out-of-phase endometrium expresses decreased PCNA levels (p < 0.05), showing that cell proliferation is diminished in this tissue. this study represents the first report describing variations at the cell proliferation and cell death levels in the out-of-phase endometrium in comparison with in-phase endometrium from infertile and recurrent abortion patients. Further studies are needed to elucidate a potential role of these alterations in the physiopathology of luteal phase deficiency.

A RP-HPLC method for quantification of diclofenac sodium released from biological macromolecules.

PubMed

Bhattacharya, Shiv Sankar; Banerjee, Subham; Ghosh, Ashoke Kumar; Chattopadhyay, Pronobesh; Verma, Anurag; Ghosh, Amitava

2013-07-01

Interpenetrating network (IPN) microbeads of sodium carboxymethyl locust bean gum (SCMLBG) and sodium carboxymethyl cellulose (SCMC) containing diclofenac sodium (DS), a nonsteroidal anti-inflammatory drug, were prepared by single water-in-water (w/w) emulsion gelation process using AlCl3 as cross-linking agent in a complete aqueous environment. Pharmacokinetic study of these IPN microbeads was then carried out by a simple and feasible high-performance liquid chromatographic method with UV detection which was developed and validated for the quantification of diclofenac sodium in rabbit plasma. The chromatographic separation was carried out in a Hypersil BDS, C18 column (250 mm × 4.6 mm; 5 m). The mobile phase was a mixture of acetonitrile and methanol (70:30, v/v) at a flow rate of 1.0 ml/min. The UV detection was set at 276 nm. The extraction recovery of diclofenac sodium in plasma of three quality control (QC) samples was ranged from 81.52% to 95.29%. The calibration curve was linear in the concentration range of 20-1000 ng/ml with the correlation coefficient (r(2)) above 0.9951. The method was specific and sensitive with the limit of quantification of 20 ng/ml. In stability tests, diclofenac sodium in rabbit plasma was stable during storage and assay procedure. Copyright © 2013. Published by Elsevier B.V.

In-line monitoring of cocrystallization process and quantification of carbamazepine-nicotinamide cocrystal using Raman spectroscopy and chemometric tools.

PubMed

Soares, Frederico L F; Carneiro, Renato L

2017-06-05

A cocrystallization process may involve several molecular species, which are generally solid under ambient conditions. Thus, accurate monitoring of different components that might appear during the reaction is necessary, as well as quantification of the final product. This work reports for the first time the synthesis of carbamazepine-nicotinamide cocrystal in aqueous media with a full conversion. The reactions were monitored by Raman spectroscopy coupled with Multivariate Curve Resolution - Alternating Least Squares, and the quantification of the final product among its coformers was performed using Raman spectroscopy and Partial Least Squares regression. The slurry reaction was made in four different conditions: room temperature, 40°C, 60°C and 80°C. The slurry reaction at 80°C enabled a full conversion of initial substrates into the cocrystal form, using water as solvent for a greener method. The employment of MCR-ALS coupled with Raman spectroscopy enabled to observe the main steps of the reactions, such as drug dissolution, nucleation and crystallization of the cocrystal. The PLS models gave mean errors of cross validation around 2.0 (% wt/wt), and errors of validation between 2.5 and 8.2 (% wt/wt) for all components. These were good results since the spectra of cocrystals and the physical mixture of the coformers present some similar peaks. Copyright © 2017 Elsevier B.V. All rights reserved.

In-line monitoring of cocrystallization process and quantification of carbamazepine-nicotinamide cocrystal using Raman spectroscopy and chemometric tools

NASA Astrophysics Data System (ADS)

Soares, Frederico L. F.; Carneiro, Renato L.

2017-06-01

A cocrystallization process may involve several molecular species, which are generally solid under ambient conditions. Thus, accurate monitoring of different components that might appear during the reaction is necessary, as well as quantification of the final product. This work reports for the first time the synthesis of carbamazepine-nicotinamide cocrystal in aqueous media with a full conversion. The reactions were monitored by Raman spectroscopy coupled with Multivariate Curve Resolution - Alternating Least Squares, and the quantification of the final product among its coformers was performed using Raman spectroscopy and Partial Least Squares regression. The slurry reaction was made in four different conditions: room temperature, 40 °C, 60 °C and 80 °C. The slurry reaction at 80 °C enabled a full conversion of initial substrates into the cocrystal form, using water as solvent for a greener method. The employment of MCR-ALS coupled with Raman spectroscopy enabled to observe the main steps of the reactions, such as drug dissolution, nucleation and crystallization of the cocrystal. The PLS models gave mean errors of cross validation around 2.0 (% wt/wt), and errors of validation between 2.5 and 8.2 (% wt/wt) for all components. These were good results since the spectra of cocrystals and the physical mixture of the coformers present some similar peaks.

Multi-analyte quantification in bioprocesses by Fourier-transform-infrared spectroscopy by partial least squares regression and multivariate curve resolution.

PubMed

Koch, Cosima; Posch, Andreas E; Goicoechea, Héctor C; Herwig, Christoph; Lendl, Bernhard

2014-01-07

This paper presents the quantification of Penicillin V and phenoxyacetic acid, a precursor, inline during Pencillium chrysogenum fermentations by FTIR spectroscopy and partial least squares (PLS) regression and multivariate curve resolution - alternating least squares (MCR-ALS). First, the applicability of an attenuated total reflection FTIR fiber optic probe was assessed offline by measuring standards of the analytes of interest and investigating matrix effects of the fermentation broth. Then measurements were performed inline during four fed-batch fermentations with online HPLC for the determination of Penicillin V and phenoxyacetic acid as reference analysis. PLS and MCR-ALS models were built using these data and validated by comparison of single analyte spectra with the selectivity ratio of the PLS models and the extracted spectral traces of the MCR-ALS models, respectively. The achieved root mean square errors of cross-validation for the PLS regressions were 0.22 g L(-1) for Penicillin V and 0.32 g L(-1) for phenoxyacetic acid and the root mean square errors of prediction for MCR-ALS were 0.23 g L(-1) for Penicillin V and 0.15 g L(-1) for phenoxyacetic acid. A general work-flow for building and assessing chemometric regression models for the quantification of multiple analytes in bioprocesses by FTIR spectroscopy is given. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Toward real-time quantification of fluorescence molecular probes using target/background ratio for guiding biopsy and endoscopic therapy of esophageal neoplasia.

PubMed

Jiang, Yang; Gong, Yuanzheng; Rubenstein, Joel H; Wang, Thomas D; Seibel, Eric J

2017-04-01

Multimodal endoscopy using fluorescence molecular probes is a promising method of surveying the entire esophagus to detect cancer progression. Using the fluorescence ratio of a target compared to a surrounding background, a quantitative value is diagnostic for progression from Barrett's esophagus to high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC). However, current quantification of fluorescent images is done only after the endoscopic procedure. We developed a Chan-Vese-based algorithm to segment fluorescence targets, and subsequent morphological operations to generate background, thus calculating target/background (T/B) ratios, potentially to provide real-time guidance for biopsy and endoscopic therapy. With an initial processing speed of 2 fps and by calculating the T/B ratio for each frame, our method provides quasireal-time quantification of the molecular probe labeling to the endoscopist. Furthermore, an automatic computer-aided diagnosis algorithm can be applied to the recorded endoscopic video, and the overall T/B ratio is calculated for each patient. The receiver operating characteristic curve was employed to determine the threshold for classification of HGD/EAC using leave-one-out cross-validation. With 92% sensitivity and 75% specificity to classify HGD/EAC, our automatic algorithm shows promising results for a surveillance procedure to help manage esophageal cancer and other cancers inspected by endoscopy.

Neurobehavioral function and low-level exposure to brominated flame retardants in adolescents: a cross-sectional study.

PubMed

Kiciński, Michał; Viaene, Mineke K; Den Hond, Elly; Schoeters, Greet; Covaci, Adrian; Dirtu, Alin C; Nelen, Vera; Bruckers, Liesbeth; Croes, Kim; Sioen, Isabelle; Baeyens, Willy; Van Larebeke, Nicolas; Nawrot, Tim S

2012-11-14

Animal and in vitro studies demonstrated a neurotoxic potential of brominated flame retardants, a group of chemicals used in many household and commercial products to prevent fire. Although the first reports of detrimental neurobehavioral effects in rodents appeared more than ten years ago, human data are sparse. As a part of a biomonitoring program for environmental health surveillance in Flanders, Belgium, we assessed the neurobehavioral function with the Neurobehavioral Evaluation System (NES-3), and collected blood samples in a group of high school students. Cross-sectional data on 515 adolescents (13.6-17 years of age) was available for the analysis. Multiple regression models accounting for potential confounders were used to investigate the associations between biomarkers of internal exposure to brominated flame retardants [serum levels of polybrominated diphenyl ether (PBDE) congeners 47, 99, 100, 153, 209, hexabromocyclododecane (HBCD), and tetrabromobisphenol A (TBBPA)] and cognitive performance. In addition, we investigated the association between brominated flame retardants and serum levels of FT3, FT4, and TSH. A two-fold increase of the sum of serum PBDE's was associated with a decrease of the number of taps with the preferred-hand in the Finger Tapping test by 5.31 (95% CI: 0.56 to 10.05, p = 0.029). The effects of the individual PBDE congeners on the motor speed were consistent. Serum levels above the level of quantification were associated with an average decrease of FT3 level by 0.18 pg/mL (95% CI: 0.03 to 0.34, p = 0.020) for PBDE-99 and by 0.15 pg/mL (95% CI: 0.004 to 0.29, p = 0.045) for PBDE-100, compared with concentrations below the level of quantification. PBDE-47 level above the level of quantification was associated with an average increase of TSH levels by 10.1% (95% CI: 0.8% to 20.2%, p = 0.033), compared with concentrations below the level of quantification. We did not observe effects of PBDE's on neurobehavioral domains other than the motor function. HBCD and TBBPA did not show consistent associations with performance in the neurobehavioral tests. This study is one of few studies and so far the largest one investigating the neurobehavioral effects of brominated flame retardants in humans. Consistently with experimental animal data, PBDE exposure was associated with changes in the motor function and the serum levels of the thyroid hormones.

Neurobehavioral function and low-level exposure to brominated flame retardants in adolescents: a cross-sectional study

PubMed Central

2012-01-01

Background Animal and in vitro studies demonstrated a neurotoxic potential of brominated flame retardants, a group of chemicals used in many household and commercial products to prevent fire. Although the first reports of detrimental neurobehavioral effects in rodents appeared more than ten years ago, human data are sparse. Methods As a part of a biomonitoring program for environmental health surveillance in Flanders, Belgium, we assessed the neurobehavioral function with the Neurobehavioral Evaluation System (NES-3), and collected blood samples in a group of high school students. Cross-sectional data on 515 adolescents (13.6-17 years of age) was available for the analysis. Multiple regression models accounting for potential confounders were used to investigate the associations between biomarkers of internal exposure to brominated flame retardants [serum levels of polybrominated diphenyl ether (PBDE) congeners 47, 99, 100, 153, 209, hexabromocyclododecane (HBCD), and tetrabromobisphenol A (TBBPA)] and cognitive performance. In addition, we investigated the association between brominated flame retardants and serum levels of FT3, FT4, and TSH. Results A two-fold increase of the sum of serum PBDE’s was associated with a decrease of the number of taps with the preferred-hand in the Finger Tapping test by 5.31 (95% CI: 0.56 to 10.05, p = 0.029). The effects of the individual PBDE congeners on the motor speed were consistent. Serum levels above the level of quantification were associated with an average decrease of FT3 level by 0.18 pg/mL (95% CI: 0.03 to 0.34, p = 0.020) for PBDE-99 and by 0.15 pg/mL (95% CI: 0.004 to 0.29, p = 0.045) for PBDE-100, compared with concentrations below the level of quantification. PBDE-47 level above the level of quantification was associated with an average increase of TSH levels by 10.1% (95% CI: 0.8% to 20.2%, p = 0.033), compared with concentrations below the level of quantification. We did not observe effects of PBDE’s on neurobehavioral domains other than the motor function. HBCD and TBBPA did not show consistent associations with performance in the neurobehavioral tests. Conclusions This study is one of few studies and so far the largest one investigating the neurobehavioral effects of brominated flame retardants in humans. Consistently with experimental animal data, PBDE exposure was associated with changes in the motor function and the serum levels of the thyroid hormones. PMID:23151181

Quantitative (13)C Solid-State NMR Spectra by Multiple-Contact Cross-polarization for Drug Delivery: From Active Principles to Excipients and Drug Carriers.

PubMed

Saïdi, Fadila; Taulelle, Francis; Martineau, Charlotte

2016-08-01

In this contribution, we present an analysis of the main parameters influencing the efficiency of the (1)H → (13)C multiple-contact cross-polarization nuclear magnetic resonance (NMR) experiment in the context of solid pharmaceutical materials. Using the optimum experimental conditions, quantitative (13)C NMR spectra are then obtained for porous metal-organic frameworks (potential drug carriers) and for components present in drug formulations (active principle ingredient and excipients, amorphous or crystalline). Finally, we show that mixtures of components can also be quantified with this method and, hence, that it represents an ideal tool for quantification of pharmaceutical formulations by (13)C cross-polarization under magic-angle spinning NMR in the industry as it is robust and easy to set up, much faster than direct (13)C polarization and is efficient for samples at natural abundance. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Vitamin D, Breast Cancer, and Bone Health

DTIC Science & Technology

2011-05-01

Margarine, fortified 1 Tbs 60 15 Pudding prepared with fortified milk 0.5 cup 50 10 Ready-to- eat cereals, fortified 0.75-1 cup 40 10 Liver, beef ...Baum M. Retrospective analysis of time to recurrence in the ATAC trial according to hormone receptor status: an hypothesis-generating study. J Clin...NTx Cross-linked N-telopeptide of type I collagen PR Partial response PTH Parathyroid hormone RR Response rate SAE Serious adverse event SD

Use of rifaximin in gastrointestinal and liver diseases.

PubMed

Shayto, Rani H; Abou Mrad, Rachel; Sharara, Ala I

2016-08-07

Rifaximin is a broad spectrum oral antibiotic with antimicrobial activity against Gram-positive and Gram-negative aerobic and anaerobic bacteria. It is poorly absorbed and thus has a highly favorable safety profile. Rifaximin has been shown to be effective in the treatment of traveler's diarrhea, functional bloating and irritable bowel syndrome, small bowel bacterial overgrowth and in the prevention of recurrent overt hepatic encephalopathy. In addition, there is emerging evidence for a possible beneficial effect of rifaximin in the treatment of uncomplicated diverticular disease and in the prevention of recurrent diverticulitis. The use of rifaximin is associated with a low incidence of development, or persistence of spontaneous bacterial mutants. Moreover, the development of important drug resistance among extra-intestinal flora during rifaximin therapy is unlikely because of minimal systemic absorption and limited cross-resistance of rifaximin with other antimicrobials. This review addresses the current and emerging role of rifaximin in the treatment of gastrointestinal and liver disorders.

Recurrent neural network based virtual detection line

NASA Astrophysics Data System (ADS)

Kadikis, Roberts

2018-04-01

The paper proposes an efficient method for detection of moving objects in the video. The objects are detected when they cross a virtual detection line. Only the pixels of the detection line are processed, which makes the method computationally efficient. A Recurrent Neural Network processes these pixels. The machine learning approach allows one to train a model that works in different and changing outdoor conditions. Also, the same network can be trained for various detection tasks, which is demonstrated by the tests on vehicle and people counting. In addition, the paper proposes a method for semi-automatic acquisition of labeled training data. The labeling method is used to create training and testing datasets, which in turn are used to train and evaluate the accuracy and efficiency of the detection method. The method shows similar accuracy as the alternative efficient methods but provides greater adaptability and usability for different tasks.

Recurrent Idiopathic Catatonia: Implications beyond the Diagnostic and Statistical Manual of Mental Disorders 5th Edition.

PubMed

Caroff, Stanley N; Hurford, Irene; Bleier, Henry R; Gorton, Gregg E; Campbell, E Cabrina

2015-08-31

We describe a case of recurrent, life-threatening, catatonic stupor, without evidence of any associated medical, toxic or mental disorder. This case provides support for the inclusion of a separate category of "unspecified catatonia" in the Diagnostic and Statistical Manual of Mental Disorders 5th edition (DSM-5) to be used to classify idiopathic cases, which appears to be consistent with Kahlbaum's concept of catatonia as a distinct disease state. But beyond the limited, cross-sectional, syndromal approach adopted in DSM-5, this case more importantly illustrates the prognostic and therapeutic significance of the longitudinal course of illness in differentiating cases of catatonia, which is better defined in the Wernicke-Kleist-Leonhard classification system. The importance of differentiating cases of catatonia is further supported by the efficacy of antipsychotics in treatment of this case, contrary to conventional guidelines.

Prevalence of epilepsy and seizure disorders as causes of apparent life- threatening event (ALTE) in children admitted to a tertiary hospital.

PubMed

Anjos, Alessandra Marques dos; Nunes, Magda Lahorgue

2009-09-01

To determine the prevalence and describe clinical characteristics of seizure disorders and epilepsy as causes of apparent life- threatening event (ALTE) in children admitted at the emergency and followed in a tertiary hospital. Cross-sectional study with prospective data collection using specific guidelines to determine the etiology of ALTE. During the study, 30 (4.2%) children admitted to the hospital had a diagnosis of ALTE. There was a predominance of males (73%) and term infants (70%). Neonatal neurological disorders and neuropsychomotor development delay were found respectively in 13.4% and 10% of the cases. Etiological investigation revealed that 50% of the cases were idiopathic, and 13.4% were caused by epilepsy or seizure disorders. Although all patients had recurrent ALTE events, epilepsy had not been previously suspected. Epilepsy should be included in the differential diagnosis of ALTE, particularly when events are recurrent.

Influence of Bony Defects on Preoperative Shoulder Function in Recurrent Anteroinferior Shoulder Instability.

PubMed

Wolke, Julia; Herrmann, Diem Anh; Krannich, Alexander; Scheibel, Markus

2016-05-01

Recurrent anteroinferior shoulder dislocations are often associated with bony glenoid and humeral defects. The influence of those bony lesions on the postoperative outcomes after arthroscopic shoulder stabilization procedures has been the subject of many studies. Little is known about the influence of those lesions on preoperative function. To evaluate the influence of glenoid and humeral bony defects on preoperative shoulder function in recurrent anteroinferior shoulder instability. Cross-sectional study; Level of evidence, 3. Included in the study were 90 patients (70 men, 20 women; mean age, 27.1 years; 24 patients with prior failed stabilization) with posttraumatic recurrent anteroinferior shoulder instability who underwent preoperative computed tomography (CT) of both shoulders. The glenoid index was used to measure glenoid defect on a 3-dimensional CT. Humeral head defect was measured on a 2-dimensional CT with evaluation of the Hill-Sachs quotient, product, sum, and difference. Preoperative evaluation also included the Rowe score, Constant score, Walch-Duplay score, Melbourne Instability Shoulder Score (MISS), Western Ontario Shoulder Instability Index (WOSI), and Subjective Shoulder Value (SSV). There was a weak but significant correlation of the Hill-Sachs quotient and the glenoid index with the Rowe score (P = .03, r = -0.22 and P = .03, r = 0.23, respectively). Furthermore, the Hill-Sachs product significantly correlated with the WOSI (P = .02); in particular, the physical symptoms subscore showed a significant correlation (P = .04). The glenoid index showed a significant correlation with the SSV (P < .01). No significant correlation was found between the Walch-Duplay score, Constant score, or MISS and bony defects. The results of this study show that objective and subjective scoring systems correlate significantly with the clinical condition of patients with recurrent shoulder instability and associated bony defects. It is recommended that clinicians use the Rowe score, WOSI, and SSV for the clinical evaluation of patients with recurrent anteroinferior shoulder instability and associated bony defects. These evaluation systems may provide an early clinical indication of bony defects. Furthermore, very poor results on these evaluations could underline the necessity of a CT scan for the diagnosis of bony defects in recurrent shoulder instability and might be helpful for decision making concerning the indication of a CT. © 2016 The Author(s).

Speech graphs provide a quantitative measure of thought disorder in psychosis.

PubMed

Mota, Natalia B; Vasconcelos, Nivaldo A P; Lemos, Nathalia; Pieretti, Ana C; Kinouchi, Osame; Cecchi, Guillermo A; Copelli, Mauro; Ribeiro, Sidarta

2012-01-01

Psychosis has various causes, including mania and schizophrenia. Since the differential diagnosis of psychosis is exclusively based on subjective assessments of oral interviews with patients, an objective quantification of the speech disturbances that characterize mania and schizophrenia is in order. In principle, such quantification could be achieved by the analysis of speech graphs. A graph represents a network with nodes connected by edges; in speech graphs, nodes correspond to words and edges correspond to semantic and grammatical relationships. To quantify speech differences related to psychosis, interviews with schizophrenics, manics and normal subjects were recorded and represented as graphs. Manics scored significantly higher than schizophrenics in ten graph measures. Psychopathological symptoms such as logorrhea, poor speech, and flight of thoughts were grasped by the analysis even when verbosity differences were discounted. Binary classifiers based on speech graph measures sorted schizophrenics from manics with up to 93.8% of sensitivity and 93.7% of specificity. In contrast, sorting based on the scores of two standard psychiatric scales (BPRS and PANSS) reached only 62.5% of sensitivity and specificity. The results demonstrate that alterations of the thought process manifested in the speech of psychotic patients can be objectively measured using graph-theoretical tools, developed to capture specific features of the normal and dysfunctional flow of thought, such as divergence and recurrence. The quantitative analysis of speech graphs is not redundant with standard psychometric scales but rather complementary, as it yields a very accurate sorting of schizophrenics and manics. Overall, the results point to automated psychiatric diagnosis based not on what is said, but on how it is said.

International validation of the consensus Immunoscore for the classification of colon cancer: a prognostic and accuracy study.

PubMed

Pagès, Franck; Mlecnik, Bernhard; Marliot, Florence; Bindea, Gabriela; Ou, Fang-Shu; Bifulco, Carlo; Lugli, Alessandro; Zlobec, Inti; Rau, Tilman T; Berger, Martin D; Nagtegaal, Iris D; Vink-Börger, Elisa; Hartmann, Arndt; Geppert, Carol; Kolwelter, Julie; Merkel, Susanne; Grützmann, Robert; Van den Eynde, Marc; Jouret-Mourin, Anne; Kartheuser, Alex; Léonard, Daniel; Remue, Christophe; Wang, Julia Y; Bavi, Prashant; Roehrl, Michael H A; Ohashi, Pamela S; Nguyen, Linh T; Han, SeongJun; MacGregor, Heather L; Hafezi-Bakhtiari, Sara; Wouters, Bradly G; Masucci, Giuseppe V; Andersson, Emilia K; Zavadova, Eva; Vocka, Michal; Spacek, Jan; Petruzelka, Lubos; Konopasek, Bohuslav; Dundr, Pavel; Skalova, Helena; Nemejcova, Kristyna; Botti, Gerardo; Tatangelo, Fabiana; Delrio, Paolo; Ciliberto, Gennaro; Maio, Michele; Laghi, Luigi; Grizzi, Fabio; Fredriksen, Tessa; Buttard, Bénédicte; Angelova, Mihaela; Vasaturo, Angela; Maby, Pauline; Church, Sarah E; Angell, Helen K; Lafontaine, Lucie; Bruni, Daniela; El Sissy, Carine; Haicheur, Nacilla; Kirilovsky, Amos; Berger, Anne; Lagorce, Christine; Meyers, Jeffrey P; Paustian, Christopher; Feng, Zipei; Ballesteros-Merino, Carmen; Dijkstra, Jeroen; van de Water, Carlijn; van Lent-van Vliet, Shannon; Knijn, Nikki; Mușină, Ana-Maria; Scripcariu, Dragos-Viorel; Popivanova, Boryana; Xu, Mingli; Fujita, Tomonobu; Hazama, Shoichi; Suzuki, Nobuaki; Nagano, Hiroaki; Okuno, Kiyotaka; Torigoe, Toshihiko; Sato, Noriyuki; Furuhata, Tomohisa; Takemasa, Ichiro; Itoh, Kyogo; Patel, Prabhu S; Vora, Hemangini H; Shah, Birva; Patel, Jayendrakumar B; Rajvik, Kruti N; Pandya, Shashank J; Shukla, Shilin N; Wang, Yili; Zhang, Guanjun; Kawakami, Yutaka; Marincola, Francesco M; Ascierto, Paolo A; Sargent, Daniel J; Fox, Bernard A; Galon, Jérôme

2018-05-26

The estimation of risk of recurrence for patients with colon carcinoma must be improved. A robust immune score quantification is needed to introduce immune parameters into cancer classification. The aim of the study was to assess the prognostic value of total tumour-infiltrating T-cell counts and cytotoxic tumour-infiltrating T-cells counts with the consensus Immunoscore assay in patients with stage I-III colon cancer. An international consortium of 14 centres in 13 countries, led by the Society for Immunotherapy of Cancer, assessed the Immunoscore assay in patients with TNM stage I-III colon cancer. Patients were randomly assigned to a training set, an internal validation set, or an external validation set. Paraffin sections of the colon tumour and invasive margin from each patient were processed by immunohistochemistry, and the densities of CD3+ and cytotoxic CD8+ T cells in the tumour and in the invasive margin were quantified by digital pathology. An Immunoscore for each patient was derived from the mean of four density percentiles. The primary endpoint was to evaluate the prognostic value of the Immunoscore for time to recurrence, defined as time from surgery to disease recurrence. Stratified multivariable Cox models were used to assess the associations between Immunoscore and outcomes, adjusting for potential confounders. Harrell's C-statistics was used to assess model performance. Tissue samples from 3539 patients were processed, and samples from 2681 patients were included in the analyses after quality controls (700 patients in the training set, 636 patients in the internal validation set, and 1345 patients in the external validation set). The Immunoscore assay showed a high level of reproducibility between observers and centres (r=0·97 for colon tumour; r=0·97 for invasive margin; p<0·0001). In the training set, patients with a high Immunoscore had the lowest risk of recurrence at 5 years (14 [8%] patients with a high Immunoscore vs 65 (19%) patients with an intermediate Immunoscore vs 51 (32%) patients with a low Immunoscore; hazard ratio [HR] for high vs low Immunoscore 0·20, 95% CI 0·10-0·38; p<0·0001). The findings were confirmed in the two validation sets (n=1981). In the stratified Cox multivariable analysis, the Immunoscore association with time to recurrence was independent of patient age, sex, T stage, N stage, microsatellite instability, and existing prognostic factors (p<0·0001). Of 1434 patients with stage II cancer, the difference in risk of recurrence at 5 years was significant (HR for high vs low Immunoscore 0·33, 95% CI 0·21-0·52; p<0·0001), including in Cox multivariable analysis (p<0·0001). Immunoscore had the highest relative contribution to the risk of all clinical parameters, including the American Joint Committee on Cancer and Union for International Cancer Control TNM classification system. The Immunoscore provides a reliable estimate of the risk of recurrence in patients with colon cancer. These results support the implementation of the consensus Immunoscore as a new component of a TNM-Immune classification of cancer. French National Institute of Health and Medical Research, the LabEx Immuno-oncology, the Transcan ERAnet Immunoscore European project, Association pour la Recherche contre le Cancer, CARPEM, AP-HP, Institut National du Cancer, Italian Association for Cancer Research, national grants and the Society for Immunotherapy of Cancer. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cognitive reactivity, self-depressed associations, and the recurrence of depression.

PubMed

Elgersma, Hermien J; de Jong, Peter J; van Rijsbergen, Gerard D; Kok, Gemma D; Burger, Huibert; van der Does, Willem; Penninx, Brenda W J H; Bockting, Claudi L H

2015-09-01

Mixed evidence exists regarding the role of cognitive reactivity (CR; cognitive responsivity to a negative mood) as a risk factor for recurrences of depression. One explanation for the mixed evidence may lie in the number of previous depressive episodes. Heightened CR may be especially relevant as a risk factor for the development of multiple depressive episodes and less so for a single depressive episode. In addition, it is theoretically plausible but not yet tested that the relationship between CR and number of episodes is moderated by the strength of automatic depression-related self-associations. To investigate (i) the strength of CR in remitted depressed individuals with a history of a single vs. multiple episodes, and (ii) the potentially moderating role of automatic negative self-associations in the relationship between the number of episodes and CR. Cross-sectional analysis of data obtained in a cohort study (Study 1) and during baseline assessments in two clinical trials (Study 2). Study 1 used data from the Netherlands Study of Depression and Anxiety (NESDA) and compared never-depressed participants (n=901) with remitted participants with either a single (n=336) or at least 2 previous episodes (n=273). Study 2 included only remitted participants with at least two previous episodes (n=273). The Leiden Index of Depression Sensitivity Revised (LEIDS-R) was used to index CR and an Implicit Association Test (IAT) to measure implicit self-associations. In Study 1, remitted depressed participants with multiple episodes had significantly higher CR than those with a single or no previous episode. The remitted individuals with multiple episodes of Study 2 had even higher CR scores than those of Study 1. Within the group of individuals with multiple episodes, CR was not heightened as a function of the number of episodes, even if individual differences in automatic negative self-associations were taken into account. The study employed a cross-sectional design, which precludes a firm conclusion with regard to the direction of this relationship. The findings are consistent with the view that high CR puts people at risk for recurrent depression and is less relevant for the development of an incidental depressive episode. This suggests that CR is an important target for interventions that aim to prevent the recurrence of depression. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of the 100-year flood plain on Upper Three Runs and selected tributaries, and the Savannah River at the Savannah River site, South Carolina, 1995

USGS Publications Warehouse

Lanier, T.H.

1996-01-01

The 100-year flood plain was determined for Upper Three Runs, its tributaries, and the part of the Savannah River that borders the Savannah River Site. The results are provided in tabular and graphical formats. The 100-year flood-plain maps and flood profiles provide water-resource managers of the Savannah River Site with a technical basis for making flood-plain management decisions that could minimize future flood problems and provide a basis for designing and constructing drainage structures along roadways. A hydrologic analysis was made to estimate the 100-year recurrence- interval flow for Upper Three Runs and its tributaries. The analysis showed that the well-drained, sandy soils in the head waters of Upper Three Runs reduce the high flows in the stream; therefore, the South Carolina upper Coastal Plain regional-rural-regression equation does not apply for Upper Three Runs. Conse- quently, a relation was established for 100-year recurrence-interval flow and drainage area using streamflow data from U.S. Geological Survey gaging stations on Upper Three Runs. This relation was used to compute 100-year recurrence-interval flows at selected points along the stream. The regional regression equations were applicable for the tributaries to Upper Three Runs, because the soil types in the drainage basins of the tributaries resemble those normally occurring in upper Coastal Plain basins. This was verified by analysis of the flood-frequency data collected from U.S. Geological Survey gaging station 02197342 on Fourmile Branch. Cross sections were surveyed throughout each reach, and other pertinent data such as flow resistance and land-use were col- lected. The surveyed cross sections and computed 100-year recurrence-interval flows were used in a step-backwater model to compute the 100-year flood profile for Upper Three Runs and its tributaries. The profiles were used to delineate the 100-year flood plain on topographic maps. The Savannah River forms the southwestern border of the Savannah River Site. Data from previously published reports were used to delineate the 100-year flood plain for the Savannah River from the downstream site boundary at the mouth of Lower Three Runs at river mile 125 to the upstream site boundary at river mile 163.

Prolonged remission from hepatic encephalopathy with rifaximin: results of a placebo crossover analysis.

PubMed

Bajaj, J S; Barrett, A C; Bortey, E; Paterson, C; Forbes, W P

2015-01-01

Rifaximin therapy reduced risk of hepatic encephalopathy (HE) recurrence and HE-related hospitalisations during a 6-month, randomised, placebo-controlled trial (RCT) and a 24-month open-label maintenance (OLM) study. However, the impact of crossover from placebo to rifaximin therapy is unclear. To study the impact of crossing over from placebo to rifaximin treatment on breakthrough HE and hospitalisation rates using a within-subjects design. Adults with cirrhosis and history of overt HE episodes, currently in HE remission, received placebo during the RCT and crossed over to rifaximin 550 mg twice daily during the OLM study. Rate of breakthrough overt HE episodes, hospitalisations and incidence and rate of adverse events (AEs) were analysed during RCT and first 6 months of OLM. Of 82 patients randomised to placebo in the RCT who crossed over to the OLM study, 39 experienced an HE episode during the RCT compared with 14 during the OLM study (P < 0.0001). Significantly lower rates of HE events were observed with rifaximin treatment compared with placebo treatment (P < 0.0001). Rates of HE-related hospitalisation were numerically lower during rifaximin treatment compared with placebo treatment, although not significant. Rates of most common AEs, serious AEs and infection-related AEs were similar between the two treatments. This analysis confirms the repeatability of results from the RCT on safety and efficacy of rifaximin 550 mg twice daily in reducing the risk of hepatic encephalopathy recurrence, and suggests these findings are translatable outside of a rigorous, controlled trial setting. © 2014 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.

Role of type-specific herpes simplex virus-1 and 2 serology as a diagnostic modality in patients with clinically suspected genital herpes: A comparative study in Indian population from a tertiary care hospital.

PubMed

Patwardhan, Vrushali; Bhalla, Preena

2016-01-01

Type-specific serology (TSS) test for herpes simplex virus (HSV) have been used as a research tool in seroepidemiological studies for some years. However, TSS as a diagnostic modality for diagnosis of current episode of genital herpes is not well documented. To measure the seroprevalence of type-specific HSV Type 1 (HSV-1) and Type 2 (HSV-2) IgG antibodies in cases provisionally diagnosed as primary and recurrent genital herpes and to evaluate the role of TSS as a diagnostic modality for diagnosis of genital herpes versus polymerase chain reaction (PCR). A cross-sectional study was performed over a period of 10 months in which 44 adult patients with clinically suspected genital herpes were recruited. An in-house glycoprotein G gene base PCR was performed directly from the genital lesion specimen for simultaneous detection and typing of HSV. TSS was performed to detect IgG antibody against HSV-1 and 2 in all patients using commercially available kits, and the results were compared. Seroprevalence of HSV-1 IgG was 43% among primary and 65% among recurrent genital herpes cases (P = 0.22). Whereas that of HSV-2 IgG was found to be 14% and 83% in respective patient group (P = 0.0001). When compared to PCR results HSV-1 IgG detection in both primary and recurrent genital herpes diagnosis had poor specificity, positive predictive value, and sensitivity. Whereas, HSV-2 serology had a sensitivity of 13.33% and 73.33% in primary and recurrent genital herpes and specificity of 83.33% and 85.71%, respectively. HSV-2 IgG detection helps in strengthening the diagnosis of recurrent HSV-2 disease, whereas the absence of HSV-2 IgG antibody helps in excluding genital herpes as a likely cause of recurrent genital ulceration. However, detection of HSV-1 IgG antibody may not be useful for diagnosis in patients of genital ulcer disease.

A Comparative Performance Analysis of Multispectral and RGB Imaging on HER2 Status Evaluation for the Prediction of Breast Cancer Prognosis.

PubMed

Liu, Wenlou; Wang, Linwei; Liu, Jiuyang; Yuan, Jingping; Chen, Jiamei; Wu, Han; Xiang, Qingming; Yang, Guifang; Li, Yan

2016-12-01

Despite the extensive application of multispectral imaging (MSI) in biomedical multidisciplinary researches, there is a paucity of data available regarding the implication of MSI in tumor prognosis prediction. We compared the behaviors of multispectral (MS) and conventional red-green-blue (RGB) images on assessment of human epidermal growth factor receptor 2 (HER2) immunohistochemistry to explore their impact on outcome in patients with invasive breast cancer (BC). Tissue microarrays containing 240 BC patients were introduced to compare the performance of MS and RGB imaging methods on the quantitative assessment of HER2 status and the prognostic value of 5-year disease-free survival (5-DFS). Both the total and average signal optical density values of HER2 MS and RGB images were analyzed, and all patients were divided into two groups based on the different 5-DFS. The quantification of HER2 MS images was negatively correlated with 5-DFS in lymph node-negative and -positive patients (P<.05), but RGB images were not in lymph node-positive patients (P=.101). Multivariate analysis indicated that the hazard ratio (HR) of HER2 MS was higher than that of HER2 RGB (HR=2.454; 95% confidence interval [CI], 1.636-3.681 vs HR=2.060; 95% CI, 1.361-3.119). Additionally, area under curve (AUC) by receiver operating characteristic analysis for HER2 MS was greater than that for HER2 RGB (AUC=0.649; 95% CI, 0.577-0.722 vs AUC=0.596; 95% CI, 0.522-0.670) in predicting the risk for recurrence. More importantly, the quantification of HER2 MS images has higher prediction accuracy than that of HER2 RGB images (69.6% vs 65.0%) on 5-DFS. Our study suggested that better information on BC prognosis could be obtained from the quantification of HER2 MS images and MS images might perform better in predicting BC prognosis than conventional RGB images. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

An overview of methods to identify and manage uncertainty for modelling problems in the water-environment-agriculture cross-sector

DOE PAGES

Jakeman, Anthony J.; Jakeman, John Davis

2018-03-14

Uncertainty pervades the representation of systems in the water–environment–agriculture cross-sector. Successful methods to address uncertainties have largely focused on standard mathematical formulations of biophysical processes in a single sector, such as partial or ordinary differential equations. More attention to integrated models of such systems is warranted. Model components representing the different sectors of an integrated model can have less standard, and different, formulations to one another, as well as different levels of epistemic knowledge and data informativeness. Thus, uncertainty is not only pervasive but also crosses boundaries and propagates between system components. Uncertainty assessment (UA) cries out for more eclecticmore » treatment in these circumstances, some of it being more qualitative and empirical. Here in this paper, we discuss the various sources of uncertainty in such a cross-sectoral setting and ways to assess and manage them. We have outlined a fast-growing set of methodologies, particularly in the computational mathematics literature on uncertainty quantification (UQ), that seem highly pertinent for uncertainty assessment. There appears to be considerable scope for advancing UA by integrating relevant UQ techniques into cross-sectoral problem applications. Of course this will entail considerable collaboration between domain specialists who often take first ownership of the problem and computational methods experts.« less

Cannabis sativa allergy: looking through the fog.

PubMed

Decuyper, I I; Van Gasse, A L; Cop, N; Sabato, V; Faber, M A; Mertens, C; Bridts, C H; Hagendorens, M M; De Clerck, L; Rihs, H P; Ebo, D G

2017-02-01

IgE-mediated Cannabis (C. sativa, marihuana) allergy seems to be on the rise. Both active and passive exposure to cannabis allergens may trigger a C. sativa sensitization and/or allergy. The clinical presentation of a C. sativa allergy varies from mild to life-threatening reactions and often seems to depend on the route of exposure. In addition, sensitization to cannabis allergens can result in various cross-allergies, mostly for plant foods. This clinical entity, designated as the 'cannabis-fruit/vegetable syndrome', might also imply cross-reactivity with tobacco, natural latex and plant-food-derived alcoholic beverages. Hitherto, these cross-allergies are predominantly reported in Europe and appear mainly to rely upon cross-reactivity between nonspecific lipid transfer proteins or thaumatin-like proteins present in C. sativa and their homologues, ubiquitously distributed throughout plant kingdom. At present, diagnosis of cannabis-related allergies predominantly rests upon a thorough history completed with skin testing using native extracts from crushed buds and leaves. However, quantification of specific IgE antibodies and basophil activation tests can also be helpful to establish correct diagnosis. In the absence of a cure, treatment comprises absolute avoidance measures. Whether avoidance of further use will halt the extension of related cross-allergies remains uncertain. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Removing Cross-Linked Telopeptides Enhances the Production of Low-Molecular-Weight Collagen Peptides from Spent Hens.

PubMed

Hong, Hui; Chaplot, Shreyak; Chalamaiah, Meram; Roy, Bimol C; Bruce, Heather L; Wu, Jianping

2017-08-30

The low-molecular-weight (LMW) peptides derived from collagen have shown a potential for various nutritional and pharmaceutical applications. However, production of LMW peptides from vertebrate collagen remains a challenge. Herein, we report a new method to produce LMW collagen peptides using pepsin pretreatment that removed cross-linked telopeptides in collagen molecules. After the pretreatment, the proportion of LMW collagen peptides (<1.4 kDa) that were obtained from pepsin-soluble collagen increased to 32.59% compared to heat-soluble collagen peptides (16.10%). Fourier transform infrared spectroscopy results indicated that telopeptide cleavage retained the triple-helical conformation of collagen. Liquid chromatography-tandem mass spectrometry analysis suggested that Gly-X-Y (X is often proline, while Y is either hydroxyproline or hydroxylysine) repeats were not the main factors that hindered the enzymatic hydrolysis of collagen molecules. However, cross-link quantification demonstrated that trivalent cross-links that included pyridinolines and pyrroles were the primary obstacles to producing small peptides from collagen of spent hens. This study demonstrated for the first time that removing cross-linked telopeptides could enhance the production of LMW peptides from spent hen collagen, which is also of interest to manufacturers who produce LMW collagen peptides from other vertebrate animals, such as bovids and porcids.

An overview of methods to identify and manage uncertainty for modelling problems in the water-environment-agriculture cross-sector

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

Jakeman, Anthony J.; Jakeman, John Davis

Uncertainty pervades the representation of systems in the water–environment–agriculture cross-sector. Successful methods to address uncertainties have largely focused on standard mathematical formulations of biophysical processes in a single sector, such as partial or ordinary differential equations. More attention to integrated models of such systems is warranted. Model components representing the different sectors of an integrated model can have less standard, and different, formulations to one another, as well as different levels of epistemic knowledge and data informativeness. Thus, uncertainty is not only pervasive but also crosses boundaries and propagates between system components. Uncertainty assessment (UA) cries out for more eclecticmore » treatment in these circumstances, some of it being more qualitative and empirical. Here in this paper, we discuss the various sources of uncertainty in such a cross-sectoral setting and ways to assess and manage them. We have outlined a fast-growing set of methodologies, particularly in the computational mathematics literature on uncertainty quantification (UQ), that seem highly pertinent for uncertainty assessment. There appears to be considerable scope for advancing UA by integrating relevant UQ techniques into cross-sectoral problem applications. Of course this will entail considerable collaboration between domain specialists who often take first ownership of the problem and computational methods experts.« less

UV-Vis Ratiometric Resonance Synchronous Spectroscopy for Determination of Nanoparticle and Molecular Optical Cross Sections.

PubMed

Nettles, Charles B; Zhou, Yadong; Zou, Shengli; Zhang, Dongmao

2016-03-01

Demonstrated herein is a UV-vis Ratiometric Resonance Synchronous Spectroscopic (R2S2, pronounced as "R-two-S-two" for simplicity) technique where the R2S2 spectrum is obtained by dividing the resonance synchronous spectrum of a NP-containing solution by the solvent resonance synchronous spectrum. Combined with conventional UV-vis measurements, this R2S2 method enables experimental quantification of the absolute optical cross sections for a wide range of molecular and nanoparticle (NP) materials that range optically from pure photon absorbers or scatterers to simultaneous photon absorbers and scatterers, simultaneous photon absorbers and emitters, and all the way to simultaneous photon absorbers, scatterers, and emitters in the UV-vis wavelength region. Example applications of this R2S2 method were demonstrated for quantifying the Rayleigh scattering cross sections of solvents including water and toluene, absorption and resonance light scattering cross sections for plasmonic gold nanoparticles, and absorption, scattering, and on-resonance fluorescence cross sections for semiconductor quantum dots (Qdots). On-resonance fluorescence quantum yields were quantified for the model molecular fluorophore Eosin Y and fluorescent Qdots CdSe and CdSe/ZnS. The insights and methodology presented in this work should be of broad significance in physical and biological science research that involves photon/matter interactions.

Long-term Results of Endovascular Stent Graft Placement of Ureteroarterial Fistula

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

Okada, Takuya, E-mail: okabone@gmail.com; Yamaguchi, Masato, E-mail: masato03310402@yahoo.co.jp; Muradi, Akhmadu, E-mail: muradiakhmadu@gmail.com

2013-08-01

PurposeTo evaluate the safety, efficacy, and long-term results of endovascular stent graft placement for ureteroarterial fistula (UAF).MethodsWe retrospectively analyzed stent graft placement for UAF performed at our institution from 2004 to 2012. Fistula location was assessed by contrast-enhanced computed tomography (CT) and angiography, and freedom from hematuria recurrence and mortality rates were estimated.ResultsStent graft placement for 11 UAFs was performed (4 men, mean age 72.8 {+-} 11.6 years). Some risk factors were present, including long-term ureteral stenting in 10 (91 %), pelvic surgery in 8 (73 %), and pelvic radiation in 5 (45 %). Contrast-enhanced CT and/or angiography revealed fistulamore » or encasement of the artery in 6 cases (55 %). In the remaining 5 (45 %), angiography revealed no abnormality, and the suspected fistula site was at the crossing area between urinary tract and artery. All procedures were successful. However, one patient died of urosepsis 37 days after the procedure. At a mean follow-up of 548 (range 35-1,386) days, 4 patients (36 %) had recurrent hematuria, and two of them underwent additional treatment with secondary stent graft placement and surgical reconstruction. The hematuria recurrence-free rates at 1 and 2 years were 76.2 and 40.6 %, respectively. The freedom from UAF-related and overall mortality rates at 2 years were 85.7 and 54.9 %, respectively.ConclusionEndovascular stent graft placement for UAF is a safe and effective method to manage acute events. However, the hematuria recurrence rate remains high. A further study of long-term results in larger number of patients is necessary.« less

NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits.

PubMed

Dittwald, Piotr; Gambin, Tomasz; Szafranski, Przemyslaw; Li, Jian; Amato, Stephen; Divon, Michael Y; Rodríguez Rojas, Lisa Ximena; Elton, Lindsay E; Scott, Daryl A; Schaaf, Christian P; Torres-Martinez, Wilfredo; Stevens, Abby K; Rosenfeld, Jill A; Agadi, Satish; Francis, David; Kang, Sung-Hae L; Breman, Amy; Lalani, Seema R; Bacino, Carlos A; Bi, Weimin; Milosavljevic, Aleksandar; Beaudet, Arthur L; Patel, Ankita; Shaw, Chad A; Lupski, James R; Gambin, Anna; Cheung, Sau Wai; Stankiewicz, Pawel

2013-09-01

We delineated and analyzed directly oriented paralogous low-copy repeats (DP-LCRs) in the most recent version of the human haploid reference genome. The computationally defined DP-LCRs were cross-referenced with our chromosomal microarray analysis (CMA) database of 25,144 patients subjected to genome-wide assays. This computationally guided approach to the empirically derived large data set allowed us to investigate genomic rearrangement relative frequencies and identify new loci for recurrent nonallelic homologous recombination (NAHR)-mediated copy-number variants (CNVs). The most commonly observed recurrent CNVs were NPHP1 duplications (233), CHRNA7 duplications (175), and 22q11.21 deletions (DiGeorge/velocardiofacial syndrome, 166). In the ∼25% of CMA cases for which parental studies were available, we identified 190 de novo recurrent CNVs. In this group, the most frequently observed events were deletions of 22q11.21 (48), 16p11.2 (autism, 34), and 7q11.23 (Williams-Beuren syndrome, 11). Several features of DP-LCRs, including length, distance between NAHR substrate elements, DNA sequence identity (fraction matching), GC content, and concentration of the homologous recombination (HR) hot spot motif 5'-CCNCCNTNNCCNC-3', correlate with the frequencies of the recurrent CNVs events. Four novel adjacent DP-LCR-flanked and NAHR-prone regions, involving 2q12.2q13, were elucidated in association with novel genomic disorders. Our study quantitates genome architectural features responsible for NAHR-mediated genomic instability and further elucidates the role of NAHR in human disease.

Psychosocial risk factors and treatment of new onset and recurrent depression during the post-partum period.

PubMed

Kettunen, Pirjo; Hintikka, Jukka

2017-07-01

When developing maternity care services, it is important to know how psychosocial factors affect the course of post-partum depression (PPD), and how depressed mothers are treated. The aim of this study is to assess how adverse childhood experiences, poor present support and violence, and low socioeconomic status (SES) associate with PPD, specifically in new onset and recurrent post-partum depression. The second aim is to assess the treatment received for PPD. This is a cross-sectional study. The study group comprises 104 mothers with a current episode of PPD, and a control group of 104 mothers without an episode. The Structured Clinical Interview for DSM-IV Axis I Disorders was used for data collection. Psychosocial risk factors, treatment issues, and the course of depression were assessed with a structured self-report questionnaire. In age-adjusted multivariate analyses, adverse childhood experiences, a low level of present support in close relationships, and a poor SES were associated significantly with PPD. Childhood adversity was associated with both new onset and recurrent depression. Nevertheless, a low level of support and a poor SES were also associated with recurrent depression. A quarter of mothers with a major depressive episode in the post-partum period attended psychiatric services. In mothers with new onset depression, the proportion was only 5%. There is an urgent need to develop the diagnostics of depression in maternity care services. An awareness of psychosocial risk factors might help in this. More depressed mothers should be referred to psychiatric services.

Subintimal Recanalization of Occluded Stents: The Substent Technique

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

Diamantopoulos, Athanasios, E-mail: adiamant@upatras.gr; Katsanos, Konstantinos; Spiliopoulos, Stavros

2013-08-01

PurposeApplication of metal stents is complicated by neointimal hyperplasia leading to vessel restenosis and reocclusion. Treatment options in cases presenting with complete occlusion of the stented segment and recurrent critical limb ischemia (CLI) are limited. We present the option of the subintimal/substent technique in dealing with occluded stents.MethodsThe study included patients presenting with recurrent CLI due to impaired blood flow as a result of complete occlusion of previously inserted metal stents and unsuccessful intraluminal crossing of the lesion via either the antegrade or retrograde approach. In these cases, crossing the occlusion through the subintimal/substent plane was attempted. Primary end pointsmore » included technical success, safety of the procedure, clinical improvement, and limb salvage, while secondary end points were patient survival, primary patency, and vessel restenosis rates at 1-year follow-up. Study end points were calculated by Kaplan-Meier survival analysis.ResultsBetween July 2006 and October 2011, a total of 14 patients (mean age 69.14 {+-} 12.59 years, 12 men) were treated with the substent technique and included in the analysis. Technical success rate was 85.71 % (12 of 14), with a total lesion length of 193.57 {+-} 90.78 mm. The mean occluded stented segment length was 90.21 {+-} 44.34 mm. In 10 (83.33 %) of 12 cases, a new stent had to be placed by the side of the old occluded one, while the remaining two cases (16.67 %) were treated only with balloon angioplasty. No serious adverse events were noted during the immediate postprocedural period. All successfully treated patients improved clinically. Estimated limb salvage was 90.9 %, and patient survival rate was 90.0 % at 1 year's follow-up. Primary patency was 45.50 % and vessel restenosis 77.30 %.ConclusionSubintimal recanalization of occluded metal stents through the substent plane is a valuable alternative treatment option, especially in patients with recurrent CLI with few alternatives.« less

Breast Cancer Diagnosis Using a Microfluidic Multiplexed Immunohistochemistry Platform

PubMed Central

Kim, Minseok S.; Kim, Taemin; Kong, Sun-Young; Kwon, Soim; Bae, Chae Yun; Choi, Jaekyu; Kim, Chul Hwan; Lee, Eun Sook; Park, Je-Kyun

2010-01-01

Background Biomarkers play a key role in risk assessment, assessing treatment response, and detecting recurrence and the investigation of multiple biomarkers may also prove useful in accurate prediction and prognosis of cancers. Immunohistochemistry (IHC) has been a major diagnostic tool to identify therapeutic biomarkers and to subclassify breast cancer patients. However, there is no suitable IHC platform for multiplex assay toward personalized cancer therapy. Here, we report a microfluidics-based multiplexed IHC (MMIHC) platform that significantly improves IHC performance in reduction of time and tissue consumption, quantification, consistency, sensitivity, specificity and cost-effectiveness. Methodology/Principal Findings By creating a simple and robust interface between the device and human breast tissue samples, we not only applied conventional thin-section tissues into on-chip without any additional modification process, but also attained perfect fluid control for various solutions, without any leakage, bubble formation, or cross-contamination. Four biomarkers, estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), progesterone receptor (PR) and Ki-67, were examined simultaneously on breast cancer cells and human breast cancer tissues. The MMIHC method improved immunoreaction, reducing time and reagent consumption. Moreover, it showed the availability of semi-quantitative analysis by comparing Western blot. Concordance study proved strong consensus between conventional whole-section analysis and MMIHC (n = 105, lowest Kendall's coefficient of concordance, 0.90). To demonstrate the suitability of MMIHC for scarce samples, it was also applied successfully to tissues from needle biopsies. Conclusions/Significance The microfluidic system, for the first time, was successfully applied to human clinical tissue samples and histopathological diagnosis was realized for breast cancers. Our results showing substantial agreement indicate that several cancer-related proteins can be simultaneously investigated on a single tumor section, giving clear advantages and technical advances over standard immunohistochemical method. This novel concept will enable histopathological diagnosis using numerous specific biomarkers at a time even for small-sized specimens, thus facilitating the individualization of cancer therapy. PMID:20454672

Prevalence and risk factors for renal scars in children with febrile UTI and/or VUR: A cross-sectional observational study of 565 consecutive patients

PubMed Central

Snodgrass, Warren T.; Shah, Anjana; Yang, Mary; Kwon, Jeannie; Villanueva, Carlos; Traylor, Janelle; Pritzker, Karen; Nakonezny, Paul A.; Haley, Robert W.; Bush, Nicol Corbin

2013-01-01

Purpose To determine prevalence and risk factors for renal scar in children referred for urologic assessment of febrile UTI and/or VUR. Methods Pre-determined risk factors for renal scar were prospectively recorded in consecutive patients referred for UTI/VUR. Age, gender, VUR grade, and reported number of febrile and non-febrile UTIs were analyzed with logistic regression to determine risk for focal cortical defects on non-acute DMSA. Results Of 565 consecutive children, 24 (4%) had congenital renal dysplasia and 84 (15.5%) had focal defect(s). VUR, especially grades IV–V, recurrent febrile UTI, and older age increased risk. For any age child with the same number of UTIs, VUR increased odds of renal defect 5.4-fold (OR = 5.4, 95% CI = 2.7–10.6, AUC = 0.759). Conclusions Focal DMSA defects were present in 15.5% of 565 consecutive children referred for febrile UTI and/or VUR; 4% had presumed congenital reflux nephropathy without cortical defect. All VUR grades increased risk for these defects, as did recurrent febrile UTIs and older age. However, 43% with grades IV–V VUR and 76% with recurrent UTI had normal DMSA. PMID:23465483

Prevalence and risk factors for renal scars in children with febrile UTI and/or VUR: a cross-sectional observational study of 565 consecutive patients.

PubMed

Snodgrass, Warren T; Shah, Anjana; Yang, Mary; Kwon, Jeannie; Villanueva, Carlos; Traylor, Janelle; Pritzker, Karen; Nakonezny, Paul A; Haley, Robert W; Bush, Nicol Corbin

2013-12-01

To determine prevalence and risk factors for renal scar in children referred for urologic assessment of febrile UTI and/or VUR. Pre-determined risk factors for renal scar were prospectively recorded in consecutive patients referred for UTI/VUR. Age, gender, VUR grade, and reported number of febrile and non-febrile UTIs were analyzed with logistic regression to determine risk for focal cortical defects on non-acute DMSA. Of 565 consecutive children, 24 (4%) had congenital renal dysplasia and 84 (15.5%) had focal defect(s). VUR, especially grades IV-V, recurrent febrile UTI, and older age increased risk. For any age child with the same number of UTIs, VUR increased odds of renal defect 5.4-fold (OR = 5.4, 95% CI = 2.7-10.6, AUC = 0.759). Focal DMSA defects were present in 15.5% of 565 consecutive children referred for febrile UTI and/or VUR; 4% had presumed congenital reflux nephropathy without cortical defect. All VUR grades increased risk for these defects, as did recurrent febrile UTIs and older age. However, 43% with grades IV-V VUR and 76% with recurrent UTI had normal DMSA. Published by Elsevier Ltd.

African Equatorial and Subtropical Ozone Plumes: Recurrences Timescales of the Brown Cloud Trans-African Plumes and Other Plumes

NASA Technical Reports Server (NTRS)

Chatfield, Robert B.; Thompson, Anne M.; Guan, Hong; Witte, Jacquelyn C.

2004-01-01

We have found repeated illustrations in the maps of Total Tropospheric Ozone (TTO) of apparent transport of ozone from the Indian Ocean to the Equatorial Atlantic Ocean. Most interesting are examples that coincide with the INDOEX observations of late northern winter, 1999. Three soundings associated with the SHADOZ (Southern Hemisphere Additional Ozonesondes) network help confirm and quantify degree of influence of pollution, lightning, and stratospheric sources, suggesting that perhaps 40% of increased Atlantic ozone could be Asian pollution during periods of maximum identified in the TTO maps. We outline recurrent periods of apparent ozone transport from Indian to Atlantic Ocean regions both during and outside the late-winter period. These are placed in the context of some general observations about factors controlling recurrence timescales for the expression of both equatorial and subtropical plumes. Low-level subtropical plumes are often controlled by frontal systems approaching the Namib coast; these direct mid-level air into either easterly equatorial plumes or westerly mid- troposphere plumes. Equatorial plumes of ozone cross Africa on an easterly path due to the occasional coincidence of two phenomena: (1) lofting of ozone to mid and upper levels, often in the Western Indian Ocean, and (2) the eastward extension of an Equatorial African easterly jet.

Possible risk factors for increased suicide following bariatric surgery.

PubMed

Mitchell, James E; Crosby, Ross; de Zwaan, Martina; Engel, Scott; Roerig, James; Steffen, Kristine; Gordon, Kathryn H; Karr, Trisha; Lavender, Jason; Wonderlich, Steve

2013-04-01

There is a growing research literature suggesting that there may be elevated risk of suicide following bariatric surgery. Most of the data reported thus far has been cross-sectional and observational, and very little is known about the possible specific causal variables involved. The purpose of this report is to review this literature and to review possible risk factors for increased suicidal risk following bariatric surgery, to delineate future research directions. First a variety of medical, biological, and genetic factors, including the persistence or recurrence of medical comorbidities after bariatric surgery, the disinhibition and impulsivity secondary to changes in the absorption of alcohol, hypoglycemia, as well as pharmacokinetic changes that may affect the absorption of various medications including antidepressant medications are reviewed. Also reviewed are possible mediating factors involving changes in various peptidergic systems such as GLP-1 and Ghrelin. A number of psychosocial issues that might be involved are discussed, including lack of improvement in quality of life after surgery, continued or recurrent physical mobility restrictions, persistence or recurrence of sexual dysfunction and relationship problems, low self-esteem, and a history of child maltreatment. Inadequate weight loss or weight regain are also discussed. A number of possible contributing factors have been identified. Possible theoretical models involved and directions for research are suggested. Copyright © 2012 The Obesity Society.

Factors associated with recurrence of alcohol-related traffic violations in southern Brazil.

PubMed

Schmitz, Aurinez R; Goldim, José R; Guimarães, Luciano S P; Lopes, Fernanda M; Kessler, Felix; Sousa, Tanara; Gonçalves, Veralice M; Pechansky, Flavio

2014-09-01

To analyze variables associated with recurrence of blood alcohol content (BAC)-related traffic violations among drivers in southern Brazil. This cross-sectional study included 12,204 driving-under-the-influence (DUI) offenders according to data provided by the Rio Grande do Sul state Transportation Department. Sociodemographic characteristics, license duration, license category, and psychological assessment results were analyzed. Drivers convicted of DUI more than once in 2009/2010 were considered recidivists. Variables were evaluated using descriptive statistical analysis and Poisson regression, adjusted by sex, age, and education level. A total of 538 (4.41%) drivers were considered recidivists. The following variables showed the strongest associations with recidivism: being aged 41-50 years (prevalence ratio [PR] = 3.41), being licensed for ≥ 12 years (PR = 1.86), being licensed for motorcycles, cars and trucks (PR = 1.36), having a license with psychological restrictions (PR = 1.33), and driving a truck or a similar vehicle at the moment of notification (PR = 1.08). In the age group with the highest risk for recurrence, drivers showed a higher probability of having a diagnosis of alcohol dependence and other psychiatric comorbidities that hinder the control of alcohol use. Psychological assessments seem to be important in predicting repeat offenses, especially when limited aptitudes are suspected, and should therefore be better investigated.

Advanced magnetic resonance imaging methods for planning and monitoring radiation therapy in patients with high-grade glioma.

PubMed

Lupo, Janine M; Nelson, Sarah J

2014-10-01

This review explores how the integration of advanced imaging methods with high-quality anatomical images significantly improves the characterization, target definition, assessment of response to therapy, and overall management of patients with high-grade glioma. Metrics derived from diffusion-, perfusion-, and susceptibility-weighted magnetic resonance imaging in conjunction with magnetic resonance spectroscopic imaging, allows us to characterize regions of edema, hypoxia, increased cellularity, and necrosis within heterogeneous tumor and surrounding brain tissue. Quantification of such measures may provide a more reliable initial representation of tumor delineation and response to therapy than changes in the contrast-enhancing or T2 lesion alone and have a significant effect on targeting resection, planning radiation, and assessing treatment effectiveness. In the long term, implementation of these imaging methodologies can also aid in the identification of recurrent tumor and its differentiation from treatment-related confounds and facilitate the detection of radiationinduced vascular injury in otherwise normal-appearing brain tissue.

Medial surface dynamics of an in vivo canine vocal fold during phonation

NASA Astrophysics Data System (ADS)

Döllinger, Michael; Berry, David A.; Berke, Gerald S.

2005-05-01

Quantitative measurement of the medial surface dynamics of the vocal folds is important for understanding how sound is generated within the larynx. Building upon previous excised hemilarynx studies, the present study extended the hemilarynx methodology to the in vivo canine larynx. Through use of an in vivo model, the medial surface dynamics of the vocal fold were examined as a function of active thyroarytenoid muscle contraction. Data were collected using high-speed digital imaging at a sampling frequency of 2000 Hz, and a spatial resolution of 1024×1024 pixels. Chest-like and fry-like vibrations were observed, but could not be distinguished based on the input stimulation current to the recurrent laryngeal nerve. The subglottal pressure did distinguish the registers, as did an estimate of the thyroarytenoid muscle activity. Upon quantification of the three-dimensional motion, the method of Empirical Eigenfunctions was used to extract the underlying modes of vibration, and to investigate mechanisms of sustained oscillation. Results were compared with previous findings from excised larynx experiments and theoretical models. .

Evidence of Mixed-mode oscillations and Farey arithmetic in double plasma system in presence of fireball

NASA Astrophysics Data System (ADS)

Mitra, Vramori; Sarma, Bornali; Sarma, Arun

2017-10-01

Plasma fireballs are luminous glowing region formed around a positively biased electrode. The present work reports the observation of mix mode oscillation (MMO) in the dynamics of plasma oscillations that are excited in the presence of fireball in a double plasma device. Source voltage and applied electrode voltage are considered as the controlling parameters for the experiment. Many sequences of distinct multi peaked periodic states reflects the presence of MMO with the variation of control parameter. The sequences of states with two patterns are characterized well by Farey arithmetic, which provides rational approximations of irrational numbers. These states can be characterized by a firing number, the ratio of the number of small amplitude oscillations to the total number of oscillations per period. The dynamical transition in plasma fireball is also demonstrated by spectral analysis, recurrence quantification analysis (RQA) and by statistical measures viz., skewness and kurtosis. The mix mode phenomenon observed in the experiment is consistent with a model that describes the dynamics of ionization instabilities.

Cannabis Allergy: What do We Know Anno 2015.

PubMed

Decuyper, Ine; Ryckebosch, Hanne; Van Gasse, Athina L; Sabato, Vito; Faber, Margaretha; Bridts, Chris H; Ebo, Didier G

2015-10-01

For about a decade, IgE-mediated cannabis (marihuana) allergy seems to be on the rise. Both active and passive exposure to cannabis allergens may lead to a cannabis sensitization and/or allergy. The clinical manifestations of a cannabis allergy can vary from mild to life-threatening reactions, often depending on the route of exposure. In addition, sensitization to cannabis allergens can trigger various secondary cross-allergies, mostly for plant-derived food. This clinical entity, which we have designated as the "cannabis-fruit/vegetable syndrome" might also imply cross-reactivity with tobacco, latex and plant-food derived alcoholic beverages. These secondary cross-allergies are mainly described in Europe and appear to result from cross-reactivity between non-specific lipid transfer proteins or thaumatin-like proteins present in Cannabis sativa and their homologues that are ubiquitously distributed throughout plant kingdom. At present, diagnosis of cannabis-related allergies rests upon a thorough history completed with skin testing using native extracts from buds and leaves. However, quantification of specific IgE antibodies and basophil activation tests can also be helpful to establish correct diagnosis. In the absence of a cure, treatment comprises absolute avoidance measures including a stop of any further cannabis (ab)use.

Spatial distribution of sediment storage types and quantification of valley fill deposits in an alpine basin, Reintal, Bavarian Alps, Germany

NASA Astrophysics Data System (ADS)

Schrott, Lothar; Hufschmidt, Gabi; Hankammer, Martin; Hoffmann, Thomas; Dikau, Richard

2003-09-01

Spatial patterns of sediment storage types and associated volumes using a novel approach for quantifying valley fill deposits are presented for a small alpine catchment (17 km 2) in the Bavarian Alps. The different sediment storage types were analysed with respect to geomorphic coupling and sediment flux activity. The most landforms in the valley in terms of surface area were found to be talus slopes (sheets and cones) followed by rockfall deposits and alluvial fans and plains. More than two-thirds of the talus slopes are relict landforms, completely decoupled from the geomorphic system. Notable sediment transport is limited to avalanche tracks, debris flows, and along floodplains. Sediment volumes were calculated using a combination of polynomial functions of cross sections, seismic refraction, and GIS modelling. A total of, 66 seismic refraction profiles were carried out throughout the valley for a more precise determination of sediment thicknesses and to check the bedrock data generated from geomorphometric analysis. We calculated the overall sediment volume of the valley fill deposits to be 0.07 km 3. This corresponds to a mean sediment thickness of 23.3 m. The seismic refraction data showed that large floodplains and sedimentation areas, which have been developed through damming effects from large rockfalls, are in general characterised by shallow sediment thicknesses (<20 m). By contrast, the thickness of several talus slopes is more than twice as much. For some locations (e.g., narrow sections of valley), the polynomial-generated cross sections resulted in overestimations of up to one order of magnitude; whereas in sections with a moderate valley shape, the modelled cross sections are in good accordance with the obtained seismic data. For the quantification of valley fill deposits, a combined application of bedrock data derived from polynomials and geophysical prospecting is highly recommended.

Combating HER2-overexpressing breast cancer through induction of calreticulin exposure by Tras-Permut CrossMab

PubMed Central

Zhang, Fan; Zhang, Jie; Liu, Moyan; Zhao, Lichao; LingHu, RuiXia; Feng, Fan; Gao, Xudong; Jiao, Shunchang; Zhao, Lei; Hu, Yi; Yang, Junlan

2015-01-01

Although trastuzumab has succeeded in breast cancer treatment, acquired resistance is one of the prime obstacles for breast cancer therapies. There is an urgent need to develop novel HER2 antibodies against trastuzumab resistance. Here, we first rational designed avidity-imporved trastuzumab and pertuzumab variants, and explored the correlation between the binding avidity improvement and their antitumor activities. After characterization of a pertuzumab variant L56TY with potent antitumor activities, a bispecific immunoglobulin G-like CrossMab (Tras-Permut CrossMab) was generated from trastuzumab and binding avidity-improved pertuzumab variant L56TY. Although, the antitumor efficacy of trastuzumab was not enhanced by improving its binding avidity, binding avidity improvement could significantly increase the anti-proliferative and antibody-dependent cellular cytotoxicity (ADCC) activities of pertuzumab. Further studies showed that Tras-Permut CrossMab exhibited exceptional high efficiency to inhibit the progression of trastuzumab-resistant breast cancer. Notably, we found that calreticulin (CRT) exposure induced by Tras-Permut CrossMab was essential for induction of tumor-specific T cell immunity against tumor recurrence. These data indicated that simultaneous blockade of HER2 protein by Tras-Permut CrossMab could trigger CRT exposure and subsequently induce potent tumor-specific T cell immunity, suggesting it could be a promising therapeutic strategy against trastuzumab resistance. PMID:25949918

Hope and mood changes throughout the primary brain tumor illness trajectory.

PubMed

Acquaye, Alvina A; Lin, Lin; Vera-Bolanos, Elizabeth; Gilbert, Mark R; Armstrong, Terri S

2016-01-01

The ambiguity of defining hope impacts the level of readiness faced by health care professionals treating patients with glioma, a disease with unpredictable outcomes. This study describes the report of hope and the relationship between hope and mood in adult brain tumor patients at various points in the illness trajectory. This was a cross-sectional study with data collection including use of the Herth Hope Index (HHI), the Profile of Mood States-Short Form (POMS-SF), and clinical information. Descriptive statistics were used to report sample characteristics. Spearman's rho and Mann-Whitney tests were used to compare and differentiate scores. Eighty-two patients ranging in age from 22 to 78 years (median, 44.5 y) participated in the study. Patients were primarily male (57.3%), married (76.8%), and had a high-grade glioma (35.4%). Nearly half had recurrence, and more than 20% were on active treatment. The overall HHI total score for the sample was 41.32 (range: 13-48). Patients with recurrence had a lower HHI interconnectedness (median = 14.00) score and higher total mood disturbance (median = 14.00) compared with patients without recurrence (median = 15.00 and median = 0.00, respectively; P < .05). All negative mood states on the POMS-SF were negatively correlated with HHI subscales. Overall, patients reporting more hope also reported less overall mood disturbance As expected, patients with tumor recurrence reported lower hope and higher mood disturbance than those who were newly diagnosed or without recurrence. Targeting interventions specifically tailored to an individual's needs for improvement in quality of life throughout the disease course may include measures to address hope in order to facilitate positive coping strategies. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Self-Consistent Scheme for Spike-Train Power Spectra in Heterogeneous Sparse Networks.

PubMed

Pena, Rodrigo F O; Vellmer, Sebastian; Bernardi, Davide; Roque, Antonio C; Lindner, Benjamin

2018-01-01

Recurrent networks of spiking neurons can be in an asynchronous state characterized by low or absent cross-correlations and spike statistics which resemble those of cortical neurons. Although spatial correlations are negligible in this state, neurons can show pronounced temporal correlations in their spike trains that can be quantified by the autocorrelation function or the spike-train power spectrum. Depending on cellular and network parameters, correlations display diverse patterns (ranging from simple refractory-period effects and stochastic oscillations to slow fluctuations) and it is generally not well-understood how these dependencies come about. Previous work has explored how the single-cell correlations in a homogeneous network (excitatory and inhibitory integrate-and-fire neurons with nearly balanced mean recurrent input) can be determined numerically from an iterative single-neuron simulation. Such a scheme is based on the fact that every neuron is driven by the network noise (i.e., the input currents from all its presynaptic partners) but also contributes to the network noise, leading to a self-consistency condition for the input and output spectra. Here we first extend this scheme to homogeneous networks with strong recurrent inhibition and a synaptic filter, in which instabilities of the previous scheme are avoided by an averaging procedure. We then extend the scheme to heterogeneous networks in which (i) different neural subpopulations (e.g., excitatory and inhibitory neurons) have different cellular or connectivity parameters; (ii) the number and strength of the input connections are random (Erdős-Rényi topology) and thus different among neurons. In all heterogeneous cases, neurons are lumped in different classes each of which is represented by a single neuron in the iterative scheme; in addition, we make a Gaussian approximation of the input current to the neuron. These approximations seem to be justified over a broad range of parameters as indicated by comparison with simulation results of large recurrent networks. Our method can help to elucidate how network heterogeneity shapes the asynchronous state in recurrent neural networks.

Identifying postoperative atrial fibrillation in cardiac surgical patients posthospital discharge, using iPhone ECG: a study protocol

PubMed Central

Lowres, Nicole; Freedman, S Ben; Gallagher, Robyn; Kirkness, Ann; Marshman, David; Orchard, Jessica; Neubeck, Lis

2015-01-01

Introduction Postoperative atrial fibrillation (AF) occurs in 30–40% of patients after cardiac surgery. Identification of recurrent postoperative AF is required to initiate evidence-based management to reduce the risk of subsequent stroke. However, as AF is often asymptomatic, recurrences may not be detected after discharge. This study determines feasibility and impact of a self-surveillance programme to identify recurrence of postoperative AF in the month of posthospital discharge. Methods and analysis This is a feasibility study, using a cross-sectional study design, of self-screening for AF using a hand-held single-lead iPhone electrocardiograph device (iECG). Participants will be recruited from the cardiothoracic surgery wards of the Royal North Shore Hospital and North Shore Private Hospital, Sydney, Australia. Cardiac surgery patients admitted in sinus rhythm and experiencing a transient episode of postoperative AF will be eligible for recruitment. Participants will be taught to take daily ECG recordings for 1 month posthospital discharge using the iECG and will be provided education regarding AF, including symptoms and health risks. The primary outcome is the feasibility of patient self-monitoring for AF recurrence using an iECG. Secondary outcomes include proportion of patients identified with recurrent AF; estimation of stroke risk and patient knowledge. Process outcomes and qualitative data related to acceptability of patient's use of the iECG and sustainability of the screening programme beyond the trial setting will also be collected. Ethics and dissemination Primary ethics approval was received on 25 February 2014 from Northern Sydney Local Health District Human Resource Ethics Committee, and on 17 July 2014 from North Shore Private Hospital Ethics Committee. Results will be disseminated via forums including, but not limited to, peer-reviewed publications and presentation at national and international conferences. Trial registration number ACTRN12614000383662. PMID:25586373

Identifying postoperative atrial fibrillation in cardiac surgical patients posthospital discharge, using iPhone ECG: a study protocol.

PubMed

Lowres, Nicole; Freedman, S Ben; Gallagher, Robyn; Kirkness, Ann; Marshman, David; Orchard, Jessica; Neubeck, Lis

2015-01-13

Postoperative atrial fibrillation (AF) occurs in 30-40% of patients after cardiac surgery. Identification of recurrent postoperative AF is required to initiate evidence-based management to reduce the risk of subsequent stroke. However, as AF is often asymptomatic, recurrences may not be detected after discharge. This study determines feasibility and impact of a self-surveillance programme to identify recurrence of postoperative AF in the month of posthospital discharge. This is a feasibility study, using a cross-sectional study design, of self-screening for AF using a hand-held single-lead iPhone electrocardiograph device (iECG). Participants will be recruited from the cardiothoracic surgery wards of the Royal North Shore Hospital and North Shore Private Hospital, Sydney, Australia. Cardiac surgery patients admitted in sinus rhythm and experiencing a transient episode of postoperative AF will be eligible for recruitment. Participants will be taught to take daily ECG recordings for 1 month posthospital discharge using the iECG and will be provided education regarding AF, including symptoms and health risks. The primary outcome is the feasibility of patient self-monitoring for AF recurrence using an iECG. Secondary outcomes include proportion of patients identified with recurrent AF; estimation of stroke risk and patient knowledge. Process outcomes and qualitative data related to acceptability of patient's use of the iECG and sustainability of the screening programme beyond the trial setting will also be collected. Primary ethics approval was received on 25 February 2014 from Northern Sydney Local Health District Human Resource Ethics Committee, and on 17 July 2014 from North Shore Private Hospital Ethics Committee. Results will be disseminated via forums including, but not limited to, peer-reviewed publications and presentation at national and international conferences. ACTRN12614000383662. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Quantification of Coffea arabica and Coffea canephora var. robusta concentration in blends by means of synchronous fluorescence and UV-Vis spectroscopies.

PubMed

Dankowska, A; Domagała, A; Kowalewski, W

2017-09-01

The potential of fluorescence, UV-Vis spectroscopies as well as the low- and mid-level data fusion of both spectroscopies for the quantification of concentrations of roasted Coffea arabica and Coffea canephora var. robusta in coffee blends was investigated. Principal component analysis was used to reduce data multidimensionality. To calculate the level of undeclared addition, multiple linear regression (PCA-MLR) models were used with lowest root mean square error of calibration (RMSEC) of 3.6% and root mean square error of cross-validation (RMSECV) of 7.9%. LDA analysis was applied to fluorescence intensities and UV spectra of Coffea arabica, canephora samples, and their mixtures in order to examine classification ability. The best performance of PCA-LDA analysis was observed for data fusion of UV and fluorescence intensity measurements at wavelength interval of 60nm. LDA showed that data fusion can achieve over 96% of correct classifications (sensitivity) in the test set and 100% of correct classifications in the training set, with low-level data fusion. The corresponding results for individual spectroscopies ranged from 90% (UV-Vis spectroscopy) to 77% (synchronous fluorescence) in the test set, and from 93% to 97% in the training set. The results demonstrate that fluorescence, UV, and visible spectroscopies complement each other, giving a complementary effect for the quantification of roasted Coffea arabica and Coffea canephora var. robusta concentration in blends. Copyright © 2017 Elsevier B.V. All rights reserved.

Automated tubule nuclei quantification and correlation with oncotype DX risk categories in ER+ breast cancer whole slide images

NASA Astrophysics Data System (ADS)

Romo-Bucheli, David; Janowczyk, Andrew; Romero, Eduardo; Gilmore, Hannah; Madabhushi, Anant

2016-03-01

Early stage estrogen receptor positive (ER+) breast cancer (BCa) treatment is based on the presumed aggressiveness and likelihood of cancer recurrence. The primary conundrum in treatment and management of early stage ER+ BCa is identifying which of these cancers are candidates for adjuvant chemotherapy and which patients will respond to hormonal therapy alone. This decision could spare some patients the inherent toxicity associated with adjuvant chemotherapy. Oncotype DX (ODX) and other gene expression tests have allowed for distinguishing the more aggressive ER+ BCa requiring adjuvant chemotherapy from the less aggressive cancers benefiting from hormonal therapy alone. However these gene expression tests tend to be expensive, tissue destructive and require physical shipping of tissue blocks for the test to be done. Interestingly breast cancer grade in these tumors has been shown to be highly correlated with the ODX risk score. Unfortunately studies have shown that Bloom-Richardson (BR) grade determined by pathologists can be highly variable. One of the constituent categories in BR grading is the quantification of tubules. The goal of this study was to develop a deep learning neural network classifier to automatically identify tubule nuclei from whole slide images (WSI) of ER+ BCa, the hypothesis being that the ratio of tubule nuclei to overall number of nuclei would correlate with the corresponding ODX risk categories. The performance of the tubule nuclei deep learning strategy was evaluated with a set of 61 high power fields. Under a 5-fold cross-validation, the average precision and recall measures were 0:72 and 0:56 respectively. In addition, the correlation with the ODX risk score was assessed in a set of 7513 high power fields extracted from 174 WSI, each from a different patient (At most 50 high power fields per patient study were used). The ratio between the number of tubule and non-tubule nuclei was computed for each WSI. The results suggests that for BCa cases with both low ODX score and low BR grade, the mean tubule nuclei ratio was significantly higher than that obtained for the BCa cases with both high ODX score and high BR grade (p < 0:01). The low ODX and low BR grade cases also presented a significantly higher average tubule nuclei ratio when compared with the rest of the BCa cases (p < 0:05). Finally, the BCa cases that presented both a high ODX and high BR grade show a mean tubule nuclei to total number of nuclei ratio which was significantly smaller than that obtained for the rest of BCa cases (p < 0:01).

Quantification of Anti-Aggregation Activity of Chaperones: A Test-System Based on Dithiothreitol-Induced Aggregation of Bovine Serum Albumin

PubMed Central

Borzova, Vera A.; Markossian, Kira A.; Kara, Dmitriy A.; Chebotareva, Natalia A.; Makeeva, Valentina F.; Poliansky, Nikolay B.; Muranov, Konstantin O.; Kurganov, Boris I.

2013-01-01

The methodology for quantification of the anti-aggregation activity of protein and chemical chaperones has been elaborated. The applicability of this methodology was demonstrated using a test-system based on dithiothreitol-induced aggregation of bovine serum albumin at 45°C as an example. Methods for calculating the initial rate of bovine serum albumin aggregation (v agg) have been discussed. The comparison of the dependences of v agg on concentrations of intact and cross-linked α-crystallin allowed us to make a conclusion that a non-linear character of the dependence of v agg on concentration of intact α-crystallin was due to the dynamic mobility of the quaternary structure of α-crystallin and polydispersity of the α-crystallin–target protein complexes. To characterize the anti-aggregation activity of the chemical chaperones (arginine, arginine ethyl ester, arginine amide and proline), the semi-saturation concentration [L]0.5 was used. Among the chemical chaperones studied, arginine ethyl ester and arginine amide reveal the highest anti-aggregation activity ([L]0.5 = 53 and 58 mM, respectively). PMID:24058554

Authenticity control of game meat products--a single method to detect and quantify adulteration of fallow deer (Dama dama), red deer (Cervus elaphus) and sika deer (Cervus nippon) by real-time PCR.

PubMed

Druml, Barbara; Grandits, Stephanie; Mayer, Walter; Hochegger, Rupert; Cichna-Markl, Margit

2015-03-01

This contribution presents a single real-time PCR assay allowing the determination of the deer content (the sum of fallow deer (Dama dama), red deer (Cervus elaphus) and sika deer (Cervus nippon)) in meat products to detect food adulteration. The PCR assay does not show cross-reactivity with 20 animal species and 43 botanical species potentially contained in game meat products. The limit of quantification is 0.5% for fallow deer and red deer and 0.1% for sika deer. The deer content in meat products is determined by relating the concentration obtained with the deer PCR assay to that obtained with a reference system which amplifies mammals and poultry DNA. The analysis of binary meat mixtures with pork, a meat mixture containing equal amounts of fallow deer, red deer and sika deer in pork and a model game sausage showed that the quantification approach is very accurate (systematic error generally <25%). Copyright © 2014 Elsevier Ltd. All rights reserved.

Inventory Uncertainty Quantification using TENDL Covariance Data in Fispact-II

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

Eastwood, J.W.; Morgan, J.G.; Sublet, J.-Ch., E-mail: jean-christophe.sublet@ccfe.ac.uk

2015-01-15

The new inventory code Fispact-II provides predictions of inventory, radiological quantities and their uncertainties using nuclear data covariance information. Central to the method is a novel fast pathways search algorithm using directed graphs. The pathways output provides (1) an aid to identifying important reactions, (2) fast estimates of uncertainties, (3) reduced models that retain important nuclides and reactions for use in the code's Monte Carlo sensitivity analysis module. Described are the methods that are being implemented for improving uncertainty predictions, quantification and propagation using the covariance data that the recent nuclear data libraries contain. In the TENDL library, above themore » upper energy of the resolved resonance range, a Monte Carlo method in which the covariance data come from uncertainties of the nuclear model calculations is used. The nuclear data files are read directly by FISPACT-II without any further intermediate processing. Variance and covariance data are processed and used by FISPACT-II to compute uncertainties in collapsed cross sections, and these are in turn used to predict uncertainties in inventories and all derived radiological data.« less

Microstructural Effects on Initiation Behavior in HMX

NASA Astrophysics Data System (ADS)

Molek, Christopher; Welle, Eric; Hardin, Barrett; Vitarelli, Jim; Wixom, Ryan; Samuels, Philip

Understanding the role microstructure plays on ignition and growth behavior has been the subject of a significant body of research within the detonation physics community. The pursuit of this understanding is important because safety and performance characteristics have been shown to strongly correlate to particle morphology. Historical studies have often correlated bulk powder characteristics to the performance or safety characteristics of pressed materials. We believe that a clearer and more relevant correlation is made between the pressed microstructure and the observed detonation behavior. This type of assessment is possible, as techniques now exist for the quantification of the pressed microstructures. Our talk will report on experimental efforts that correlate directly measured microstructural characteristics to initiation threshold behavior of HMX based materials. The internal microstructures were revealed using an argon ion cross-sectioning technique. This technique enabled the quantification of density and interface area of the pores within the pressed bed using methods of stereology. These bed characteristics are compared to the initiation threshold behavior of three HMX based materials using an electric gun based test method. Finally, a comparison of experimental threshold data to supporting theoretical efforts will be made.

Separation and quantification of monoclonal-antibody aggregates by hollow-fiber-flow field-flow fractionation.

PubMed

Fukuda, Jun; Iwura, Takafumi; Yanagihara, Shigehiro; Kano, Kenji

2014-10-01

Hollow-fiber-flow field-flow fractionation (HF5) separates protein molecules on the basis of the difference in the diffusion coefficient, and can evaluate the aggregation ratio of proteins. However, HF5 is still a minor technique because information on the separation conditions is limited. We examined in detail the effect of different settings, including the main-flow rate, the cross-flow rate, the focus point, the injection amount, and the ionic strength of the mobile phase, on fractographic characteristics. On the basis of the results, we proposed optimized conditions of the HF5 method for quantification of monoclonal antibody in sample solutions. The HF5 method was qualified regarding the precision, accuracy, linearity of the main peak, and quantitation limit. In addition, the HF5 method was applied to non-heated Mab A and heat-induced-antibody-aggregate-containing samples to evaluate the aggregation ratio and the distribution extent. The separation performance was comparable with or better than that of conventional methods including analytical ultracentrifugation-sedimentation velocity and asymmetric-flow field-flow fractionation.

A new QRT-PCR assay designed for the differentiation between elements provided from Agrobacterium sp. in GMOs plant events and natural Agrobacterium sp. bacteria.

PubMed

Nabi, Nesrine; Chaouachi, Maher; Zellama, Mohamed Salem; Ben Hafsa, Ahmed; Mrabet, Besma; Saïd, Khaled; Fathia, Harzallah Skhiri

2016-04-01

The question asked in the present work was how to differentiate between contamination of field samples with and GM plants contained sequences provided from this bacterium in order to avoid false positives in the frame of the detection and the quantification of GMO. For this, new set of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target Agrobacterium sp. using the tumor-morphology-shooty gene (TMS1). Final standard curves were calculated for each pathogen by plotting the threshold cycle value against the bacterial number (log (colony forming units) per milliliter) via linear regression. The method designed was highly specific and sensitive, with a detection limit of 10CFU/ml. No significant cross-reaction was observed. Results from this study showed that TaqMan real-time PCR, is potentially an effective method for the rapid and reliable quantification of Agrobacterium sp. in samples containing GMO or non GMO samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Partial synthesis of ganglioside and lysoganglioside lipoforms as internal standards for MS quantification.

PubMed

Gantner, Martin; Schwarzmann, Günter; Sandhoff, Konrad; Kolter, Thomas

2014-12-01

Within recent years, ganglioside patterns have been increasingly analyzed by MS. However, internal standards for calibration are only available for gangliosides GM1, GM2, and GM3. For this reason, we prepared homologous internal standards bearing nonnatural fatty acids of the major mammalian brain gangliosides GM1, GD1a, GD1b, GT1b, and GQ1b, and of the tumor-associated gangliosides GM2 and GD2. The fatty acid moieties were incorporated after selective chemical or enzymatic deacylation of bovine brain gangliosides. For modification of the sphingoid bases, we developed a new synthetic method based on olefin cross metathesis. This method was used for the preparation of a lyso-GM1 and a lyso-GM2 standard. The total yield of this method was 8.7% for the synthesis of d17:1-lyso-GM1 from d20:1/18:0-GM1 in four steps. The title compounds are currently used as calibration substances for MS quantification and are also suitable for functional studies. Copyright © 2014 by the American Society for Biochemistry and Molecular Biology, Inc.

Three Dimensional Characterization of Tin Crystallography and Cu6Sn5 Intermetallics in Solder Joints by Multiscale Tomography

NASA Astrophysics Data System (ADS)

Kirubanandham, A.; Lujan-Regalado, I.; Vallabhaneni, R.; Chawla, N.

2016-11-01

Decreasing pitch size in electronic packaging has resulted in a drastic decrease in solder volumes. The Sn grain crystallography and fraction of intermetallic compounds (IMCs) in small-scale solder joints evolve much differently at the smaller length scales. A cross-sectional study limits the morphological analysis of microstructural features to two dimensions. This study utilizes serial sectioning technique in conjunction with electron backscatter diffraction to investigate the crystallographic orientation of both Sn grains and Cu6Sn5 IMCs in Cu/Pure Sn/Cu solder joints in three dimensional (3D). Quantification of grain aspect ratio is affected by local cooling rate differences within the solder volume. Backscatter electron imaging and focused ion beam serial sectioning enabled the visualization of morphology of both nanosized Cu6Sn5 IMCs and the hollow hexagonal morphology type Cu6Sn5 IMCs in 3D. Quantification and visualization of microstructural features in 3D thus enable us to better understand the microstructure and deformation mechanics within these small scale solder joints.

Quantification and Compensation of Eddy-Current-Induced Magnetic Field Gradients

PubMed Central

Spees, William M.; Buhl, Niels; Sun, Peng; Ackerman, Joseph J.H.; Neil, Jeffrey J.; Garbow, Joel R.

2011-01-01

Two robust techniques for quantification and compensation of eddy-current-induced magnetic-field gradients and static magnetic-field shifts (ΔB0) in MRI systems are described. Purpose-built 1-D or 6-point phantoms are employed. Both procedures involve measuring the effects of a prior magnetic-field-gradient test pulse on the phantom’s free induction decay (FID). Phantom-specific analysis of the resulting FID data produces estimates of the time-dependent, eddy-current-induced magnetic field gradient(s) and ΔB0 shift. Using Bayesian methods, the time dependencies of the eddy-current-induced decays are modeled as sums of exponentially decaying components, each defined by an amplitude and time constant. These amplitudes and time constants are employed to adjust the scanner’s gradient pre-emphasis unit and eliminate undesirable eddy-current effects. Measurement with the six-point sample phantom allows for simultaneous, direct estimation of both on-axis and cross-term eddy-current-induced gradients. The two methods are demonstrated and validated on several MRI systems with actively-shielded gradient coil sets. PMID:21764614

Quantification and compensation of eddy-current-induced magnetic-field gradients.

PubMed

Spees, William M; Buhl, Niels; Sun, Peng; Ackerman, Joseph J H; Neil, Jeffrey J; Garbow, Joel R

2011-09-01

Two robust techniques for quantification and compensation of eddy-current-induced magnetic-field gradients and static magnetic-field shifts (ΔB0) in MRI systems are described. Purpose-built 1-D or six-point phantoms are employed. Both procedures involve measuring the effects of a prior magnetic-field-gradient test pulse on the phantom's free induction decay (FID). Phantom-specific analysis of the resulting FID data produces estimates of the time-dependent, eddy-current-induced magnetic field gradient(s) and ΔB0 shift. Using Bayesian methods, the time dependencies of the eddy-current-induced decays are modeled as sums of exponentially decaying components, each defined by an amplitude and time constant. These amplitudes and time constants are employed to adjust the scanner's gradient pre-emphasis unit and eliminate undesirable eddy-current effects. Measurement with the six-point sample phantom allows for simultaneous, direct estimation of both on-axis and cross-term eddy-current-induced gradients. The two methods are demonstrated and validated on several MRI systems with actively-shielded gradient coil sets. Copyright © 2011 Elsevier Inc. All rights reserved.

Regional flux analysis for discovering and quantifying anatomical changes: An application to the brain morphometry in Alzheimer's disease.

PubMed

Lorenzi, M; Ayache, N; Pennec, X

2015-07-15

In this study we introduce the regional flux analysis, a novel approach to deformation based morphometry based on the Helmholtz decomposition of deformations parameterized by stationary velocity fields. We use the scalar pressure map associated to the irrotational component of the deformation to discover the critical regions of volume change. These regions are used to consistently quantify the associated measure of volume change by the probabilistic integration of the flux of the longitudinal deformations across the boundaries. The presented framework unifies voxel-based and regional approaches, and robustly describes the volume changes at both group-wise and subject-specific level as a spatial process governed by consistently defined regions. Our experiments on the large cohorts of the ADNI dataset show that the regional flux analysis is a powerful and flexible instrument for the study of Alzheimer's disease in a wide range of scenarios: cross-sectional deformation based morphometry, longitudinal discovery and quantification of group-wise volume changes, and statistically powered and robust quantification of hippocampal and ventricular atrophy. Copyright © 2015 Elsevier Inc. All rights reserved.

A Tissue-Specific Approach to the Analysis of Metabolic Changes in Caenorhabditis elegans

PubMed Central

Pujol, Claire; Ipsen, Sabine; Brodesser, Susanne; Mourier, Arnaud; Tolnay, Markus; Frank, Stephan; Trifunović, Aleksandra

2011-01-01

The majority of metabolic principles are evolutionarily conserved from nematodes to humans. Caenorhabditis elegans has widely accelerated the discovery of new genes important to maintain organismic metabolic homeostasis. Various methods exist to assess the metabolic state in worms, yet they often require large animal numbers and tend to be performed as bulk analyses of whole worm homogenates, thereby largely precluding a detailed studies of metabolic changes in specific worm tissues. Here, we have adapted well-established histochemical methods for the use on C. elegans fresh frozen sections and demonstrate their validity for analyses of morphological and metabolic changes on tissue level in wild type and various mutant strains. We show how the worm presents on hematoxylin and eosin (H&E) stained sections and demonstrate their usefulness in monitoring and the identification of morphological abnormalities. In addition, we demonstrate how Oil-Red-O staining on frozen worm cross-sections permits quantification of lipid storage, avoiding the artifact-prone fixation and permeabilization procedures of traditional whole-mount protocols. We also adjusted standard enzymatic stains for respiratory chain subunits (NADH, SDH, and COX) to monitor metabolic states of various C. elegans tissues. In summary, the protocols presented here provide technical guidance to obtain robust, reproducible and quantifiable tissue-specific data on worm morphology as well as carbohydrate, lipid and mitochondrial energy metabolism that cannot be obtained through traditional biochemical bulk analyses of worm homogenates. Furthermore, analysis of worm cross-sections overcomes the common problem with quantification in three-dimensional whole-mount specimens. PMID:22162770

Specific and quantitative detection of human polyomaviruses BKV, JCV, and SV40 by real time PCR.

PubMed

McNees, Adrienne L; White, Zoe S; Zanwar, Preeti; Vilchez, Regis A; Butel, Janet S

2005-09-01

The polyomaviruses that infect humans, BK virus (BKV), JC virus (JCV), and simian virus 40 (SV40), typically establish subclinical persistent infections. However, reactivation of these viruses in immunocompromised hosts is associated with renal nephropathy and hemorrhagic cystitis (HC) caused by BKV and with progressive multifocal leukoencephalopathy (PML) caused by JCV. Additionally, SV40 is associated with several types of human cancers including primary brain and bone cancers, mesotheliomas, and non-Hodgkin's lymphoma. Advancements in detection of these viruses may contribute to improved diagnosis and treatment of affected patients. To develop sensitive and specific real time quantitative polymerase chain reaction (RQ-PCR) assays for the detection of T-antigen DNA sequences of the human polyomaviruses BKV, JCV, and SV40 using the ABI Prism 7000 Sequence Detection System. Assays for absolute quantification of the viral T-ag sequences were designed and the sensitivity and specificity were evaluated. A quantitative assay to measure the single copy human RNAse P gene was also developed and evaluated in order to normalize viral gene copy numbers to cell numbers. Quantification of the target genes is sensitive and specific over a 7 log dynamic range. Ten copies each of the viral and cellular genes are reproducibly and accurately detected. The sensitivity of detection of the RQ-PCR assays is increased 10- to 100-fold compared to conventional PCR and agarose gel protocols. The primers and probes used to detect the viral genes are specific for each virus and there is no cross reactivity within the dynamic range of the standard dilutions. The sensitivity of detection for these assays is not reduced in human cellular extracts; however, different DNA extraction protocols may affect quantification. These assays provide a technique for rapid and specific quantification of polyomavirus genomes per cell in human samples.

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data.

PubMed

Mitchell, Christopher J; Kim, Min-Sik; Na, Chan Hyun; Pandey, Akhilesh

2016-08-01

Quantitative mass spectrometry data necessitates an analytical pipeline that captures the accuracy and comprehensiveness of the experiments. Currently, data analysis is often coupled to specific software packages, which restricts the analysis to a given workflow and precludes a more thorough characterization of the data by other complementary tools. To address this, we have developed PyQuant, a cross-platform mass spectrometry data quantification application that is compatible with existing frameworks and can be used as a stand-alone quantification tool. PyQuant supports most types of quantitative mass spectrometry data including SILAC, NeuCode, (15)N, (13)C, or (18)O and chemical methods such as iTRAQ or TMT and provides the option of adding custom labeling strategies. In addition, PyQuant can perform specialized analyses such as quantifying isotopically labeled samples where the label has been metabolized into other amino acids and targeted quantification of selected ions independent of spectral assignment. PyQuant is capable of quantifying search results from popular proteomic frameworks such as MaxQuant, Proteome Discoverer, and the Trans-Proteomic Pipeline in addition to several standalone search engines. We have found that PyQuant routinely quantifies a greater proportion of spectral assignments, with increases ranging from 25-45% in this study. Finally, PyQuant is capable of complementing spectral assignments between replicates to quantify ions missed because of lack of MS/MS fragmentation or that were omitted because of issues such as spectra quality or false discovery rates. This results in an increase of biologically useful data available for interpretation. In summary, PyQuant is a flexible mass spectrometry data quantification platform that is capable of interfacing with a variety of existing formats and is highly customizable, which permits easy configuration for custom analysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.